Critical Error: Unable to gunzip input file:

Infrastructure and utilities bioBakery workflows
1

Task 61 failed
Name: kneaddata____BIKE016A_lib515676_7680_3
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/anaconda3/envs/metaphlan/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `kneaddata --input /mnt/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/BIKE016A_lib515676_7680_3.R1.fastq.gz --output /mnt/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/mnt/e/workflow_output/kneaddata/main --threads 1 --output-prefix BIKE016A_lib515676_7680_3 --input /mnt/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/BIKE016A_lib515676_7680_3.R2.fastq.gz --cat-final-output --reference-db /mnt/e/biobakery_workflow_databases/kneaddata_db_human_genome --serial --run-trf ’ failed.
Out: b’Decompressing gzipped file …\n\nDecompressing gzipped file …\n\n’
Err: b’Critical Error: Unable to gunzip input file: /mnt/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/BIKE016A_lib515676_7680_3.R2.fastq.gz\n’

Task 119 failed
Name: metaphlan____BIKE016A_lib515676_7680_3
Original error:
Task failed because parent task `61’ failed
Task 325 failed
Name: strainphlan_sample2markers____BIKE016A_lib515676_7680_3
Original error:

2

Hello, Thank you for providing the full error traceback. Can you check to see if the file /mnt/d/DATOSSECUENCIACION/MVT-prj10_rendimiento_deportivo/BIKE/BIKE016A_lib515676_7680_3.R2.fastq.gz is indeed a gzip file and if so it you can gunzip it? It looks like the software is having an issue trying to decompress the file.

Thank you,
Lauren