TypeError in wgbs.map Step

[ebprideaux]

Describe the bug At the wgbs.map step, I get a TypeError:

==== NAME=wgbs.map, STATUS=Failed, PARENT= SHARD_IDX=1, RC=1, JOB_ID=9608 START=2021-10-15T03:04:21.289Z, END=2021-10-15T03:09:23.663Z STDOUT=/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/stdout STDERR=/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/stderr STDERR_CONTENTS= : : Command map started at 2021-10-14 20:08:16.349606 : : ------------ Mapping Parameters ------------ : Sample barcode : sample_1 : Data set : 1 : No. threads : 8 : Index : indexes/hg38.BS.gem : Paired : False : Read non stranded: False : Type : SINGLE : Input Files : ./fastq/1/Control_S1_L004_R2_001.fastq.gz : Output dir : ./mapping/sample_1 : : Bisulfite Mapping... TypeError: sequence item 14: expected str instance, NoneType found ln: failed to access '/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/mapping//*.bam': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/mapping//.csi': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/mapping/**/.bam.md5': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed_Caper/wgbs/9f04e4dd-2a84-4af6-8731-d3c49f6e2782/call-map/shard-1/attempt-2/execution/mapping/**/*.json': No such file or directory

How can I resolve this error?

OS/Platform

• OS/Platform: Linux 7 CentOS on a Slurm-managed HPC
• Conda version: conda 4.10.3
• Pipeline version: 1.1.7
• Caper version: 1.6.3

Caper configuration file default.conf.txt

Error log Caper automatically runs a troubleshooter for failed workflows. If it doesn't then get a WORKFLOW_ID of your failed workflow with caper list or directly use a metadata.json file on Caper's output directory.

$ caper debug [WORKFLOW_ID_OR_METADATA_JSON_FILE]

cromwell.out.txt

Input JSON File json_input.txt