Error during: extract-metagene-profiles (no files in without-rrna folder)

[HeyLifeHD]

Dear rp-bp authors, sorry for bothering again. While running "run-all-rpbp-instances" I get the following error: run-all-rpbp-instances \

/icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/191217_config.yaml \ --num-cpus 7 \ --merge-replicates \ --run-replicates \ --overwrite 61702418 reads; of these: 61702418 (100.00%) were unpaired; of these: 49678892 (80.51%) aligned 0 times 29570 (0.05%) aligned exactly 1 time 11993956 (19.44%) aligned >1 times 19.49% overall alignment rate Dec 18 11:23:07 ..... started STAR run Dec 18 11:23:08 ..... loading genome Dec 18 11:23:24 ..... processing annotations GTF Dec 18 11:23:44 ..... inserting junctions into the genome indices Dec 18 11:25:55 ..... started mapping Dec 18 11:25:57 ..... finished mapping Dec 18 11:25:58 ..... started sorting BAM Dec 18 11:25:58 ..... finished successfully WARNING root 2019-12-18 11:26:02,253 : [utils.create_symlink]: file already exists at: ' /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/hg19ensembl75_testRun/without-r rna-mapping/DAC-CHX-rep1.191217Ribo.bam'. It will be removed 0it [00:00, ?it/s] Traceback (most recent call last):
File "/home/heyj/miniconda3/envs/rbbp/bin/extract-metagene-profiles", line 8, in sys.exit(main()) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/ribo/pgrms/extract_m etagene_profiles.py", line 257, in main all_metagene_profile_dfs = pd.concat(all_metagene_profile_dfs) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pandas/core/reshape/conca t.py", line 228, in concat copy=copy, sort=sort) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pandas/core/reshape/conca t.py", line 262, in init raise ValueError('No objects to concatenate') ValueError: No objects to concatenate Traceback (most recent call last):
File "/home/heyj/miniconda3/envs/rbbp/bin/create-orf-profiles", line 11, in load_entry_point('rpbp==2.0.0', 'console_scripts', 'create-orf-profiles')() File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/rpbp/orf_profile_construc tion/create_orf_profiles.py", line 212, in main overwrite=args.overwrite, call=call) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py" , line 346, in call_if_not_exists
ret_code = check_call(cmd, call=call, raise_on_error=raise_on_error) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 194, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 177, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'extract-metagene-profiles /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/hg19ensembl75_testRun/without-rrna-mapping/DAC-CHX-rep1.191217Ribo-unique.bam /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/index/hg19ensembl75/hg19ensembl75/hg19ensembl75.annotated.bed.gz /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/hg19ensembl75_testRun/metagene-profiles/DAC-CHX-rep1.191217Ribo-unique.metagene-profile.csv.gz --num-cpus 7 --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --start-upstream 300 --start-downstream 300 --end-upstream 300 --end-downstream 300' returned non-zero exit status 1. Traceback (most recent call last):
File "/home/heyj/miniconda3/envs/rbbp/bin/run-rpbp-pipeline", line 11, in load_entry_point('rpbp==2.0.0', 'console_scripts', 'run-rpbp-pipeline')() File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/rpbp/run_rpbp_pipeline.py", line 139, in main shell_utils.check_call(cmd) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 194, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 177, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'create-orf-profiles /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/raw_data/DAC_CHX.fastq.gz /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/191217_config.yaml DAC-CHX-rep1 --num-cpus 7 --mem 2G --overwrite --logging-level WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR ' returned non-zero exit status 1. Traceback (most recent call last):
File "/home/heyj/miniconda3/envs/rbbp/bin/run-all-rpbp-instances", line 11, in load_entry_point('rpbp==2.0.0', 'console_scripts', 'run-all-rpbp-instances')() File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/rpbp/run_all_rpbp_instances.py", line 171, in main job_id = slurm.check_sbatch(cmd, args=args) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/slurm.py", line 183, in check_sbatch shell_utils.check_call(cmd, call=call) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 194, in check_call return check_call_step(cmd, call=call, raise_on_error=raise_on_error) File "/home/heyj/miniconda3/envs/rbbp/lib/python3.6/site-packages/pbio/misc/shell_utils.py", line 177, in check_call_step raise subprocess.CalledProcessError(ret_code, cmd) subprocess.CalledProcessError: Command 'run-rpbp-pipeline /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/raw_data/DAC_CHX.fastq.gz /icgc/dkfzlsdf/analysis/C010/tinat/191204_Riboseq/191217_rbbp/191217_config.yaml DAC-CHX-rep1 --num-cpus 7 --mem 2G --overwrite --logging-lev el WARNING --file-logging-level NOTSET --stdout-logging-level NOTSET --stderr-logging-level NOTSET --star-executable STAR ' returned non-zero exit status 1.

I think it is due to the missing input file in the without-rrna folder, but dont know how to prevent is. Thank you a lot in advance.

Best,

Joschka

[eboileau]

Hi, can you please use the template when creating a bug report? Please check that you have satisfied all the requirements, and make sure you are able to reproduce the error. It seems it could only be due to corrupted/empty files.