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qiaseq / smcounter-v2-paper

Data and code supporting smCounter-v2-paper
https://www.biorxiv.org/content/early/2018/03/14/281659
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error with smcounter2 #3

Open lijuanzhang218 opened 4 years ago

lijuanzhang218 commented 4 years ago

Hi, I'm trying to use smcounter2 to detect SNV on my UMI-based data. But I got a error like this when I use M0253.bam to test.

started at 2020-01-15 17:24:49.944421 ('repBed', '/apps/user/zhanglijuan/software/smcounter2/share/smcounter2-0.1.2018.08.28-0/data/annotation/hg19/simpleRepeat.full.bed') ('bamFile', '/apps/user/zhanglijuan/618G/UMI/smcounter2/M0253.bam') ('rpb', 5.0) ('mismatchThr', 6.0) ('hpLen', 8) ('inputVCF', 'none') ('srBed', '/apps/user/zhanglijuan/software/smcounter2/share/smcounter2-0.1.2018.08.28-0/data/annotation/hg19/SR_LC_SL.full.bed') ('bamType', 'raw') ('refGenome', '/apps/database/hg19/ucsc.hg19.fasta') ('nCPU', 40) ('maxAltAllele', 3) ('primerDist', 2) ('bedTarget', '/apps/user/zhanglijuan/618G/UMI/smcounter2/DHS-101Z.primer3.roi.bed') ('primerSide', 1) ('mtThreshold', 0.8) ('runPath', '/apps/user/zhanglijuan/618G/UMI/smcounter2/result_M0253') ('outPrefix', 'M0253') ('ds', 10000) ('minBQ', 25) ('isRna', False) ('minMQ', 50) ('minAltUMI', 3) rpb = 5.0, given by user Traceback (most recent call last): File "/apps/user/zhanglijuan/software/smcounter2/bin/smCounter2", line 177, in main(args) File "/apps/user/zhanglijuan/software/smcounter2/bin/smCounter2", line 131, in main for interval_result in pool.map(func,locList): File "/apps/user/zhanglijuan/software/Python-2.7.6/build/lib/python2.7/multiprocessing/pool.py", line 250, in map return self.map_async(func, iterable, chunksize).get() File "/apps/user/zhanglijuan/software/Python-2.7.6/build/lib/python2.7/multiprocessing/pool.py", line 554, in get raise self._value UnboundLocalError: local variable 'pos' referenced before assignment

Can you help me to solve this? Hoping to your reply. Thanks!

lijuanzhang218 commented 4 years ago

And can you tell me how do you add UMI to bam file as such format "Mi:Z:chr1-1-115251626-CTGGGCTTGTTA pr:Z:chr1-1-115252239-32 re:i:0 NM:i:0 AS:i:127 XS:i:0 mi:Z:CTGGGCTTGTTA"? In my own bam file added UMI, there's only has this "SA:Z:chr17,22020694,+,45S105M,3,6; MC:Z:7H143M MD:Z:27C50 RG:Z:41128051 NM:i:1 AS:i:73 XS:i:0 RX:Z:GGGTACGAA"

left-castle commented 4 years ago

Maybe it is a matter of pysam. Which version of pysam do you use? I had same error with pysam 0.15.4. Now I use pysam 0.11.2.2, so it works.