Segmentation fault when activating soloMultiMappers

[pietermonsieurs]

Hi,
I have problems running the STAR solo implementation with the multimapper function enabled. The problem description is very similar to this (solved) issue: #1166

When I run the command without the --soloMultiMappers flag enable, everything works ok. However, when enabling this flag, I get a segmentation fault after "started Solo counting". This error occurs with any of the mulitmapper algorithms (uniform, PropUnique, EM, Rescue).

Strange thing is that - using exactly the same command and input files - this runs (with multimapper enabled) without any error on my MacBook, however, it fails when installed on our supercomputer (both for 2.7.9.a and 2.7.10.a). Any idea what can go wrong? I also copy-paste the full error message. Log files are not produced when segmentation fault is raised.

Thanks!
Kind regards,
Pieter

Mar 22 13:45:58 ..... started STAR run
Mar 22 13:46:04 ..... loading genome
Mar 22 13:46:05 ..... started mapping
Mar 22 13:46:07 ..... finished mapping
Mar 22 13:46:07 ..... started Solo counting
Segmentation fault (core dumped)

*** Error in `/user/antwerpen/205/vsc20587/data/STAR/source/STAR': double free or corruption (out): 0x000000001ead9fe0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b4d201f9329]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x41fa67]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x44a316]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x4706f5]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x46b742]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x40ef1d]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b4d2019a555]
/user/antwerpen/205/vsc20587/data/STAR/source/STAR[0x41b0c0]
======= Memory map: ========
00400000-005c8000 r-xp 00000000 00:2c 19428077601 /data/antwerpen/205/vsc20587/STAR/source/STAR
007c8000-007c9000 r--p 001c8000 00:2c 19428077601 /data/antwerpen/205/vsc20587/STAR/source/STAR
007c9000-007d7000 rw-p 001c9000 00:2c 19428077601 /data/antwerpen/205/vsc20587/STAR/source/STAR
007d7000-007d9000 rw-p 00000000 00:00 0
00ea0000-1eb06000 rw-p 00000000 00:00 0 [heap]
2b4d1f0dc000-2b4d1f0fe000 r-xp 00000000 08:03 297682 /usr/lib64/ld-2.17.so
2b4d1f0fe000-2b4d1f101000 rw-p 00000000 00:00 0
2b4d1f10f000-2b4d1f196000 rw-p 00000000 00:00 0
2b4d1f2fd000-2b4d1f2fe000 r--p 00021000 08:03 297682 /usr/lib64/ld-2.17.so
2b4d1f2fe000-2b4d1f2ff000 rw-p 00022000 08:03 297682 /usr/lib64/ld-2.17.so
2b4d1f2ff000-2b4d1f300000 rw-p 00000000 00:00 0
2b4d1f300000-2b4d1f315000 r-xp 00000000 08:03 296909 /usr/lib64/libz.so.1.2.7
2b4d1f315000-2b4d1f514000 ---p 00015000 08:03 296909 /usr/lib64/libz.so.1.2.7
2b4d1f514000-2b4d1f515000 r--p 00014000 08:03 296909 /usr/lib64/libz.so.1.2.7
2b4d1f515000-2b4d1f516000 rw-p 00015000 08:03 296909 /usr/lib64/libz.so.1.2.7
2b4d1f516000-2b4d1f5ff000 r-xp 00000000 08:03 297065 /usr/lib64/libstdc++.so.6.0.19
2b4d1f5ff000-2b4d1f7ff000 ---p 000e9000 08:03 297065 /usr/lib64/libstdc++.so.6.0.19
2b4d1f7ff000-2b4d1f807000 r--p 000e9000 08:03 297065 /usr/lib64/libstdc++.so.6.0.19
2b4d1f807000-2b4d1f809000 rw-p 000f1000 08:03 297065 /usr/lib64/libstdc++.so.6.0.19
2b4d1f809000-2b4d1f81e000 rw-p 00000000 00:00 0
2b4d1f81e000-2b4d1f91f000 r-xp 00000000 08:03 297258 /usr/lib64/libm-2.17.so
2b4d1f91f000-2b4d1fb1e000 ---p 00101000 08:03 297258 /usr/lib64/libm-2.17.so
2b4d1fb1e000-2b4d1fb1f000 r--p 00100000 08:03 297258 /usr/lib64/libm-2.17.so
2b4d1fb1f000-2b4d1fb20000 rw-p 00101000 08:03 297258 /usr/lib64/libm-2.17.so
2b4d1fb20000-2b4d1fb45000 r-xp 00000000 08:03 297409 /usr/lib64/libgomp.so.1.0.0
2b4d1fb45000-2b4d1fd44000 ---p 00025000 08:03 297409 /usr/lib64/libgomp.so.1.0.0
2b4d1fd44000-2b4d1fd45000 r--p 00024000 08:03 297409 /usr/lib64/libgomp.so.1.0.0
2b4d1fd45000-2b4d1fd46000 rw-p 00025000 08:03 297409 /usr/lib64/libgomp.so.1.0.0
2b4d1fd46000-2b4d1fd5b000 r-xp 00000000 08:03 297435 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b4d1fd5b000-2b4d1ff5a000 ---p 00015000 08:03 297435 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b4d1ff5a000-2b4d1ff5b000 r--p 00014000 08:03 297435 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b4d1ff5b000-2b4d1ff5c000 rw-p 00015000 08:03 297435 /usr/lib64/libgcc_s-4.8.5-20150702.so.1
2b4d1ff5c000-2b4d1ff73000 r-xp 00000000 08:03 297132 /usr/lib64/libpthread-2.17.so
2b4d1ff73000-2b4d20172000 ---p 00017000 08:03 297132 /usr/lib64/libpthread-2.17.so
2b4d20172000-2b4d20173000 r--p 00016000 08:03 297132 /usr/lib64/libpthread-2.17.so
2b4d20173000-2b4d20174000 rw-p 00017000 08:03 297132 /usr/lib64/libpthread-2.17.so
2b4d20174000-2b4d20178000 rw-p 00000000 00:00 0
2b4d20178000-2b4d2033c000 r-xp 00000000 08:03 297554 /usr/lib64/libc-2.17.so
2b4d2033c000-2b4d2053b000 ---p 001c4000 08:03 297554 /usr/lib64/libc-2.17.so
2b4d2053b000-2b4d2053f000 r--p 001c3000 08:03 297554 /usr/lib64/libc-2.17.so
2b4d2053f000-2b4d20541000 rw-p 001c7000 08:03 297554 /usr/lib64/libc-2.17.so
2b4d20541000-2b4d2391e000 rw-p 00000000 00:00 0
2b4d2444c000-2b4d3ba80000 rw-p 00000000 00:00 0
2b4d3c4f9000-2b4d4526e000 rw-p 00000000 00:00 0
2b4d48000000-2b4d48021000 rw-p 00000000 00:00 0
2b4d48021000-2b4d4c000000 ---p 00000000 00:00 0
7ffe3361f000-7ffe33668000 rw-p 00000000 00:00 0 [stack]
7ffe336f0000-7ffe336f2000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)

[alexdobin]

Hi Pieter,

please try this patch that may have some seg-faults.
If it does not help, I would ask you for a minimal example and STAR parameter to reproduce the problem.

Thanks,
Alex

[pietermonsieurs]

Hi Alex,
Thanks for the reply.
Installing the latest version still results in a segmentation fault:

I have create a minimal example, added to this issue (debug.zip). This contains examples fastq files (R1 with UMI and barcode information and R2 with transcript information), the reference genome information and the barcode whitelist file.
debug.zip

The command I am using:
STAR
--readFilesCommand zcat
--readFilesIn gex_sample01_debug_S1_L001_R2_001.fastq.gz gex_sample01_debug_S1_L001_R1_001.fastq.gz
--soloType CB_UMI_Simple
--soloCBwhitelist 3M-february-2018.txt
--soloCBstart 1 --soloCBlen 16
--soloUMIstart 17 --soloUMIlen 12
--soloFeatures Gene
--genomeDir ./Ldon
--soloMultiMappers Uniform
--outFileNamePrefix ./debug/
--outSAMtype BAM SortedByCoordinate

Kind regards,
Pieter

[rlinder02]

Hi Alex,

Hope all is well! I am having a very similar issue as Pieter- when I run --soloMultiMappers, I get a segmentation fault; if I run STAR without this parameter, everything runs smoothly. I haven't tried running it on my macbook (having some issues getting it to build), but when I run it using either RedHat or Ubuntu distributions of Linux, I get the segmentation fault error. The container I'm using to run it is in docker hub under rlinder02/starsolo-sc-rnaseq. I'm attaching a screenshot of the Valgrind output with all the parameters used listed. Let me know if there's anything else you need. Thanks!!

Best,
Rob

[alexdobin]

Hi Rob,

please try this patch, I think it should have fixed this bug:
https://github.com/alexdobin/STAR/releases/tag/2.7.10a_alpha_220818

[rlinder02]

Hi Alex,

Thanks so much! This seems to have fixed it- runs without errors :) Have a great week!

Best,
Rob