Error in rule concat_annotations
Closed this issue · 3 comments
AFAIK this is one of the remaining steps before the genomes/annotations/kegg_modules.tsv file, which I require in order to do functional analysis much like that done in the tutorial repo.
Removing temporary output genomes/all_contigs.fasta.
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Provided resources: mem_mb=60000, mem_mib=57221, disk_mb=1000, disk_mib=954, time=2, mem=60, time_min=120
Singularity containers: ignored
Select jobs to execute...
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 23/23 [00:00<00:00, 74.69it/s]
[Sat Apr 15 09:06:17 2023]
Error in rule concat_annotations:
jobid: 0
input: genomes/annotations/dram/intermediate_files/MAG18, genomes/annotations/dram/intermediate_files/MAG16, genomes/annotations/dram/intermediate_files/MAG19, genomes/annotations/dram/intermediate_files/MAG21, genomes/annotations/dram/intermediate_files/MAG15, genomes/annotations/dram/intermediate_files/MAG11, genomes/annotations/dram/intermediate_files/MAG04, genomes/annotations/dram/intermediate_files/MAG06, genomes/annotations/dram/intermediate_files/MAG01, genomes/annotations/dram/intermediate_files/MAG17, genomes/annotations/dram/intermediate_files/MAG22, genomes/annotations/dram/intermediate_files/MAG05, genomes/annotations/dram/intermediate_files/MAG13, genomes/annotations/dram/intermediate_files/MAG02, genomes/annotations/dram/intermediate_files/MAG09, genomes/annotations/dram/intermediate_files/MAG14, genomes/annotations/dram/intermediate_files/MAG12, genomes/annotations/dram/intermediate_files/MAG07, genomes/annotations/dram/intermediate_files/MAG20, genomes/annotations/dram/intermediate_files/MAG03, genomes/annotations/dram/intermediate_files/MAG08, genomes/annotations/dram/intermediate_files/MAG10, genomes/annotations/dram/intermediate_files/MAG23
output: genomes/annotations/dram/annotations.tsv, genomes/annotations/dram/rrnas.tsv, genomes/annotations/dram/trnas.tsv
RuleException:
FileNotFoundError in file /home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/atlas/workflow/rules/dram.smk, line 120:
[Errno 2] No such file or directory: 'genomes/annotations/dram/intermediate_files/MAG18/rrnas.tsv'
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/atlas/workflow/rules/dram.smk", line 120, in __rule_concat_annotations
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/atlas/workflow/scripts/utils/io.py", line 204, in pandas_concat
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/atlas/workflow/scripts/utils/io.py", line 131, in _pandas_concat_disck_based
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/util/_decorators.py", line 311, in wrapper
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 678, in read_csv
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 575, in _read
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 932, in init
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1216, in _make_engine
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/site-packages/pandas/io/common.py", line 786, in get_handle
File "/home/mrasic2/.conda/envs/atlas215/lib/python3.10/concurrent/futures/thread.py", line 58, in run
Removing output files of failed job concat_annotations since they might be corrupted:
genomes/annotations/dram/annotations.tsv
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Ok, could you check if the annotation for the genome MAG18 run correctly?
check the log logs/dram/run_dram/MAG18.log
Maybe you can delete the whole folder genomes/annotations/dram/intermediate_files/MAG18 and rerun atlas.
check if other genomes filed too.
I think it would generate (even with only a header) genomes/annotations/dram/intermediate_files/MAG18/rrnas.tsv
I think the header file would occur in a previous version, (either in 2.14.3 or 2.15 or previous DRAM), but since I updated this error started to appear. I checked my previous runs which also have logs that state that
"no rrnas were found so rrnas.tsv not created"
Possibly a change in dram.smk since 2.13? Additionally I know DRAM was upgraded so it could be something on their end that changed.
I was able to manually workaround this by creating rrnas.tsv with just the header so that pandas concat could work. The rule completed successfully and I was able to generate a kegg_modules file.
I am having issues to dram destill still but I will open in a separate issue.
There was no activity since some time. I hope your issue is solved in the mean time.
This issue will automatically close soon if no further activity occurs.
Thank you for your contributions.