I am not sure how to resolve this issue. It ran on the full dataset a few weeks ago but now I receive the error below. I have uninstalled and reinstalled phyluce and miniconda and checked that the paths and names of Gblocks and the files are match in the phyluce.conf file and in bin/. I have looked for typos in paths, commands, etc. but cannot find one.
I have changed the number of cores from 1-33 and added in commands for input and output formats. I have confirmed the files are there but none are uce-##.fasta-gb. They are uce-###.fasta as they were when it ran successfully a few weeks ago. The only thing I can think of that is different is that I made a new taxon-set.conf file for the rerun for phyluce_assembly_get_match_counts but directed to the original contigs folder, which had more contigs in it than I had selected for the trimmed rerun.
I am running in Linux HPC with bash phyluce_Gblock_int_trim_Sibo-trimmed.sh
I can share the taxon-sets folder if needed; it is too large to attach here. Here is the tree and files in the /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed; 
2026-03-08 13:47:33,337 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Starting phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Version: 1.7.3
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Commit: None
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --alignments: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b1: 0.5
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b2: 0.85
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b3: 8
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b4: 10
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --cores: 33
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --input_format: fasta
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --log_path: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/log
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --output: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed-gblocks
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --output_format: nexus
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --verbosity: INFO
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Getting aligned sequences for trimming
2026-03-08 13:47:33,427 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Alignment trimming begins.
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 141, in get_and_trim_alignments
with open(trimmed_aln_file, "rU") as trimmed_aln:
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed/uce-990291357.fasta-gb'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 224, in
main()
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 208, in main
alignments = pool.map(get_and_trim_alignments, params)
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed/uce-990291357.fasta-gb'
I am not sure how to resolve this issue. It ran on the full dataset a few weeks ago but now I receive the error below. I have uninstalled and reinstalled phyluce and miniconda and checked that the paths and names of Gblocks and the files are match in the phyluce.conf file and in bin/. I have looked for typos in paths, commands, etc. but cannot find one.
I have changed the number of cores from 1-33 and added in commands for input and output formats. I have confirmed the files are there but none are uce-##.fasta-gb. They are uce-###.fasta as they were when it ran successfully a few weeks ago. The only thing I can think of that is different is that I made a new taxon-set.conf file for the rerun for phyluce_assembly_get_match_counts but directed to the original contigs folder, which had more contigs in it than I had selected for the trimmed rerun.
I am running in Linux HPC with bash phyluce_Gblock_int_trim_Sibo-trimmed.sh
I can share the taxon-sets folder if needed; it is too large to attach here. Here is the tree and files in the /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed;
2026-03-08 13:47:33,337 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Starting phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Version: 1.7.3
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Commit: None
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --alignments: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b1: 0.5
2026-03-08 13:47:33,338 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b2: 0.85
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b3: 8
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --b4: 10
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --cores: 33
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --input_format: fasta
2026-03-08 13:47:33,339 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --log_path: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/log
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --output: /scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed-gblocks
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --output_format: nexus
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Argument --verbosity: INFO
2026-03-08 13:47:33,340 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Getting aligned sequences for trimming
2026-03-08 13:47:33,427 - phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed - INFO - Alignment trimming begins.
..............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 141, in get_and_trim_alignments
with open(trimmed_aln_file, "rU") as trimmed_aln:
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed/uce-990291357.fasta-gb'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 224, in
main()
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/bin/phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", line 208, in main
alignments = pool.map(get_and_trim_alignments, params)
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 266, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home1/05600/eeeaston/miniconda3/envs/phyluce-1.7.3/lib/python3.6/multiprocessing/pool.py", line 644, in get
raise self._value
FileNotFoundError: [Errno 2] No such file or directory: '/scratch/05600/eeeaston/trim_Sibo/taxon-sets-trimmed/all/mafft-nexus-internal-trimmed/uce-990291357.fasta-gb'