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ewels / clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
https://ewels.github.io/clusterflow/
GNU General Public License v3.0
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Bismark methylation extractor error #20

Closed ewels closed 9 years ago

ewels commented 9 years ago

Bismark methylation extrator module threw the following warning and later failed:

Reference found where even-sized list expected at /bi/apps/clusterflow/0.4_devel/modules/../source/CF/Helpers.pm line 262.

This somehow seems to then lead to bismark not being given a reference genome:

bismark_methylation_extractor --multi 4  --ignore_r2 2 --bedGraph --counts  --cytosine_report --gzip -p --no_overlap --report  lane2_5pc_SCM_ox_ATCACGTT_L002_R1_val_1.fq.gz_bismark_bt2_pe.deduplicated.bam
Please specify a genome folder to proceed (full path only)

Note - I was messing around with this command recently to get it to do the coverage analysis, so the first warning could be a red herring.

ewels commented 9 years ago

@FelixKrueger - I'm a bit confused by this bug report. I think our code bases must be different as line 262 shouldn't be able to generate that first warning.

Could you dig a little further back from the warning messages to find the code responsible please? Or let me know the steps I need to do to reproduce the error..

FelixKrueger commented 9 years ago

Maybe it is not worth digging much deeper for this at the current time, we have changed so many things lately. How about I report back if I find a new problem? Apparently I’ve now got push access to our BI_devel version for CF, from which you can merge things…

ewels commented 9 years ago

Ok, I'm closing this for now then. Feel free to re-open or create a new issue if this turns up again.