Open ebprideaux opened 2 years ago
This issue in gemBS is almost exactly the same as yours: https://github.com/heathsc/gemBS/issues/37 , although I'm not sure if it is relevant to the version of gemBS used in the pipeline. You may be able to work around by passing in "wgbs.underconversion_sequence_name": "chrL"
in your input. Since it looks like you used a lambda control you probably want to have this value there anyway so you can get the QC value for the bisulfite conversion rate.
FYI Conda isn't supported by this pipeline. I'd recommend using Docker, or if your HPC doesn't allow it then Singularity would be an option. In theory it should "just work" but in practice there can be quirks due to differences between the runtimes. I haven't tested this pipeline myself with Singularity so I can't say for sure.
By the way, looking at your input files, it looks like you might have paired-end data? You have it specified as
"wgbs.fastqs": [
[
[
"/resource3/data/WGBS/RawData/222_S2_L004_R1_001.fastq.gz"
],
[
"/resource3/data/WGBS/RawData/222_S2_L004_R2_001.fastq.gz"
]
],
[
[
"/resource3/data/WGBS/RawData/Control_S1_L004_R1_001.fastq.gz"
],
[
"/resource3/data/WGBS/RawData/Control_S1_L004_R2_001.fastq.gz"
]
]
],
but if they are in fact paired, the two files should be placed in the same array like this:
"wgbs.fastqs": [
[
[
"/resource3/data/WGBS/RawData/222_S2_L004_R1_001.fastq.gz",
"/resource3/data/WGBS/RawData/222_S2_L004_R2_001.fastq.gz"
]
],
[
[
"/resource3/data/WGBS/RawData/Control_S1_L004_R1_001.fastq.gz",
"/resource3/data/WGBS/RawData/Control_S1_L004_R2_001.fastq.gz"
]
]
],
I went ahead and changed the json input to reflect paired-end data. Thank you!
I believe my original json input already had:
"wgbs.underconversion_sequence_name": "chrL"
Is this what you were referring to?
Our HPC doesn't allow Docker. I don't have experience with Singularity, but may need to talk with our sysadmin about adding it (I don't have root privileges).
I am re-running with updated json input to see if error is replicated. Will follow up with results. RHwgbsinput copy.json.update.txt
Yeah sorry I missed that in the input, that's what I was referring to. In that case it looks OK then. If it still fails I would double check your gemBS version. You can see how it is installed in the pipeline here:
Confirming it failed on the same task:
==== NAME=wgbs.map, STATUS=Failed, PARENT= SHARD_IDX=1, RC=1, JOB_ID=17853 START=2021-10-15T19:22:17.505Z, END=2021-10-15T19:27:35.017Z STDOUT=/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/stdout STDERR=/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/stderr STDERR_CONTENTS= : : Command map started at 2021-10-15 12:26:08.265708 : : ------------ Mapping Parameters ------------ : Sample barcode : sample_1 : Data set : 1 : No. threads : 8 : Index : indexes/hg38.BS.gem : Paired : True : Read non stranded: False : Type : PAIRED : Input Files : ./fastq/1/Control_S1_L004_R1_001.fastq.gz,./fastq/1/Control_S1_L004_R2_001.fastq.gz : Output dir : ./mapping/sample_1 : : Bisulfite Mapping... TypeError: sequence item 17: expected str instance, NoneType found ln: failed to access '/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/mapping//*.bam': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/mapping/*/.csi': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/mapping//*.bam.md5': No such file or directory ln: failed to access '/resource3/data/WGBS/Processed/wgbs/2ef10817-0cfc-4575-b976-16e85d0a46a3/call-map/shard-1/attempt-2/execution/mapping/*/.json': No such file or directory
Looks like the gemBS conda installed is gembs-3.2.0 (released june 2018). I think this is likely the problem. From your link earlier, they pushed a new version that incorporated changes fixing this TypeError. Will try updating and get back to you.
Describe the bug At the wgbs.map step, I get a TypeError:
How can I resolve this error?
OS/Platform
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 withcaper list
or directly use ametadata.json
file on Caper's output directory.cromwell.out.txt
Input JSON File json_input.txt