nanopolish not executing

[tzcoolman]

Hi Luca,

Thanks for the pipeline.
I was running mop_tail and encountered the issue people previously reported:
#20
I was able to get away with it by doing 'nextflow -self-update'
The program was able to download nanopolish, however, this is what I got from the log file:

executor > local (12)
[- ] process > TAILFINDR_ESTIMATE_TAIL:est... -
[- ] process > collect_tailfindr_results -
[15/f6ce7b] process > checkRef (Checking GRCh38.p... [100%] 1 of 1 ✔
[db/430059] process > filter_bam (SGNex_Myeloma-N... [100%] 4 of 4 ✔
[19/ed9f58] process > SAMTOOLS_INDEX:indexBam (SG... [100%] 4 of 4 ✔
[- ] process > NANOPOLISH_POLYA_LEN:polyAtail -
[- ] process > NANOPOLISH_POLYA_LEN:collec... -
[- ] process > join_nanotail_results -
[c1/8a13a1] process > TAILFINDR_VER:getVersion [100%] 1 of 1 ✔
[0b/108860] process > NANOPOLISH_VER:getVersion [100%] 1 of 1 ✔
[f8/9a5349] process > SAMTOOLS_VER:getVersion [100%] 1 of 1 ✔
Pipeline BIOCORE@CRG Master of Pore completed!
Started at 2024-02-26T14:10:21.925352849-05:00
Finished at 2024-02-26T14:16:11.289517940-05:00
Time elapsed: 5m 49s
Execution status: OK
Completed at: 26-Feb-2024 14:16:11
Duration : 5m 49s
CPU hours : 0.7
Succeeded : 12

The nanopolish img was there. Iooks like it was not executed. Is there anyway to fix it? Thx.

tzcoolman

[lucacozzuto]

can you send me the log, please?

[tzcoolman]

log.txt

Hi Luca,

Here it is.

[lucacozzuto]

Hi, so I used the test data and it worked. Can you check you got all the outputs from mop_preprocess?

[lucacozzuto]

In particular you need the following outputs:

/alignment/*_s.bam
/alignment/*_s.bam.bai
/fastq_files/*.fq.gz
/fast5_files/*
/assigned/*.assigned

[tzcoolman]

I double-checked those files and they were there.
Is there any verbose mode that I can use to see more tail of the processing results?

[lucacozzuto]

you can checkk the .nextflow.log in which more info are stored. I'm actually surprised. Can you also check the toy dataset?

[tzcoolman]

Yes. The pipeline works with toy dataset. I directly used fastq files as input for mop_preprocess thus got error in mop_tail steps. Thank you Luca.