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sunnyisgalaxy / moabs

A comprehensive, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data
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Segmentation Faulting #23

Open Atalasia opened 4 years ago

Atalasia commented 4 years ago

Hello, I am trying to run mcall module but segfaulting. I've tried to google/solve it myself, but I haven't had any success.

I am running a target position specific bisulfite sequencing (not WGBS, RRBS) following the programs method listed in a paper (Targeted bisulfite sequencing of the dynamic DNA methylome, Ziller et al. 2016). Essentially it's following Bismark -> Picard (dedup, sort) -> mcall

I've used a precompiled binary in the moabs-1.3.8.7 version and 1.3.8.6 but still, the same error. Following is from stdout.

This is the command that I used. mcall -m <bam> -r <hg38.fa> *I've used one sample in this example, but running multiple samples still show the same error.

./moabs.sh /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam
Options are saved in file run.config and printed here:
cytosineMinScore=20
excludedFlag=0
fullMode=0
keepTemp=0
mappedFiles=/data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam
minFragSize=0
minMMFragSize=0
nextBaseMinScore=3
processPEOverlapSeq=1
qualityScoreBase=0
reference=/data/REFERENCE/hg38/hg38.fa
reportCHX=X
reportCpX=G
requiredFlag=0
skipRandomChrom=1
statsOnly=0
threads=1
trimRRBSEndRepairSeq=2
trimWGBSEndRepairPE1Seq=3
trimWGBSEndRepairPE2Seq=3
Program started
From the extension of file /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam, program is parsing file according to BAM foramt
XR:Z or ZR:Z:, or ZS:Z: field not found, that is totally fine.
For file /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam, the quality score format is Sanger format based at 33!
Protocol and read length are detected as WGBS and 151 bases for file /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam
For file /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam the number of all reads is 17360352 and the number of mapped reads is 17360352
Start processing file /data/PMP/p_test/02.bm_bam/CRC_1124_1_bismark_bt2_pe.srt.bam on chrom chr1
./moabs.sh: line 9: 21517 Segmentation fault      $mcall -m $inbam -r $ref
lijinbio commented 4 years ago

Due to version changes, a Bismark BAM file is not suitable for MCALL. Please try to generate the BAM file using BSMAP, which is also a component in MOABS.

paulmenzel commented 3 years ago

@Atalasia, it’d be great, if you followed up on this issue.