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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Issue with bowtie2 #390

Closed ckntav closed 3 years ago

ckntav commented 3 years ago

Hello, I'm trying to run HiC-Pro through the singularity container with the test data. It seems that there is an error with bowtie2:

Run HiC-Pro 2.11.4

Mon Dec 14 15:19:17 EST 2020 Bowtie2 alignment step1 ... Logs: logs/dixon_2M/mapping_step1.log Exit: Error in reads alignment - Exit make: *** [/usr/local/bin/HiC-Pro_2.11.4/bin/../scripts//Makefile:88: bowtie_global] Error 1

Here is what it is written in SRR400264_00_R2_bowtie2.log:

HiC-Pro mapping

perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "fr_CA.UTF-8", LANG = "C" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Error: Bad function type 'sL'. Should be C (constant), L (linear), S (square root) or G (natural log). Error: Encountered internal Bowtie 2 exception (#1) Command: /usr/local/anaconda/bin/bowtie2-align-s --wrapper basic-0 --very-sensitive -L 30 --score-min sL,-0.6,-0.2 --end-to-end --reorder --rg-id BMG --rg SM:SRR400264_00_R2 -p 1 -x path_to/input/bowtie_indexes/hg19 --passthrough -U rawdata/dixon_2M/SRR400264_00_R2.fastq.gz (ERR): bowtie2-align exited with value 1

NB: I replace the absolute path of bowtie2 indexes with path_to

Do you have an idea of what happened?

Thanks,

Chris

nservant commented 3 years ago

Hi Chris, I think it has nothing to do with HiC-Pro itself ... but more with bowtie2. My feeling is that bowtie2 is not proprely installed. best

ckntav commented 3 years ago

Hello, thank you for your feedback. I finally installed HiC-Pro from source on the cluster. It seems to run well but I'm concerned about one message in the log file. That message is described in Issue #227, so I commented there. Best