snakepipes: error in chip-seq using Genrich as mapper

I stumbled upon this error:

Sample sheet found and header is ok!

---- This analysis has been done using snakePipes version 2.7.3 ----
Sample sheet found and header is ok!
Building DAG of jobs...
InputFunctionException in line 164 of /home/tgeorgom/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile:
Error:
  TypeError: can only concatenate str (not "bool") to str
Wildcards:
  group=DMSO_POLII
Traceback:
  File "/home/tgeorgom/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile", line 167, in <lambda>
  File "/home/tgeorgom/mambaforge/envs/snakePipes/lib/python3.11/site-packages/snakePipes/shared/rules/ChIP_peak_calling_spikein.snakefile", line 167, in <listcomp>

 Spikein genome detected - at least one spikeIn chromosome found with extention _spikein .


Error: snakemake returned an error code of 1, so processing is incomplete!

the command is:

ChIP-seq -d /mnt/c/AP04/ -j 8 --local --useSpikeInForNorm --getSizeFactorsFrom genome --peakCaller Genrich  --sampleSheet /mnt/c/AP04/PolII.tsv --w
indowSize 500 --plotFormat "pdf"  mm10_gencodeM19_spikesTEST /mnt/c/AP04/PolII_ChIPtype.yalm

the samplelist is:

name    condition
A006850324_209957_S1_L000       DMSO_POLII
A006850324_209960_S2_L000       DMSO_POLII
A006850324_209962_S3_L000       DMSO_POLII
A006850324_209964_S4_L000       AA5_POLII
A006850324_209966_S5_L000       AA5_POLII
A006850324_209968_S6_L000       AA5_POLII

and the yalm file for the peak type is:

chip_dict:
  A006850324_209957_S1_L000:
    broad: False
  A006850324_209960_S2_L000:
    broad: False
  A006850324_209962_S3_L000:
    broad: False
  A006850324_209964_S4_L000:
    broad: False
  A006850324_209966_S5_L000:
    broad: Fasle
  A006850324_209968_S6_L000:
    broad: False

the -d folder contains the following:

Bowtie2
ChIP-seq.cluster_config.yaml
ChIP-seq.config.yaml
ChIP-seq_organism.yaml
ChIP-seq_run-4.log
DNA-mapping.cluster_config.yaml
DNA-mapping.config.yaml
DNA-mapping_organism.yaml
DNA-mapping_run-4.log
DNA-mapping_tools.txt
FASTQ_fastp
FastQC
FastQC_trimmed
PolII.tsv
PolII_ChIPtype.yalm
PolII_ChIPtype_all.yalm
Sambamba
Ser5PolII.tsv
bamCoverage
chip_samples.yaml
chip_seq_sample_config.PREDICTED.yaml
cluster_logs
deepTools_qc
fastq
filter_rules
filtered_bam
multiQC

About this issue

  • Original URL
  • State: closed
  • Created 8 months ago
  • Comments: 21

Most upvoted comments

In addition, shouldn’t I first activate the snakepipes_develop and then do pip install --upgrade . ? because where pip will do the update? I assume in the base environment

ah sorry, it should perhaps read git clone instead of git checkout