Issue running default settings #57

antoinekoehl · 2021-02-02T22:27:00Z

Hi,

I get the following issue when trying to run PASTA using default settings:
$run_pasta.py -i input_aln.fasta -d protein

PASTA INFO: Reading input sequences from 'input_aln.fasta'...
PASTA INFO: Masking alignment sites with less than 0 sites before running the tree step
PASTA INFO: Configuration written to "/home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob2_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /home/akoehl/.pasta/pastajob/temprW0DGL
PASTA INFO: Name translation information saved to /home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob2_temp_name_translation.txt as safe name, original name, blank line format.
PASTA INFO: Creating a starting tree for the PASTA algorithm...
PASTA INFO: Input sequences assumed to be aligned (based on sequence lengths).
PASTA INFO: Performing initial tree search to get starting tree...
PASTA INFO: Starting PASTA algorithm on initial tree...
PASTA INFO: Max subproblem set to 71
PASTA INFO: Step 0. Realigning with decomposition strategy set to mincluster
Process Worker dying. Error in job.start = Traceback (most recent call last):
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in call
plj.run()
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run
process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Process Worker dying. Error in job.start = Traceback (most recent call last):
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in call
plj.run()
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run
process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Is this a case of providing too few files? The idea was to use a (small) set of well-aligned sequences to create a reference tree, that I would then use as input to align a much larger set of unaligned sequences.

The text was updated successfully, but these errors were encountered:

smirarab · 2021-02-02T22:34:19Z

My guess is that something is wrong with the installation. Can you try the installation steps one more time and make sure nothing fails? If that didn't help, can you turn on debug information and send me the debug info? To do so, look at this: https://github.com/smirarab/pasta/#debug

…

On Tue, Feb 2, 2021 at 2:27 PM antoinekoehl ***@***.***> wrote: Hi, I get the following issue when trying to run PASTA using default settings: $run_pasta.py -i input_aln.fasta -d protein PASTA INFO: Reading input sequences from 'input_aln.fasta'... PASTA INFO: Masking alignment sites with less than 0 sites before running the tree step PASTA INFO: Configuration written to "/home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob2_temp_pasta_config.txt". PASTA INFO: Directory for temporary files created at /home/akoehl/.pasta/pastajob/temprW0DGL PASTA INFO: Name translation information saved to /home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob2_temp_name_translation.txt as safe name, original name, blank line format. PASTA INFO: Creating a starting tree for the PASTA algorithm... PASTA INFO: Input sequences assumed to be aligned (based on sequence lengths). PASTA INFO: Performing initial tree search to get starting tree... PASTA INFO: Starting PASTA algorithm on initial tree... PASTA INFO: Max subproblem set to 71 PASTA INFO: Step 0. Realigning with decomposition strategy set to mincluster Process Worker dying. Error in job.start = Traceback (most recent call last): File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in *call* plj.run() File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k) File "/usr/lib/python2.7/subprocess.py", line 394, in *init* errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Process Worker dying. Error in job.start = Traceback (most recent call last): File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in *call* plj.run() File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k) File "/usr/lib/python2.7/subprocess.py", line 394, in *init* errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory It's able to read my input file, as I find a correct alignment file at ~/.pasta/pastajob/temp1UUOA5/init_aln/query-0.fasta Is this a case of providing too few files? The idea was to use a (small) set of well-aligned sequences to create a reference tree, that I would then use as input to align a much larger set of unaligned sequences. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#57>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXOBUUGFXQFGIVAFAF4DS5B34LANCNFSM4W7XNKCA> .

-- Siavash Mirarab

antoinekoehl · 2021-02-02T22:43:19Z

Thanks so much for the quick reply! I re-ran installation. This error did pop up:

/usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'app'
warnings.warn(msg)

I then re-ran the simple default run with debug information:

PASTA INFO: Reading input sequences from 'input_aln.fasta'...
[02/02/21 14:38:37] alignment.py (line 735): DEBUG: using read function from SequenceDataset class with careful_parse = False
[02/02/21 14:38:37] alignment.py (line 569): DEBUG: Will be using custom Fasta reader
[02/02/21 14:38:37] alignment.py (line 582): DEBUG: Legal characters are: *-?ABCDEFGHIKLMNPQRSTUVWXYZabcdefghiklmnpqrstuvwxyz
[02/02/21 14:38:37] alignment.py (line 637): DEBUG: Custom reader finished reading alignment with 141 sequences .
[02/02/21 14:38:37] alignment.py (line 756): DEBUG: File read. checking input ...
[02/02/21 14:38:37] alignment.py (line 877): DEBUG: sd.datatype = PROTEIN
[02/02/21 14:38:37] alignment.py (line 789): DEBUG: Checking sequences are valid
[02/02/21 14:38:37] alignment.py (line 823): DEBUG: Sequence validity check done.
[02/02/21 14:38:37] alignment.py (line 918): DEBUG: creating dendropy dataset
[02/02/21 14:38:37] alignment.py (line 934): DEBUG: dendropy dataset created and locked
PASTA INFO: Masking alignment sites with less than 0 sites before running the tree step
PASTA INFO: Configuration written to "/home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob_temp_pasta_config.txt".

[02/02/21 14:38:37] usersettingclasses.py (line 359): [02/02/21 14:38:37] usersettingclasses.py (line 378): [02/02/21 14:38:37] usersettingclasses.py (line 359): [02/02/21 14:38:37] usersettingclasses.py (line 378): [02/02/21 14:38:37] usersettingclasses.py (line 391): [02/02/21 14:38:37] usersettingclasses.py (line 409): [02/02/21 14:38:37] usersettingclasses.py (line 417): [02/02/21 14:38:37] usersettingclasses.py (line 436): [02/02/21 14:38:37] usersettingclasses.py (line 417): [02/02/21 14:38:37] usersettingclasses.py (line 436): PASTA INFO: Directory for temporary [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 236): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] alignment.py (line 937): [02/02/21 14:38:37] scheduler.py (line 137): PASTA INFO: Name translation information PASTA INFO: Creating a starting tree PASTA INFO: Performing initial alignment [02/02/21 14:38:37] mainpasta.py (line 280): [02/02/21 14:38:37] mainpasta.py (line 284): [02/02/21 14:38:37] scheduler.py (line 42): [02/02/21 14:38:37] scheduler.py (line 139): [02/02/21 14:38:37] scheduler.py (line 87): [02/02/21 14:38:37] scheduler.py (line 179): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:37] scheduler.py (line 137): [02/02/21 14:38:39] scheduler.py (line 122): Return code: 0; None
[02/02/21 14:38:39] scheduler.py (line 137): [02/02/21 14:38:39] scheduler.py (line 183): [02/02/21 14:38:39] filemgr.py (line 215): [02/02/21 14:38:39] scheduler.py (line 42): [02/02/21 14:38:39] scheduler.py (line 179): [02/02/21 14:38:39] scheduler.py (line 139): [02/02/21 14:38:39] scheduler.py (line 87): [02/02/21 14:38:40] scheduler.py (line 122): Return code: 0; None
[02/02/21 14:38:40] scheduler.py (line 137): [02/02/21 14:38:40] scheduler.py (line 183): [02/02/21 14:38:40] filemgr.py (line 215): [02/02/21 14:38:40] alignment.py (line 1211): [02/02/21 14:38:40] alignment.py (line 1213): [02/02/21 14:38:40] alignment.py (line 1217): [02/02/21 14:38:40] alignment.py (line 1252): [02/02/21 14:38:40] filemgr.py (line 215): PASTA INFO: Performing initial tree [02/02/21 14:38:40] alignment.py (line 1256): [02/02/21 14:38:40] alignment.py (line 1260): [02/02/21 14:38:40] scheduler.py (line 42): [02/02/21 14:38:40] scheduler.py (line 179): [02/02/21 14:38:40] scheduler.py (line 139): [02/02/21 14:38:40] scheduler.py (line 87): [02/02/21 14:38:43] scheduler.py (line 122): Return code: 0; None
[02/02/21 14:38:43] scheduler.py (line 183): [02/02/21 14:38:43] scheduler.py (line 137): [02/02/21 14:38:43] filemgr.py (line 215): [02/02/21 14:38:43] filemgr.py (line 215): [02/02/21 14:38:43] mainpasta.py (line 342): [02/02/21 14:38:43] treeholder.py (line 162): [02/02/21 14:38:43] treeholder.py (line 148): [02/02/21 14:38:43] treeholder.py (line 166): [02/02/21 14:38:43] treeholder.py (line 51): [02/02/21 14:38:43] treeholder.py (line 60): [02/02/21 14:38:43] treeholder.py (line 91): [02/02/21 14:38:43] treeholder.py (line 94): [02/02/21 14:38:43] treeholder.py (line 174): [02/02/21 14:38:43] treeholder.py (line 176): PASTA INFO: Starting PASTA algorithm PASTA INFO: Max subproblem set to 71
[02/02/21 14:38:43] pastajob.py (line 493): PASTA INFO: Step 0. Realigning with [02/02/21 14:38:43] treeholder.py (line 162): [02/02/21 14:38:43] treeholder.py (line 148): [02/02/21 14:38:43] treeholder.py (line 166): [02/02/21 14:38:43] treeholder.py (line 174): [02/02/21 14:38:43] treeholder.py (line 176): [02/02/21 14:38:43] pastaalignerjob.py (line 111): [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Creating aligner mafft
DEBUG: Creating instance of MafftAligner
DEBUG: Creating aligner hmmeralign
DEBUG: Creating instance of HMMERAlignAligner
DEBUG: Creating merger opal
DEBUG: Creating instance of OpalMerger
DEBUG: Creating tree estimator fasttree
DEBUG: Creating instance of FastTree
DEBUG: Creating tree estimator Raxml
DEBUG: Creating instance of Raxml
files created at /home/akoehl/.pasta/pastajob/temp8KFltX
DEBUG: Launching Worker thread #0
DEBUG: Launching Worker thread #1
DEBUG: Launching Worker thread #2
DEBUG: Process Worker 0 ticking on queue <Queue.Queue instance at 0x7f284b1c0780> of size 0
DEBUG: Launching Worker thread #3
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DEBUG: Process Worker 31 ticking on queue <Queue.Queue instance at 0x7f284817daa0> of size 0
DEBUG: start relabeling for PASTA
DEBUG: Process Worker 32 ticking on queue <Queue.Queue instance at 0x7f284817b320> of size 0
saved to /home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob_temp_name_translation.txt as safe name, original name, blank line format.
for the PASTA algorithm...
of the entire data matrix...
DEBUG: Will align the remaining 41 sequences in 1 chunks
DEBUG: Chunk with 41 sequences built
DEBUG: initalign_mafft queued
DEBUG: Process Worker 0 found a job to run
DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 40 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3/input.fasta.
DEBUG: Worker 0 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c0780>
DEBUG: Process Worker 33 ticking on queue <Queue.Queue instance at 0x7f284817be60> of size 0
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DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 40 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3/input.fasta.
DEBUG: Process Worker 0 ticking on queue <Queue.Queue instance at 0x7f284b1c0780> of size 0
DEBUG: Worker 0 joined on queue <Queue.Queue instance at 0x7f284b1c0780>
DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3'
DEBUG: initalign-hmmeralign queued
DEBUG: Worker 1 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6050>
DEBUG: Process Worker 1 found a job to run
DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/hmmeralign /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/query-0.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.aligned amino.
DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/hmmeralign /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/query-0.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.aligned amino.
DEBUG: Process Worker 1 ticking on queue <Queue.Queue instance at 0x7f284b1c6050> of size 0
DEBUG: Worker 1 joined on queue <Queue.Queue instance at 0x7f284b1c6050>
DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB'
DEBUG: Transitive Merge Started. ID:1 - Rows: 100,141
DEBUG: Shared seq: 100
DEBUG: Insertion Columns: 0,192
DEBUG: Transitive Merge Finished. ID:1; cols after: 529
DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln'
search to get starting tree...
DEBUG: Masking alignment sites with fewer than 0 characters from alignment with 529 columns
DEBUG: 0 Columns identified for masking
DEBUG: inittree_fasttree queued
DEBUG: Worker 2 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6550>
DEBUG: Process Worker 2 found a job to run
DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/fasttreeMP -quiet -wag -gamma -fastest -log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/input.fasta.
DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/fasttreeMP -quiet -wag -gamma -fastest -log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/input.fasta.
DEBUG: Worker 2 joined on queue <Queue.Queue instance at 0x7f284b1c6550>
DEBUG: Process Worker 2 ticking on queue <Queue.Queue instance at 0x7f284b1c6550> of size 0
DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_tree'
DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH'
DEBUG: We have the tree and whole_alignment, partitions...
DEBUG: start generating tree from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.07670)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.727
DEBUG: NOT covered in tests
DEBUG: tree generated from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272
DEBUG: start resolving polytomies
DEBUG: Found 1 polytomies
DEBUG: polytomies resolution - updating splits
DEBUG: polytomies resolved.
DEBUG: calculating splits
DEBUG: end generating tree from string
on initial tree...
DEBUG: directory /home/akoehl/.pasta/pastajob/temp8KFltX/step0 created
decomposition strategy set to mincluster
DEBUG: start generating tree from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272
DEBUG: NOT covered in tests
DEBUG: tree generated from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272
DEBUG: calculating splits
DEBUG: end generating tree from string
DEBUG: Number of children of the root at the start: 3
DEBUG: Comparing expected_number_of_taxa=141 and max_subproblem_size=71

[02/02/21 14:38:43] pastaalignerjob.py (line 396): DEBUG: tree before bipartition by mincluster = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ...
[02/02/21 14:38:43] pastaalignerjob.py (line 41): DEBUG: bisecting tree...
[02/02/21 14:38:43] pastaalignerjob.py (line 55): DEBUG: breaking using min-cluster strategy
[02/02/21 14:38:43] pastaalignerjob.py (line 406): DEBUG: tree1 = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ...
[02/02/21 14:38:43] pastaalignerjob.py (line 407): DEBUG: tree2 = (((5ht7rhuman:0.00081,(5ht7rrat:0.00082,5ht7rmouse:0.00506)0.736:0.005)1.000:1.07042,((5ht5ahuman:0.05944,(5ht5arat:0.03393,5ht5amouse:0.03541)0.629:0.04211)1.000:1.23679,((5ht1amouse:0.00517,(5ht1ara ...
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 3
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2
[02/02/21 14:38:43] pastaalignerjob.py (line 287): DEBUG: self.multilocus_dataset.get_num_taxa = 141...Recursing
[02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=73 and max_subproblem_size=71

[02/02/21 14:38:43] pastaalignerjob.py (line 396): DEBUG: tree before bipartition by mincluster = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ...
[02/02/21 14:38:43] pastaalignerjob.py (line 41): DEBUG: bisecting tree...
[02/02/21 14:38:43] pastaalignerjob.py (line 55): DEBUG: breaking using min-cluster strategy
[02/02/21 14:38:43] pastaalignerjob.py (line 406): DEBUG: tree1 = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ...
[02/02/21 14:38:43] pastaalignerjob.py (line 407): DEBUG: tree2 = ((5ht6rrat:0.00081,((5ht6rhuman:0.00566,5ht6rpantr:0.00082)0.993:0.04646,5ht6rmouse:0.0227)0.002:0.00519)1.000:1.51891,(((hrh1bovin:0.00081,((hrh1pantr:0.0,hrh1human:0.0):0.05074,(hrh1rat:0.02156,hrh1 ...
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2
[02/02/21 14:38:43] pastaalignerjob.py (line 287): DEBUG: self.multilocus_dataset.get_num_taxa = 73...Recursing
[02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=36 and max_subproblem_size=71

[02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 36...Calling Aligner
[02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=37 and max_subproblem_size=71

[02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 37...Calling Aligner
[02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=68 and max_subproblem_size=71

[02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 68...Calling Aligner
[02/02/21 14:38:43] pastajob.py (line 522): DEBUG: Build PASTA merge jobs
[02/02/21 14:38:43] pastajob.py (line 351): DEBUG: START building heuristic spanning tree
[02/02/21 14:38:43] pastajob.py (line 366): DEBUG: leafs labeled
[02/02/21 14:38:43] pastajob.py (line 377): DEBUG: Subset Labeling (start):
[&R] ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.72727,((taar1macmu:0.01837,(taar1human:0.0095,taar1pantr:0.00955)0.908:0.02047)0.905:0.11361,(taar1rat:0.06774,taar1mouse:0.1308)0.958:0.17053)1.000:1.24363)0.902:0.26282)0.873:0.071355,(((((drd1mouse:0.00081,drd1rat:0.00907)0.994:0.05601,(drd1bovin:0.02607,(drd1macmu:0.00082,drd1human:0.00447)0.985:0.03002)0.342:0.00082)0.978:0.26126,(drd5human:0.09522,(drd5mouse:0.01203,drd5rat:0.02821)0.858:0.06112)0.948:0.18411)1.000:0.77389,(((adrb3mouse:0.01968,adrb3rat:0.02647)0.882:0.04959,(adrb3bovin:0.0583,(adrb3macmu:0.01806,adrb3human:0.02519)0.929:0.0303)0.717:0.04577)1.000:0.68251,(((adrb2macmu:0.0008,adrb2human:0.01783)0.929:0.03541,((adrb2rat:0.0008,adrb2mouse:0.02863)0.983:0.03718,adrb2bovin:0.05049)0.713:0.00811)1.000:0.50278,(adrb1melga:0.16969,((adrb1human:0.0,adrb1macmu:0.0):0.00951,(adrb1bovin:0.10734,(adrb1mouse:0.00081,adrb1rat:0.00494)0.762:0.00632)0.239:0.009)0.996:0.15444)0.831:0.13157)0.246:0.08697)1.000:0.75617)0.784:0.06344,((5ht6rrat:0.00081,((5ht6rhuman:0.00566,5ht6rpantr:0.00082)0.993:0.04646,5ht6rmouse:0.0227)0.002:0.00519)1.000:1.51891,(((hrh1bovin:0.00081,((hrh1pantr:0.0,hrh1human:0.0):0.05074,(hrh1rat:0.02156,hrh1mouse:0.03026)0.993:0.07298)0.441:0.06731)1.000:1.17448,(((((acm2rat:0.0,acm2mouse:0.0):0.00457,(acm2pantr:0.00081,(acm2bovin:0.0,acm2human:0.0):0.00082)1.000:0.0009)0.998:0.18133,(acm4human:0.01054,(acm4mouse:0.00081,acm4rat:0.00475)0.790:0.01393)0.974:0.13135)0.995:0.325,((((acm3bovin:0.0067,(acm3mouse:0.00552,acm3rat:0.00082)0.794:0.00465)0.979:0.03052,acm3pantr:0.00081)0.791:0.00567,acm3human:0.0008)0.986:0.10695,(((acm5mouse:0.00082,acm5rat:0.00586)0.893:0.02691,(acm5pantr:0.00498,(acm5macmu:0.00991,acm5human:0.00574)0.791:0.00552)0.981:0.00081)0.999:0.17848,((acm1human:0.00081,acm1macmu:0.00081)0.835:0.00459,(acm1mouse:0.00081,acm1rat:0.00081)0.688:0.00081)1.000:0.30313)0.765:0.04994)0.889:0.13894)0.998:0.62569,((hrh3human:0.01116,(hrh3mouse:0.00565,hrh3rat:0.01085)0.839:0.01646)0.965:0.33345,(hrh4human:0.14604,(hrh4mouse:0.10063,hrh4rat:0.07696)0.942:0.20322)1.000:0.98033)1.000:0.91595)0.954:0.31226)0.989:0.47329,(((5ht7rhuman:0.00081,(5ht7rrat:0.00082,5ht7rmouse:0.00506)0.736:0.005)1.000:1.07042,((5ht5ahuman:0.05944,(5ht5arat:0.03393,5ht5amouse:0.03541)0.629:0.04211)1.000:1.23679,((5ht1amouse:0.00517,(5ht1arat:0.00904,(5ht1apantr:0.00081,5ht1ahuman:0.00502)0.848:0.00131)0.790:0.01492)1.000:0.62116,(((5ht1bhuman:0.00127,(5ht1bpantr:0.00081,(5ht1bmouse:0.00503,5ht1brat:0.005)0.999:0.06239)0.883:0.01537)0.998:0.22001,(5ht1dhuman:0.02432,(5ht1dmouse:0.00548,5ht1drat:0.00438)0.965:0.07563)0.998:0.27729)0.985:0.23494,((5ht1epantr:0.0,5ht1ehuman:0.0):0.43751,((5ht1fhuman:0.00081,5ht1fpantr:0.00081)0.915:0.03568,(5ht1fmouse:0.00319,5ht1frat:0.052)0.755:0.0111)0.993:0.2877)0.995:0.31861)0.980:0.25538)0.809:0.14938)0.909:0.18277)0.854:0.10181,(((((ada1arat:0.00743,ada1amouse:0.015)0.858:0.01729,ada1abovin:0.02986)0.926:0.02491,ada1ahuman:0.00081)0.975:0.24606,((ada1dhuman:0.0008,(ada1drat:0.01231,ada1dmouse:0.0054)0.943:0.03287)1.000:0.38249,(ada1bhuman:0.0104,(ada1brat:0.0008,ada1bmouse:0.03411)0.900:0.02043)0.987:0.1782)0.785:0.15188)1.000:0.9518,(((ada2abovin:0.00081,(ada2ahuman:0.03765,(ada2amouse:0.00082,ada2arat:0.00518)0.995:0.06917)0.915:0.04047)0.925:0.16274,((ada2chuman:0.01504,(ada2cmouse:0.04483,ada2crat:0.0053)0.319:0.00082)0.999:0.32117,(ada2bhuman:0.03057,(ada2brat:0.0053,ada2bmouse:0.00548)0.902:0.06113)1.000:0.32506)0.153:0.10924)1.000:0.9672,((((5ht2chuman:0.00985,5ht2cpantr:0.00081)0.793:0.0144,(5ht2cmouse:0.01599,5ht2crat:0.00136)0.832:0.0209)0.861:0.11854,((5ht2abovin:0.00749,((5ht2amacmu:0.0,5ht2ahuman:0.0):0.00473,(5ht2arat:0.00467,5ht2amouse:0.00081)0.891:0.00936)0.855:0.01713)0.999:0.28119,(5ht2bhuman:0.03925,(5ht2brat:0.07167,5ht2bmouse:0.04787)0.972:0.07868)1.000:0.5473)0.742:0.12056)1.000:1.37701,((drd4human:0.0963,(drd4mouse:0.01959,drd4rat:0.01965)0.821:0.06574)1.000:1.07887,(((drd3rat:0.01033,drd3mouse:0.0008)0.909:0.03224,(drd3human:0.00518,drd3pantr:0.0008)0.835:0.02047)0.998:0.39429,(drd2melga:0.08777,(drd2bovin:0.00434,((drd2rat:0.0,drd2mouse:0.0):0.01009,(drd2pantr:0.00081,drd2human:0.01095)0.956:0.02079)0.773:0.00601)0.908:0.06638)0.944:0.15718)0.970:0.36475)0.860:0.22186)0.762:0.16142)0.761:0.1736)0.851:0.11832)0.711:0.0937)0.974:0.2097)0.000:0.0008):0.071355);

[02/02/21 14:38:43] pastajob.py (line 406): DEBUG: Before final round, the tree is:
[&R] (('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1';

[02/02/21 14:38:43] pastajob.py (line 440): DEBUG: Spanning tree is:
(('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1';

[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1
[02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 3 subsets
[02/02/21 14:38:43] pastaalignerjob.py (line 505): DEBUG: subsets tree: (('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1';
... recursing further
[02/02/21 14:38:43] pastaalignerjob.py (line 512): DEBUG: rerooted to: ('r0/d2':0.0937,:0.0008)'r1/d2';
...
[02/02/21 14:38:43] pastaalignerjob.py (line 526): DEBUG: child = ('r0/d2':0.0937)'r1/d2';
...
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1
[02/02/21 14:38:43] pastaalignerjob.py (line 526): DEBUG: child = (:0.0008)'r1/d2';
...
[02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1
[02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 2 subsets
[02/02/21 14:38:43] pastaalignerjob.py (line 494): DEBUG: subsets tree: ('r0/d2':0.0937)'r1/d2';
... pairwise merge
[02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 2 subsets
[02/02/21 14:38:43] pastaalignerjob.py (line 494): DEBUG: subsets tree: (:0.0008)'r1/d2';
... pairwise merge
[02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued
[02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued
[02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued
[02/02/21 14:38:43] pastaalignerjob.py (line 386): DEBUG: waiting for merge events to be queued
[02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 4 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c94b0>
[02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 4 found a job to run
[02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ/input.fasta.
[02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 3 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6cd0>
[02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 3 found a job to run
[02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift/input.fasta.
[02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 5 put a job tuple on queue <Queue.Queue instance at 0x7f284b1ce320>
[02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 5 found a job to run
[02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx/input.fasta.
[02/02/21 14:38:44] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift/input.fasta.
Return code: 0; None
[02/02/21 14:38:44] scheduler.py (line 183): DEBUG: Worker 3 joined on queue <Queue.Queue instance at 0x7f284b1c6cd0>
[02/02/21 14:38:44] scheduler.py (line 137): DEBUG: Process Worker 3 ticking on queue <Queue.Queue instance at 0x7f284b1c6cd0> of size 0
[02/02/21 14:38:44] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift'
[02/02/21 14:38:45] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ/input.fasta.
Return code: 0; None
[02/02/21 14:38:45] scheduler.py (line 183): DEBUG: Worker 4 joined on queue <Queue.Queue instance at 0x7f284b1c94b0>
[02/02/21 14:38:45] scheduler.py (line 137): DEBUG: Process Worker 4 ticking on queue <Queue.Queue instance at 0x7f284b1c94b0> of size 0
[02/02/21 14:38:45] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ'
[02/02/21 14:38:45] scheduler.py (line 42): DEBUG: merger0_opal queued
[02/02/21 14:38:45] scheduler.py (line 179): DEBUG: Worker 4 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c94b0>
[02/02/21 14:38:45] scheduler.py (line 139): DEBUG: Process Worker 4 found a job to run
[02/02/21 14:38:45] scheduler.py (line 87): DEBUG: launching java -Xmx1024m -jar /home/akoehl/Software/pasta-code/pasta/bin/opal.jar --in /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/1_U2X.fasta --in2 /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/2_U2X.fasta --out /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/out_rep.fasta --align_method profile.
[02/02/21 14:38:45] scheduler.py (line 148): ERROR: Process Worker dying. Error in job.start = Traceback (most recent call last):
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in call
plj.run()
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run
process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

Process Process-6:
Traceback (most recent call last):
File "/usr/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap
self.run()
File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run
self._target(*self._args, **self._kwargs)
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in call
plj.run()
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run
process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
[02/02/21 14:38:47] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx/input.fasta.
Return code: 0; None
[02/02/21 14:38:47] scheduler.py (line 137): DEBUG: Process Worker 5 ticking on queue <Queue.Queue instance at 0x7f284b1ce320> of size 0
[02/02/21 14:38:47] scheduler.py (line 183): DEBUG: Worker 5 joined on queue <Queue.Queue instance at 0x7f284b1ce320>
[02/02/21 14:38:47] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx'
[02/02/21 14:38:47] scheduler.py (line 42): DEBUG: merger0_opal queued
[02/02/21 14:38:47] pastaalignerjob.py (line 388): DEBUG: merge events to be queued. signal received.
[02/02/21 14:38:47] scheduler.py (line 179): DEBUG: Worker 5 put a job tuple on queue <Queue.Queue instance at 0x7f284b1ce320>
[02/02/21 14:38:47] scheduler.py (line 139): DEBUG: Process Worker 5 found a job to run
[02/02/21 14:38:47] scheduler.py (line 87): DEBUG: launching java -Xmx1024m -jar /home/akoehl/Software/pasta-code/pasta/bin/opal.jar --in /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/1_U2X.fasta --in2 /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/2_U2X.fasta --out /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/out_rep.fasta --align_method profile.
[02/02/21 14:38:47] scheduler.py (line 148): ERROR: Process Worker dying. Error in job.start = Traceback (most recent call last):
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in call
plj.run()
File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run
process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k)
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

smirarab · 2021-02-02T22:58:43Z

Ah, I see. You likely don't have java installed. Try typing java --version in your terminal. If nothing shows up that is the problem.

…

On Tue, Feb 2, 2021 at 2:43 PM antoinekoehl ***@***.***> wrote: Thanks so much for the quick reply! I re-ran installation. This error did pop up: /usr/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'app' warnings.warn(msg) I then re-ran the simple default run with debug information: PASTA INFO: Reading input sequences from 'input_aln.fasta'... [02/02/21 14:38:37] alignment.py (line 735): DEBUG: using read function from SequenceDataset class with careful_parse = False [02/02/21 14:38:37] alignment.py (line 569): DEBUG: Will be using custom Fasta reader [02/02/21 14:38:37] alignment.py (line 582): DEBUG: Legal characters are: *-?ABCDEFGHIKLMNPQRSTUVWXYZabcdefghiklmnpqrstuvwxyz [02/02/21 14:38:37] alignment.py (line 637): DEBUG: Custom reader finished reading alignment with 141 sequences . [02/02/21 14:38:37] alignment.py (line 756): DEBUG: File read. checking input ... [02/02/21 14:38:37] alignment.py (line 877): DEBUG: sd.datatype = PROTEIN [02/02/21 14:38:37] alignment.py (line 789): DEBUG: Checking sequences are valid [02/02/21 14:38:37] alignment.py (line 823): DEBUG: Sequence validity check done. [02/02/21 14:38:37] alignment.py (line 918): DEBUG: creating dendropy dataset [02/02/21 14:38:37] alignment.py (line 934): DEBUG: dendropy dataset created and locked PASTA INFO: Masking alignment sites with less than 0 sites before running the tree step PASTA INFO: Configuration written to "/home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob_temp_pasta_config.txt". [02/02/21 14:38:37] usersettingclasses.py (line 359): DEBUG: Creating aligner mafft [02/02/21 14:38:37] usersettingclasses.py (line 378): DEBUG: Creating instance of MafftAligner [02/02/21 14:38:37] usersettingclasses.py (line 359): DEBUG: Creating aligner hmmeralign [02/02/21 14:38:37] usersettingclasses.py (line 378): DEBUG: Creating instance of HMMERAlignAligner [02/02/21 14:38:37] usersettingclasses.py (line 391): DEBUG: Creating merger opal [02/02/21 14:38:37] usersettingclasses.py (line 409): DEBUG: Creating instance of OpalMerger [02/02/21 14:38:37] usersettingclasses.py (line 417): DEBUG: Creating tree estimator fasttree [02/02/21 14:38:37] usersettingclasses.py (line 436): DEBUG: Creating instance of FastTree [02/02/21 14:38:37] usersettingclasses.py (line 417): DEBUG: Creating tree estimator Raxml [02/02/21 14:38:37] usersettingclasses.py (line 436): DEBUG: Creating instance of Raxml PASTA INFO: Directory for temporary files created at /home/akoehl/.pasta/pastajob/temp8KFltX [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #1 <#1> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #2 <#2> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 0 ticking on queue <Queue.Queue instance at 0x7f284b1c0780> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #3 <#3> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 1 ticking on queue <Queue.Queue instance at 0x7f284b1c6050> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #4 <#4> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 2 ticking on queue <Queue.Queue instance at 0x7f284b1c6550> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 3 ticking on queue <Queue.Queue instance at 0x7f284b1c6cd0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #5 <#5> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #6 <#6> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 4 ticking on queue <Queue.Queue instance at 0x7f284b1c94b0> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 5 ticking on queue <Queue.Queue instance at 0x7f284b1ce320> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #7 <#7> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #8 <#8> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 6 ticking on queue <Queue.Queue instance at 0x7f284b1ce9b0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #9 <#9> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 7 ticking on queue <Queue.Queue instance at 0x7f284b1d1640> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #10 <#10> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 8 ticking on queue <Queue.Queue instance at 0x7f284b1d1c80> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #11 <#11> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 9 ticking on queue <Queue.Queue instance at 0x7f284b1d6820> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #12 <#12> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 10 ticking on queue <Queue.Queue instance at 0x7f284b1d9050> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #13 <#13> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #14 <#14> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 11 ticking on queue <Queue.Queue instance at 0x7f284b1d9910> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 12 ticking on queue <Queue.Queue instance at 0x7f284b1dd460> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #15 <#15> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 13 ticking on queue <Queue.Queue instance at 0x7f284b1ddc30> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #16 <#16> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #17 <#17> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 14 ticking on queue <Queue.Queue instance at 0x7f284b1e2410> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #18 <#18> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #19 <#19> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 15 ticking on queue <Queue.Queue instance at 0x7f284b1e2eb0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #20 <#20> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #21 <#21> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 16 ticking on queue <Queue.Queue instance at 0x7f284b1e5a00> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #22 <#22> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 17 ticking on queue <Queue.Queue instance at 0x7f284b1ea640> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #23 <#23> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 18 ticking on queue <Queue.Queue instance at 0x7f284b1eaaa0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #24 <#24> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 19 ticking on queue <Queue.Queue instance at 0x7f2848169320> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #25 <#25> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #26 <#26> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 20 ticking on queue <Queue.Queue instance at 0x7f2848169dc0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #27 <#27> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 21 ticking on queue <Queue.Queue instance at 0x7f284816c5a0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #28 <#28> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 22 ticking on queue <Queue.Queue instance at 0x7f284816cb40> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #29 <#29> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 23 ticking on queue <Queue.Queue instance at 0x7f28481713c0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #30 <#30> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 24 ticking on queue <Queue.Queue instance at 0x7f2848171dc0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #31 <#31> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 25 ticking on queue <Queue.Queue instance at 0x7f2848173550> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #32 <#32> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 26 ticking on queue <Queue.Queue instance at 0x7f2848173e10> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #33 <#33> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #34 <#34> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 27 ticking on queue <Queue.Queue instance at 0x7f28481775f0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #35 <#35> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 28 ticking on queue <Queue.Queue instance at 0x7f2848177dc0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #36 <#36> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 29 ticking on queue <Queue.Queue instance at 0x7f2848179870> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #37 <#37> [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #38 <#38> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 30 ticking on queue <Queue.Queue instance at 0x7f284817d1e0> of size 0 [02/02/21 14:38:37] scheduler.py (line 236): DEBUG: Launching Worker thread #39 <#39> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 31 ticking on queue <Queue.Queue instance at 0x7f284817daa0> of size 0 [02/02/21 14:38:37] alignment.py (line 937): DEBUG: start relabeling for PASTA [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 32 ticking on queue <Queue.Queue instance at 0x7f284817b320> of size 0 PASTA INFO: Name translation information saved to /home/akoehl/Projects/deorphanization/coevolution/data/aminergics/pastajob_temp_name_translation.txt as safe name, original name, blank line format. PASTA INFO: Creating a starting tree for the PASTA algorithm... PASTA INFO: Performing initial alignment of the entire data matrix... [02/02/21 14:38:37] mainpasta.py (line 280): DEBUG: Will align the remaining 41 sequences in 1 chunks [02/02/21 14:38:37] mainpasta.py (line 284): DEBUG: Chunk with 41 sequences built [02/02/21 14:38:37] scheduler.py (line 42): DEBUG: initalign_mafft queued [02/02/21 14:38:37] scheduler.py (line 139): DEBUG: Process Worker 0 found a job to run [02/02/21 14:38:37] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 40 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3/input.fasta. [02/02/21 14:38:37] scheduler.py (line 179): DEBUG: Worker 0 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c0780> [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 33 ticking on queue <Queue.Queue instance at 0x7f284817be60> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 34 ticking on queue <Queue.Queue instance at 0x7f2848184690> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 35 ticking on queue <Queue.Queue instance at 0x7f2848184af0> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 36 ticking on queue <Queue.Queue instance at 0x7f2848189370> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 37 ticking on queue <Queue.Queue instance at 0x7f2848189d20> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 38 ticking on queue <Queue.Queue instance at 0x7f284818b370> of size 0 [02/02/21 14:38:37] scheduler.py (line 137): DEBUG: Process Worker 39 ticking on queue <Queue.Queue instance at 0x7f284818bbe0> of size 0 [02/02/21 14:38:39] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 40 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3/input.fasta. Return code: 0; None [02/02/21 14:38:39] scheduler.py (line 137): DEBUG: Process Worker 0 ticking on queue <Queue.Queue instance at 0x7f284b1c0780> of size 0 [02/02/21 14:38:39] scheduler.py (line 183): DEBUG: Worker 0 joined on queue <Queue.Queue instance at 0x7f284b1c0780> [02/02/21 14:38:39] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/tempmafftBdOli3' [02/02/21 14:38:39] scheduler.py (line 42): DEBUG: initalign-hmmeralign queued [02/02/21 14:38:39] scheduler.py (line 179): DEBUG: Worker 1 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6050> [02/02/21 14:38:39] scheduler.py (line 139): DEBUG: Process Worker 1 found a job to run [02/02/21 14:38:39] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/hmmeralign /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/query-0.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.aligned amino. [02/02/21 14:38:40] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/hmmeralign /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/query-0.fasta /home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB/input.aligned amino. Return code: 0; None [02/02/21 14:38:40] scheduler.py (line 137): DEBUG: Process Worker 1 ticking on queue <Queue.Queue instance at 0x7f284b1c6050> of size 0 [02/02/21 14:38:40] scheduler.py (line 183): DEBUG: Worker 1 joined on queue <Queue.Queue instance at 0x7f284b1c6050> [02/02/21 14:38:40] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln/temphmmeralignWkpcaB' [02/02/21 14:38:40] alignment.py (line 1211): DEBUG: Transitive Merge Started. ID:1 - Rows: 100,141 [02/02/21 14:38:40] alignment.py (line 1213): DEBUG: Shared seq: 100 [02/02/21 14:38:40] alignment.py (line 1217): DEBUG: Insertion Columns: 0,192 [02/02/21 14:38:40] alignment.py (line 1252): DEBUG: Transitive Merge Finished. ID:1; cols after: 529 [02/02/21 14:38:40] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_aln' PASTA INFO: Performing initial tree search to get starting tree... [02/02/21 14:38:40] alignment.py (line 1256): DEBUG: Masking alignment sites with fewer than 0 characters from alignment with 529 columns [02/02/21 14:38:40] alignment.py (line 1260): DEBUG: 0 Columns identified for masking [02/02/21 14:38:40] scheduler.py (line 42): DEBUG: inittree_fasttree queued [02/02/21 14:38:40] scheduler.py (line 179): DEBUG: Worker 2 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6550> [02/02/21 14:38:40] scheduler.py (line 139): DEBUG: Process Worker 2 found a job to run [02/02/21 14:38:40] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/fasttreeMP -quiet -wag -gamma -fastest -log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/input.fasta. [02/02/21 14:38:43] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/fasttreeMP -quiet -wag -gamma -fastest -log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/log /home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH/input.fasta. Return code: 0; None [02/02/21 14:38:43] scheduler.py (line 183): DEBUG: Worker 2 joined on queue <Queue.Queue instance at 0x7f284b1c6550> [02/02/21 14:38:43] scheduler.py (line 137): DEBUG: Process Worker 2 ticking on queue <Queue.Queue instance at 0x7f284b1c6550> of size 0 [02/02/21 14:38:43] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_tree' [02/02/21 14:38:43] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/init_tree/tempfasttreeRMY2gH' [02/02/21 14:38:43] mainpasta.py (line 342): DEBUG: We have the tree and whole_alignment, partitions... [02/02/21 14:38:43] treeholder.py (line 162): DEBUG: start generating tree from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.07670)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.727 [02/02/21 14:38:43] treeholder.py (line 148): DEBUG: NOT covered in tests [02/02/21 14:38:43] treeholder.py (line 166): DEBUG: tree generated from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 [02/02/21 14:38:43] treeholder.py (line 51): DEBUG: start resolving polytomies [02/02/21 14:38:43] treeholder.py (line 60): DEBUG: Found 1 polytomies [02/02/21 14:38:43] treeholder.py (line 91): DEBUG: polytomies resolution - updating splits [02/02/21 14:38:43] treeholder.py (line 94): DEBUG: polytomies resolved. [02/02/21 14:38:43] treeholder.py (line 174): DEBUG: calculating splits [02/02/21 14:38:43] treeholder.py (line 176): DEBUG: end generating tree from string PASTA INFO: Starting PASTA algorithm on initial tree... PASTA INFO: Max subproblem set to 71 [02/02/21 14:38:43] pastajob.py (line 493): DEBUG: directory /home/akoehl/.pasta/pastajob/temp8KFltX/step0 created PASTA INFO: Step 0. Realigning with decomposition strategy set to mincluster [02/02/21 14:38:43] treeholder.py (line 162): DEBUG: start generating tree from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 [02/02/21 14:38:43] treeholder.py (line 148): DEBUG: NOT covered in tests [02/02/21 14:38:43] treeholder.py (line 166): DEBUG: tree generated from string ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 [02/02/21 14:38:43] treeholder.py (line 174): DEBUG: calculating splits [02/02/21 14:38:43] treeholder.py (line 176): DEBUG: end generating tree from string [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 3 [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=141 and max_subproblem_size=71 [02/02/21 14:38:43] pastaalignerjob.py (line 396): DEBUG: tree before bipartition by mincluster = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ... [02/02/21 14:38:43] pastaalignerjob.py (line 41): DEBUG: bisecting tree... [02/02/21 14:38:43] pastaalignerjob.py (line 55): DEBUG: breaking using min-cluster strategy [02/02/21 14:38:43] pastaalignerjob.py (line 406): DEBUG: tree1 = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ... [02/02/21 14:38:43] pastaalignerjob.py (line 407): DEBUG: tree2 = (((5ht7rhuman:0.00081,(5ht7rrat:0.00082,5ht7rmouse:0.00506)0.736:0.005)1.000:1.07042,((5ht5ahuman:0.05944,(5ht5arat:0.03393,5ht5amouse:0.03541)0.629:0.04211)1.000:1.23679,((5ht1amouse:0.00517,(5ht1ara ... [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 3 [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2 [02/02/21 14:38:43] pastaalignerjob.py (line 287): DEBUG: self.multilocus_dataset.get_num_taxa = 141...Recursing [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=73 and max_subproblem_size=71 [02/02/21 14:38:43] pastaalignerjob.py (line 396): DEBUG: tree before bipartition by mincluster = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ... [02/02/21 14:38:43] pastaalignerjob.py (line 41): DEBUG: bisecting tree... [02/02/21 14:38:43] pastaalignerjob.py (line 55): DEBUG: breaking using min-cluster strategy [02/02/21 14:38:43] pastaalignerjob.py (line 406): DEBUG: tree1 = ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.7272 ... [02/02/21 14:38:43] pastaalignerjob.py (line 407): DEBUG: tree2 = ((5ht6rrat:0.00081,((5ht6rhuman:0.00566,5ht6rpantr:0.00082)0.993:0.04646,5ht6rmouse:0.0227)0.002:0.00519)1.000:1.51891,(((hrh1bovin:0.00081,((hrh1pantr:0.0,hrh1human:0.0):0.05074,(hrh1rat:0.02156,hrh1 ... [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2 [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 2 [02/02/21 14:38:43] pastaalignerjob.py (line 287): DEBUG: self.multilocus_dataset.get_num_taxa = 73...Recursing [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=36 and max_subproblem_size=71 [02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 36...Calling Aligner [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=37 and max_subproblem_size=71 [02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 37...Calling Aligner [02/02/21 14:38:43] pastaalignerjob.py (line 255): DEBUG: Comparing expected_number_of_taxa=68 and max_subproblem_size=71 [02/02/21 14:38:43] pastaalignerjob.py (line 258): DEBUG: self.multilocus_dataset.get_num_taxa = 68...Calling Aligner [02/02/21 14:38:43] pastajob.py (line 522): DEBUG: Build PASTA merge jobs [02/02/21 14:38:43] pastajob.py (line 351): DEBUG: START building heuristic spanning tree [02/02/21 14:38:43] pastajob.py (line 366): DEBUG: leafs labeled [02/02/21 14:38:43] pastajob.py (line 377): DEBUG: Subset Labeling (start): [&R] ((((hrh2human:0.00081,hrh2pantr:0.00081)0.802:0.04561,(hrh2rat:0.02012,hrh2mouse:0.03349)0.546:0.0767)1.000:0.98355,((5ht4rmouse:0.00081,(5ht4rrat:0.03507,5ht4rhuman:0.07477)0.558:0.02397)1.000:0.72727,((taar1macmu:0.01837,(taar1human:0.0095,taar1pantr:0.00955)0.908:0.02047)0.905:0.11361,(taar1rat:0.06774,taar1mouse:0.1308)0.958:0.17053)1.000:1.24363)0.902:0.26282)0.873:0.071355,(((((drd1mouse:0.00081,drd1rat:0.00907)0.994:0.05601,(drd1bovin:0.02607,(drd1macmu:0.00082,drd1human:0.00447)0.985:0.03002)0.342:0.00082)0.978:0.26126,(drd5human:0.09522,(drd5mouse:0.01203,drd5rat:0.02821)0.858:0.06112)0.948:0.18411)1.000:0.77389,(((adrb3mouse:0.01968,adrb3rat:0.02647)0.882:0.04959,(adrb3bovin:0.0583,(adrb3macmu:0.01806,adrb3human:0.02519)0.929:0.0303)0.717:0.04577)1.000:0.68251,(((adrb2macmu:0.0008,adrb2human:0.01783)0.929:0.03541,((adrb2rat:0.0008,adrb2mouse:0.02863)0.983:0.03718,adrb2bovin:0.05049)0.713:0.00811)1.000:0.50278,(adrb1melga:0.16969,((adrb1human:0.0,adrb1macmu:0.0):0.00951,(adrb1bovin:0.10734,(adrb1mouse:0.00081,adrb1rat:0.00494)0.762:0.00632)0.239:0.009)0.996:0.15444)0.831:0.13157)0.246:0.08697)1.000:0.75617)0.784:0.06344,((5ht6rrat:0.00081,((5ht6rhuman:0.00566,5ht6rpantr:0.00082)0.993:0.04646,5ht6rmouse:0.0227)0.002:0.00519)1.000:1.51891,(((hrh1bovin:0.00081,((hrh1pantr:0.0,hrh1human:0.0):0.05074,(hrh1rat:0.02156,hrh1mouse:0.03026)0.993:0.07298)0.441:0.06731)1.000:1.17448,(((((acm2rat:0.0,acm2mouse:0.0):0.00457,(acm2pantr:0.00081,(acm2bovin:0.0,acm2human:0.0):0.00082)1.000:0.0009)0.998:0.18133,(acm4human:0.01054,(acm4mouse:0.00081,acm4rat:0.00475)0.790:0.01393)0.974:0.13135)0.995:0.325,((((acm3bovin:0.0067,(acm3mouse:0.00552,acm3rat:0.00082)0.794:0.00465)0.979:0.03052,acm3pantr:0.00081)0.791:0.00567,acm3human:0.0008)0.986:0.10695,(((acm5mouse:0.00082,acm5rat:0.00586)0.893:0.02691,(acm5pantr:0.00498,(acm5macmu:0.00991,acm5human:0.00574)0.791:0.00552)0.981:0.00081)0.999:0.17848,((acm1human:0.00081,acm1macmu:0.00081)0.835:0.00459,(acm1mouse:0.00081,acm1rat:0.00081)0.688:0.00081)1.000:0.30313)0.765:0.04994)0.889:0.13894)0.998:0.62569,((hrh3human:0.01116,(hrh3mouse:0.00565,hrh3rat:0.01085)0.839:0.01646)0.965:0.33345,(hrh4human:0.14604,(hrh4mouse:0.10063,hrh4rat:0.07696)0.942:0.20322)1.000:0.98033)1.000:0.91595)0.954:0.31226)0.989:0.47329,(((5ht7rhuman:0.00081,(5ht7rrat:0.00082,5ht7rmouse:0.00506)0.736:0.005)1.000:1.07042,((5ht5ahuman:0.05944,(5ht5arat:0.03393,5ht5amouse:0.03541)0.629:0.04211)1.000:1.23679,((5ht1amouse:0.00517,(5ht1arat:0.00904,(5ht1apantr:0.00081,5ht1ahuman:0.00502)0.848:0.00131)0.790:0.01492)1.000:0.62116,(((5ht1bhuman:0.00127,(5ht1bpantr:0.00081,(5ht1bmouse:0.00503,5ht1brat:0.005)0.999:0.06239)0.883:0.01537)0.998:0.22001,(5ht1dhuman:0.02432,(5ht1dmouse:0.00548,5ht1drat:0.00438)0.965:0.07563)0.998:0.27729)0.985:0.23494,((5ht1epantr:0.0,5ht1ehuman:0.0):0.43751,((5ht1fhuman:0.00081,5ht1fpantr:0.00081)0.915:0.03568,(5ht1fmouse:0.00319,5ht1frat:0.052)0.755:0.0111)0.993:0.2877)0.995:0.31861)0.980:0.25538)0.809:0.14938)0.909:0.18277)0.854:0.10181,(((((ada1arat:0.00743,ada1amouse:0.015)0.858:0.01729,ada1abovin:0.02986)0.926:0.02491,ada1ahuman:0.00081)0.975:0.24606,((ada1dhuman:0.0008,(ada1drat:0.01231,ada1dmouse:0.0054)0.943:0.03287)1.000:0.38249,(ada1bhuman:0.0104,(ada1brat:0.0008,ada1bmouse:0.03411)0.900:0.02043)0.987:0.1782)0.785:0.15188)1.000:0.9518,(((ada2abovin:0.00081,(ada2ahuman:0.03765,(ada2amouse:0.00082,ada2arat:0.00518)0.995:0.06917)0.915:0.04047)0.925:0.16274,((ada2chuman:0.01504,(ada2cmouse:0.04483,ada2crat:0.0053)0.319:0.00082)0.999:0.32117,(ada2bhuman:0.03057,(ada2brat:0.0053,ada2bmouse:0.00548)0.902:0.06113)1.000:0.32506)0.153:0.10924)1.000:0.9672,((((5ht2chuman:0.00985,5ht2cpantr:0.00081)0.793:0.0144,(5ht2cmouse:0.01599,5ht2crat:0.00136)0.832:0.0209)0.861:0.11854,((5ht2abovin:0.00749,((5ht2amacmu:0.0,5ht2ahuman:0.0):0.00473,(5ht2arat:0.00467,5ht2amouse:0.00081)0.891:0.00936)0.855:0.01713)0.999:0.28119,(5ht2bhuman:0.03925,(5ht2brat:0.07167,5ht2bmouse:0.04787)0.972:0.07868)1.000:0.5473)0.742:0.12056)1.000:1.37701,((drd4human:0.0963,(drd4mouse:0.01959,drd4rat:0.01965)0.821:0.06574)1.000:1.07887,(((drd3rat:0.01033,drd3mouse:0.0008)0.909:0.03224,(drd3human:0.00518,drd3pantr:0.0008)0.835:0.02047)0.998:0.39429,(drd2melga:0.08777,(drd2bovin:0.00434,((drd2rat:0.0,drd2mouse:0.0):0.01009,(drd2pantr:0.00081,drd2human:0.01095)0.956:0.02079)0.773:0.00601)0.908:0.06638)0.944:0.15718)0.970:0.36475)0.860:0.22186)0.762:0.16142)0.761:0.1736)0.851:0.11832)0.711:0.0937)0.974:0.2097)0.000:0.0008):0.071355); [02/02/21 14:38:43] pastajob.py (line 406): DEBUG: Before final round, the tree is: [&R] (('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1'; [02/02/21 14:38:43] pastajob.py (line 440): DEBUG: Spanning tree is: (('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1'; [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1 [02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 3 subsets [02/02/21 14:38:43] pastaalignerjob.py (line 505): DEBUG: subsets tree: (('r0/d2':0.0937)'r1/d2':0.0008)'r1/d1'; ... recursing further [02/02/21 14:38:43] pastaalignerjob.py (line 512): DEBUG: rerooted to: ('r0/d2':0.0937,:0.0008)'r1/d2'; ... [02/02/21 14:38:43] pastaalignerjob.py (line 526): DEBUG: child = ('r0/d2':0.0937)'r1/d2'; ... [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1 [02/02/21 14:38:43] pastaalignerjob.py (line 526): DEBUG: child = (:0.0008)'r1/d2'; ... [02/02/21 14:38:43] pastaalignerjob.py (line 111): DEBUG: Number of children of the root at the start: 1 [02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 2 subsets [02/02/21 14:38:43] pastaalignerjob.py (line 494): DEBUG: subsets tree: ('r0/d2':0.0937)'r1/d2'; ... pairwise merge [02/02/21 14:38:43] pastaalignerjob.py (line 490): DEBUG: Recursive merge on a branch with 2 subsets [02/02/21 14:38:43] pastaalignerjob.py (line 494): DEBUG: subsets tree: (:0.0008)'r1/d2'; ... pairwise merge [02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued [02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued [02/02/21 14:38:43] scheduler.py (line 42): DEBUG: align0_mafft queued [02/02/21 14:38:43] pastaalignerjob.py (line 386): DEBUG: waiting for merge events to be queued [02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 4 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c94b0> [02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 4 found a job to run [02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ/input.fasta. [02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 3 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c6cd0> [02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 3 found a job to run [02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift/input.fasta. [02/02/21 14:38:43] scheduler.py (line 179): DEBUG: Worker 5 put a job tuple on queue <Queue.Queue instance at 0x7f284b1ce320> [02/02/21 14:38:43] scheduler.py (line 139): DEBUG: Process Worker 5 found a job to run [02/02/21 14:38:43] scheduler.py (line 87): DEBUG: launching /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx/input.fasta. [02/02/21 14:38:44] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift/input.fasta. Return code: 0; None [02/02/21 14:38:44] scheduler.py (line 183): DEBUG: Worker 3 joined on queue <Queue.Queue instance at 0x7f284b1c6cd0> [02/02/21 14:38:44] scheduler.py (line 137): DEBUG: Process Worker 3 ticking on queue <Queue.Queue instance at 0x7f284b1c6cd0> of size 0 [02/02/21 14:38:44] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d2/tempmafftys4ift' [02/02/21 14:38:45] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ/input.fasta. Return code: 0; None [02/02/21 14:38:45] scheduler.py (line 183): DEBUG: Worker 4 joined on queue <Queue.Queue instance at 0x7f284b1c94b0> [02/02/21 14:38:45] scheduler.py (line 137): DEBUG: Process Worker 4 ticking on queue <Queue.Queue instance at 0x7f284b1c94b0> of size 0 [02/02/21 14:38:45] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r1/d1/tempmaffttPPaRQ' [02/02/21 14:38:45] scheduler.py (line 42): DEBUG: merger0_opal queued [02/02/21 14:38:45] scheduler.py (line 179): DEBUG: Worker 4 put a job tuple on queue <Queue.Queue instance at 0x7f284b1c94b0> [02/02/21 14:38:45] scheduler.py (line 139): DEBUG: Process Worker 4 found a job to run [02/02/21 14:38:45] scheduler.py (line 87): DEBUG: launching java -Xmx1024m -jar /home/akoehl/Software/pasta-code/pasta/bin/opal.jar --in /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/1_U2X.fasta --in2 /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/2_U2X.fasta --out /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r1d1/tempopalpdgiDl/out_rep.fasta --align_method profile. [02/02/21 14:38:45] scheduler.py (line 148): ERROR: Process Worker dying. Error in job.start = Traceback (most recent call last): File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in *call* plj.run() File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k) File "/usr/lib/python2.7/subprocess.py", line 394, in *init* errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory Process Process-6: Traceback (most recent call last): File "/usr/lib/python2.7/multiprocessing/process.py", line 267, in _bootstrap self.run() File "/usr/lib/python2.7/multiprocessing/process.py", line 114, in run self._target(*self._args, **self._kwargs) File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in *call* plj.run() File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k) File "/usr/lib/python2.7/subprocess.py", line 394, in *init* errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory [02/02/21 14:38:47] scheduler.py (line 122): DEBUG: Finished /home/akoehl/Software/pasta-code/pasta/bin/mafft --localpair --maxiterate 1000 --ep 0.123 --quiet --thread 1 --anysymbol /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx/input.fasta. Return code: 0; None [02/02/21 14:38:47] scheduler.py (line 137): DEBUG: Process Worker 5 ticking on queue <Queue.Queue instance at 0x7f284b1ce320> of size 0 [02/02/21 14:38:47] scheduler.py (line 183): DEBUG: Worker 5 joined on queue <Queue.Queue instance at 0x7f284b1ce320> [02/02/21 14:38:47] filemgr.py (line 215): DEBUG: Cleaning temp dir: '/home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/r0/d2/tempmafftxdOVqx' [02/02/21 14:38:47] scheduler.py (line 42): DEBUG: merger0_opal queued [02/02/21 14:38:47] pastaalignerjob.py (line 388): DEBUG: merge events to be queued. signal received. [02/02/21 14:38:47] scheduler.py (line 179): DEBUG: Worker 5 put a job tuple on queue <Queue.Queue instance at 0x7f284b1ce320> [02/02/21 14:38:47] scheduler.py (line 139): DEBUG: Process Worker 5 found a job to run [02/02/21 14:38:47] scheduler.py (line 87): DEBUG: launching java -Xmx1024m -jar /home/akoehl/Software/pasta-code/pasta/bin/opal.jar --in /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/1_U2X.fasta --in2 /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/2_U2X.fasta --out /home/akoehl/.pasta/pastajob/temp8KFltX/step0/mincluster/pw/r1d2_r0d2/tempopalCKGYcz/out_rep.fasta --align_method profile. [02/02/21 14:38:47] scheduler.py (line 148): ERROR: Process Worker dying. Error in job.start = Traceback (most recent call last): File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 141, in *call* plj.run() File "/home/akoehl/Software/pasta-code/pasta/pasta/scheduler.py", line 106, in run process = Popen(self._invocation, stdin = PIPE, universal_newlines=True, **k) File "/usr/lib/python2.7/subprocess.py", line 394, in *init* errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXOCWCHC5K3XBE2HVUNLS5B5ZNANCNFSM4W7XNKCA> .

-- Siavash Mirarab

antoinekoehl · 2021-02-02T23:56:32Z

Ahhh, that's embarrassing. Had to do a full system reinstall not that long ago, totally forgot about java. That fixed it! Thanks so much!

smirarab · 2021-02-03T02:29:14Z

Glad it worked.

…

On Tue, Feb 2, 2021 at 3:56 PM antoinekoehl ***@***.***> wrote: Ahhh, that's embarrassing. Had to do a full system reinstall not that long ago, totally forgot about java. That fixed it! Thanks so much! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#57 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGJXODILA352DJED2KKCEDS5CGMBANCNFSM4W7XNKCA> .

-- Siavash Mirarab

antoinekoehl closed this as completed Feb 7, 2021

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Issue running default settings #57

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antoinekoehl commented Feb 2, 2021 •

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Issue running default settings #57

Issue running default settings #57

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antoinekoehl commented Feb 2, 2021 •

edited

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