Error in PI step: Invalid index

[linshutian02]

Hi
Few days ago, I downloaded the MetaCHIP(V1.10.9) and succeeded in testing the example data. But when I run MetaCHIP with the data myself, the error occur below:

command: MetaCHIP PI -p sample_3 -r c -t 6 -i sample_3_bins -x fasta -taxon sample_3_bins_GTDB.tsv

[2022-01-13 22:57:18] Input genomes grouped into 3 classes.
[2022-01-13 22:57:18] Total number of qualified genomes for HGT detection: 10.
[2022-01-13 22:57:19] Grouping file exported to: sample_3_grouping_c3.txt.
[2022-01-13 22:57:19] Running Prodigal for 10 qualified genomes with 6 cores (1-3 minutes per genome per core).
[2022-01-13 22:57:28] Get SCG tree: running hmmsearch with 6 cores.
[2022-01-13 22:57:30] Get SCG tree: running hmmalign with 6 cores.

Error: File existence/permissions problem in trying to open HMM file sample_3_MetaCHIP_wd/sample_3_c_get_SCG_tree_wd/sample_3_c_hmm_profile_fetched/.hmm.
HMM file sample_3_MetaCHIP_wd/sample_3_c_get_SCG_tree_wd/sample_3_c_hmm_profile_fetched/.hmm not found (nor an .h3m binary of i

[2022-01-13 22:57:35] Get SCG tree: concatenating alignments.
[2022-01-13 22:57:35] Get SCG tree: removing columns from concatenated alignment represented by <50% of genomes and with amino acid consensus <25%.
Traceback (most recent call last):
File "/miniconda3/bin/MetaCHIP", line 166, in
PI(args, MetaCHIP_config.config_dict)
File "/miniconda3/lib/python3.7/site-packages/MetaCHIP/PI.py", line 974, in PI
remove_low_cov_and_consensus_columns(pwd_combined_alignment_file_tmp, minimal_cov_in_msa, min_consensus_in_msa, pwd_combined_alignment_file)
File "/miniconda3/lib/python3.7/site-packages/MetaCHIP/PI.py", line 533, in remove_low_cov_and_consensus_columns
alignment_cov = remove_low_cov_columns(alignment, minimal_cov)
File "/miniconda3/lib/python3.7/site-packages/MetaCHIP/PI.py", line 492, in remove_low_cov_columns
alignment_new = remove_columns_from_msa(alignment_in, low_cov_columns)
File "/miniconda3/lib/python3.7/site-packages/MetaCHIP/PI.py", line 460, in remove_columns_from_msa
segment_value = alignment_in[:, segment[0]]
File "/miniconda3/lib/python3.7/site-packages/Bio/Align/init.py", line 760, in getitem
rec[col_index] for rec in self._records[row_index]
File "/miniconda3/lib/python3.7/site-packages/Bio/Align/init.py", line 160, in init
self.extend(records)
File "/miniconda3/lib/python3.7/site-packages/Bio/Align/init.py", line 450, in extend
rec = next(records)
File "/miniconda3/lib/python3.7/site-packages/Bio/Align/init.py", line 760, in
rec[col_index] for rec in self._records[row_index]
File "/miniconda3/lib/python3.7/site-packages/Bio/SeqRecord.py", line 519, in getitem
raise ValueError("Invalid index")
ValueError: Invalid index

By the way, the version of biopython is V1.79.
What's wrong with it?

[bahiyahazli]

Hello! I received the same error too! I have 2 sample groups and both return the same error.

I do not know whether the problem is due to Error: File existence/permissions problem in trying to open HMM file sample_3_MetaCHIP_wd/sample_3_c_get_SCG_tree_wd/sample_3_c_hmm_profile_fetched/.hmm. HMM file sample_3_MetaCHIP_wd/sample_3_c_get_SCG_tree_wd/sample_3_c_hmm_profile_fetched/.hmm not found that causes the next step to have an invalid index, or something else.

Have you perhaps found a solution for this error?

Thanks