mskcc/facets-suite

Please update docker image

zhouzhendiao opened this issue · 0 comments

Recently I used this pipeline in docker. It's very convenient to generate downstream outputs, thanks!
However, I encountered some issues during the analysis.

  1. Error when running snp-pileup binary
docker run -v $PWD:/work philipjonsson/facets-suite:dev /usr/bin/snp-pileup \
    --count-orphans \
    --gzip \
    --pseudo-snps 50 \
    --max-depth 4000 \
    /work/common.sample.vcf.gz \
    /work/TCRBOA6.csv.gz \
    /work/TCRBOA6-N-WEX.sample.bam \
    /work/TCRBOA6-T-WEX.sample.bam
*** Error in `/usr/bin/snp-pileup': double free or corruption (out): 0x000055a0042a45e0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x70bfb)[0x7ff3c0f52bfb]
/lib/x86_64-linux-gnu/libc.so.6(+0x76fc6)[0x7ff3c0f58fc6]
/lib/x86_64-linux-gnu/libc.so.6(+0x7780e)[0x7ff3c0f5980e]
/usr/lib/x86_64-linux-gnu/libtasn1.so.6(+0xb33f)[0x7ff3bbe9b33f]
/usr/lib/x86_64-linux-gnu/libtasn1.so.6(asn1_delete_structure2+0xf7)[0x7ff3bbe9c4b7]
/usr/lib/x86_64-linux-gnu/libgnutls.so.30(+0x4e42f)[0x7ff3bd7cb42f]
/lib64/ld-linux-x86-64.so.2(+0xfd6a)[0x7ff3c1dd9d6a]
/lib/x86_64-linux-gnu/libc.so.6(+0x35940)[0x7ff3c0f17940]
/lib/x86_64-linux-gnu/libc.so.6(+0x3599a)[0x7ff3c0f1799a]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf8)[0x7ff3c0f022e8]
/usr/bin/snp-pileup(+0x221a)[0x55a0031ef21a]
======= Memory map: ========
55a0031ed000-55a0031f8000 r-xp 00000000 00:25e 26                        /usr/bin/snp-pileup
55a0033f7000-55a0033f8000 r--p 0000a000 00:25e 26                        /usr/bin/snp-pileup
55a0033f8000-55a0033f9000 rw-p 0000b000 00:25e 26                        /usr/bin/snp-pileup
55a004299000-55a00432f000 rw-p 00000000 00:00 0                          [heap]
...
  1. bugs in run-facets-wrapper_fixbug.R, I think these are due to not updating to the latest version.
    e.g. not initialize variable ploidy in function gene_level_changes, not parse argument --diplogr as "double".