Hi.
**However, I am getting this error. I tried multiple things, including installing and reinstalling packages, changing versions, but nothing seems to work. My understanding is that the alignment files aren't being generated, but I can't figure out why. Any thought how I can make this work? **
INFO - - - - - - - - - - - - - - - - - - - -
INFO Paralog wgd analysis for species [poatr]
INFO Wed Jun 1 21:01:56 2022
INFO - - - - - - - - - - - - - - - - - - - -
INFO Checking if sequence data files exist and if sequence IDs are compatible with wgd pipeline...
WARNING Poa trivialis: sequence IDs in FASTA file [cds_final.fasta] could raise an error due to:
WARNING - ID length longer than 50 characters, it is advised to shorten them
WARNING - ID name contains one or more characters that are not allowed: =
INFO Completed
INFO Running wgd paralog Ks pipeline...
INFO Paralog blast data poatr.blast.tsv already exists, will skip wgd all versus all Blastp
INFO Paralog gene family data poatr.mcl.tsv already exists, will skip wgd mcl
INFO No paralog Ks data, will run wgd Ks analysis
INFO ---
INFO Checking external software...
INFO muscle 5.1.linux64 []
INFO AAML in paml version 4.9j, February 2020
INFO Usage for FastTree version 2.1.11 Double precision (No SSE3):
INFO Translating CDS file cds_final.fasta...
INFO ---
INFO Running whole paranome Ks analysis...
WARNING Filtered out the 3 largest gene families because their size is > 200
WARNING If you want to analyse these large families anyhow, please raise the `max_gene_family_size` parameter
INFO Started analysis of 5019 gene families in parallel using 4 threads
INFO Performing analysis on gene family GF_000004 (size 165)
ERROR Unexpected internal error during analysis of gene family GF_000004:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000004.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000005 (size 138)
ERROR Unexpected internal error during analysis of gene family GF_000005:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000005.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000006 (size 129)
ERROR Unexpected internal error during analysis of gene family GF_000006:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000006.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000007 (size 122)
ERROR Unexpected internal error during analysis of gene family GF_000007:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000007.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000008 (size 122)
ERROR Unexpected internal error during analysis of gene family GF_000008:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000008.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000009 (size 120)
ERROR Unexpected internal error during analysis of gene family GF_000009:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000009.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000010 (size 117)
ERROR Unexpected internal error during analysis of gene family GF_000010:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000010.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000011 (size 115)
ERROR Unexpected internal error during analysis of gene family GF_000011:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000011.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000012 (size 111)
ERROR Unexpected internal error during analysis of gene family GF_000012:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000012.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000013 (size 110)
ERROR Unexpected internal error during analysis of gene family GF_000013:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000013.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000014 (size 107)
ERROR Unexpected internal error during analysis of gene family GF_000014:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000014.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000015 (size 95)
ERROR Unexpected internal error during analysis of gene family GF_000015:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000015.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000016 (size 92)
ERROR Unexpected internal error during analysis of gene family GF_000016:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000016.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000017 (size 89)
ERROR Unexpected internal error during analysis of gene family GF_000017:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000017.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000018 (size 89)
ERROR Unexpected internal error during analysis of gene family GF_000018:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000018.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000019 (size 86)
ERROR Unexpected internal error during analysis of gene family GF_000019:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000019.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000020 (size 81)
ERROR Unexpected internal error during analysis of gene family GF_000020:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000020.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000021 (size 79)
ERROR Unexpected internal error during analysis of gene family GF_000021:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000021.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000022 (size 79)
ERROR Unexpected internal error during analysis of gene family GF_000022:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000022.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000023 (size 75)
ERROR Unexpected internal error during analysis of gene family GF_000023:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000023.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000024 (size 73)
ERROR Unexpected internal error during analysis of gene family GF_000024:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000024.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000025 (size 72)
ERROR Unexpected internal error during analysis of gene family GF_000025:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000025.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000026 (size 69)
ERROR Unexpected internal error during analysis of gene family GF_000026:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000026.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000027 (size 67)
ERROR Unexpected internal error during analysis of gene family GF_000027:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000027.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000028 (size 67)
ERROR Unexpected internal error during analysis of gene family GF_000028:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000028.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000029 (size 64)
ERROR Unexpected internal error during analysis of gene family GF_000029:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000029.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000030 (size 64)
ERROR Unexpected internal error during analysis of gene family GF_000030:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000030.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000031 (size 62)
ERROR Unexpected internal error during analysis of gene family GF_000031:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000031.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000032 (size 61)
ERROR Unexpected internal error during analysis of gene family GF_000032:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000032.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000033 (size 59)
ERROR Unexpected internal error during analysis of gene family GF_000033:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000033.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000034 (size 57)
ERROR Unexpected internal error during analysis of gene family GF_000034:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000034.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000035 (size 56)
ERROR Unexpected internal error during analysis of gene family GF_000035:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000035.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000036 (size 55)
ERROR Unexpected internal error during analysis of gene family GF_000036:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000036.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000037 (size 55)
ERROR Unexpected internal error during analysis of gene family GF_000037:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000037.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000038 (size 52)
ERROR Unexpected internal error during analysis of gene family GF_000038:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000038.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000039 (size 51)
ERROR Unexpected internal error during analysis of gene family GF_000039:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000039.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000040 (size 50)
ERROR Unexpected internal error during analysis of gene family GF_000040:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000040.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000041 (size 49)
ERROR Unexpected internal error during analysis of gene family GF_000041:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000041.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000042 (size 48)
ERROR Unexpected internal error during analysis of gene family GF_000042:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000042.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000043 (size 48)
ERROR Unexpected internal error during analysis of gene family GF_000043:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000043.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000044 (size 46)
ERROR Unexpected internal error during analysis of gene family GF_000044:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000044.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000045 (size 46)
ERROR Unexpected internal error during analysis of gene family GF_000045:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000045.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000046 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000046:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000046.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000047 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000047:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000047.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000048 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000048:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000048.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000049 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000049:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000049.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000050 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000050:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000050.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000051 (size 45)
ERROR Unexpected internal error during analysis of gene family GF_000051:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000051.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000052 (size 44)
ERROR Unexpected internal error during analysis of gene family GF_000052:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000052.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000053 (size 44)
ERROR Unexpected internal error during analysis of gene family GF_000053:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000053.fasta.msa'
ERROR Skipping gene family
INFO Performing analysis on gene family GF_000054 (size 44)
ERROR Unexpected internal error during analysis of gene family GF_000054:
Traceback (most recent call last):
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 278, in analyse_family_try_except
analysis_function(family_id, family, nucleotide, tmp, codeml, preserve,
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/ks_distribution.py", line 371, in analyse_family
msa_path, stats, successful = prepare_aln(msa_path_protein, nucleotide)
File "/storage/home/cpb5881/.local/lib/python3.8/site-packages/wgd_ksrates/alignment.py", line 43, in prepare_aln
with open(msa_file, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp/GF_000054.fasta.msa'
ERROR Skipping gene family
ERROR Too many gene family analyses failed, terminating threads...
ERROR Too many gene family analyses failed, terminating threads...
ERROR Too many gene family analyses failed, terminating threads...
ERROR --
ERROR The analyses of more than 1% of gene families [51/5019] have failed due to unexpected internal errors
ERROR Please check the nature of the error(s), remove the tmp directory [/storage/group/cpb5881/default/WGD/wgd/paralog_distributions/wgd_poatr/poatr.ks_tmp] and rerun the Ks analysis
ERROR See the tracebacks above for the following gene family IDs:
ERROR GF_000004
ERROR GF_000005
ERROR GF_000006
ERROR GF_000007
ERROR GF_000008
ERROR GF_000009
ERROR GF_000010
ERROR GF_000011
ERROR GF_000012
ERROR GF_000013
ERROR GF_000014
ERROR GF_000015
ERROR GF_000016
ERROR GF_000017
ERROR GF_000018
ERROR GF_000019
ERROR GF_000020
ERROR GF_000021
ERROR GF_000022
ERROR GF_000023
ERROR GF_000024
ERROR GF_000025
ERROR GF_000026
ERROR GF_000027
ERROR GF_000028
ERROR GF_000029
ERROR GF_000030
ERROR GF_000031
ERROR GF_000032
ERROR GF_000033
ERROR GF_000034
ERROR GF_000035
ERROR GF_000036
ERROR GF_000037
ERROR GF_000038
ERROR GF_000039
ERROR GF_000040
ERROR GF_000041
ERROR GF_000042
ERROR GF_000043
ERROR GF_000044
ERROR GF_000045
ERROR GF_000046
ERROR GF_000047
ERROR GF_000048
ERROR GF_000049
ERROR GF_000050
ERROR GF_000051
ERROR GF_000052
ERROR GF_000053
ERROR GF_000054
ERROR Exiting