squid

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squid running errors

2

Hello, when I analyze my BWA mapped BAM files, I got the following error: squid: src/SegmentGraph.cpp:2489: void SegmentGraph_t::CompressNode(): Assertion `LinkedNode.s ize()!=0' failed. /var/spool/torque/mom_priv/jobs/10249993.mesabim3.msi.umn.edu.SC: line 9: 6359 Aborted (core dumped) squid...

cauyrd

squid errors

1

[Mon Oct 7 13:51:39 2019] Start reading bam file. [Mon Oct 7 13:51:58 2019] Finish sorting Chimeric bam reads. [Mon Oct 7 13:52:00 2019] Finish removing PCR duplicates. [Mon Oct...

jchenpku

Increase sensitivity of SQUID

1

Hi, I'm wonder if there is a parameter where you can increase the sensitivity of SQUID by lowering the number of reads supporting the fusion (the SCORE field in the...

readmanchiu

void segmentGraph aborted

5

I attempt to identify the variants in our samples using squid. I aligned the reads using STAR 2-pass including chimeric bam. Squid run was aborted after build nodes, finish seeding...

srajedwin

Bioconda package?

3

Hi, did you have a look at making a Bioconda package for this? Would make installation easy and you will get automatically a Docker container for the tool resolving for...

apeltzer

Hi Looks very interesting would it be possible for you guys to setup a docker image? It would make installation so much easier, thanks cheers, Fabian

FabianGrammes

Long-read data

1

Hi, Stupid question from rookie; Is this working for long read data, like Oxford Nanopore? Thank you! Peny

OxPen

Segmentation fault: 11

8

Trying to run squid with star-fusion output but it terminates with segmentation fault: 11 Any suggestions on how to fix this issue?

ghost

Question: removing PCR duplicates

1

Dear all, should PCR duplicates be removed from the BAM file before running SQUID? I see a message saying that SQUID is removing PCR duplicates but it is quite fast,...

fgvieira

Error: munmap_chunk(): invalid pointer: xxxxxx

4

I build squid from source and tried it on one of my sample, but encountered an error and it aborted: ``` $ ./squid-1.0/bin/squid -b Aligned.sortedByCoord.out.bam -c Chimeric.bam -G 1 -CO...

ycl6