Closed mladen5000 closed 1 year ago
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.
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