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alexdobin / STAR

RNA-seq aligner
MIT License
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Seg fault on CentOS_7.9.2009 #1907

Open yagam-fluent opened 1 year ago

yagam-fluent commented 1 year ago

Hi Alex,

Please see below. All relevant files are attached. Everything works just fine on other Linux distributions, including an earlier version of CentOS. Using another index works fine, it's just this one that has issues.

cat /etc/os-release NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

/home/centos/pipeline/src/STAR/linux/STAR --genomeDir /home/centos/pipeline/test/test_data/STAR_index --readFilesIn /tmp/tmpebnim5/threads_0/out/barcoded_fastqs/barcoded_1_R2.fastq.gz,/tmp/tmpebnim5/threads_0/out/barcoded_fastqs/barcoded_2_R2.fastq.gz /tmp/tmpebnim5/threads_0/out/barcoded_fastqs/barcoded_1_R1.fastq.gz,/tmp/tmpebnim5/threads_0/out/barcoded_fastqs/barcoded_2_R1.fastq.gz --soloCBwhitelist /tmp/tmpebnim5/threads_0/out/barcodes/barcode_whitelist.txt --outFileNamePrefix /tmp/tmpebnim5/threads_0/out/starsolo/ --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --runThreadN 8 --alignIntronMin 20 --soloType CB_UMI_Simple --soloUMIdedup 1MM_CR --outFilterMultimapNmax 20 --soloCellFilter None --soloCellReadStats Standard --soloBarcodeMate 0 --soloCBmatchWLtype Exact --limitOutSJcollapsed 3000000 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --soloFeatures GeneFull --outSAMtype BAM Unsorted --outSAMmode NoQS --outSAMreadID Number --outSAMattributes gx HI CR UR --soloMultiMappers Unique --readFilesCommand zcat

    STAR version: 2.7.10a_alpha_220818   compiled: 2022-09-27T13:54:45+0000 :/home/STAR-2.7.10a_alpha_220818/source

Jul 20 23:56:50 ..... started STAR run Jul 20 23:56:50 ..... loading genome Error in `/home/centos/pipeline/src/STAR/linux/STAR': corrupted size vs. prev_size: 0x00000000024756a0 ======= Backtrace: ========= /lib64/libc.so.6(+0x7f474)[0x7f038b8d9474] /lib64/libc.so.6(+0x8156b)[0x7f038b8db56b] /lib64/libc.so.6(fclose+0x177)[0x7f038b8c8247] /lib64/libstdc++.so.6(_ZNSt12basic_fileIcE5closeEv+0x3e)[0x7f038c5fe54e] /lib64/libstdc++.so.6(_ZNSt13basic_filebufIcSt11char_traitsIcEE5closeEv+0xae)[0x7f038c6396ce] /home/centos/pipeline/src/STAR/linux/STAR[0x51f9eb] /home/centos/pipeline/src/STAR/linux/STAR[0x40f357] /lib64/libc.so.6(libc_start_main+0xf5)[0x7f038b87c555] /home/centos/pipeline/src/STAR/linux/STAR[0x41b110] ======= Memory map: ======== 00400000-005c9000 r-xp 00000000 103:01 5267212 /home/centos/pipeline/src/STAR/linux/STAR 007c8000-007c9000 r--p 001c8000 103:01 5267212 /home/centos/pipeline/src/STAR/linux/STAR 007c9000-007d7000 rw-p 001c9000 103:01 5267212 /home/centos/pipeline/src/STAR/linux/STAR 007d7000-007d9000 rw-p 00000000 00:00 0 02452000-0254d000 rw-p 00000000 00:00 0 [heap] 7f0384000000-7f0384021000 rw-p 00000000 00:00 0 7f0384021000-7f0388000000 ---p 00000000 00:00 0 7f038b7fc000-7f038b85a000 rw-p 00000000 00:00 0 7f038b85a000-7f038ba1e000 r-xp 00000000 103:01 12583931 /usr/lib64/libc-2.17.so 7f038ba1e000-7f038bc1d000 ---p 001c4000 103:01 12583931 /usr/lib64/libc-2.17.so 7f038bc1d000-7f038bc21000 r--p 001c3000 103:01 12583931 /usr/lib64/libc-2.17.so 7f038bc21000-7f038bc23000 rw-p 001c7000 103:01 12583931 /usr/lib64/libc-2.17.so 7f038bc23000-7f038bc28000 rw-p 00000000 00:00 0 7f038bc28000-7f038bc3f000 r-xp 00000000 103:01 12583965 /usr/lib64/libpthread-2.17.so 7f038bc3f000-7f038be3e000 ---p 00017000 103:01 12583965 /usr/lib64/libpthread-2.17.so 7f038be3e000-7f038be3f000 r--p 00016000 103:01 12583965 /usr/lib64/libpthread-2.17.so 7f038be3f000-7f038be40000 rw-p 00017000 103:01 12583965 /usr/lib64/libpthread-2.17.so 7f038be40000-7f038be44000 rw-p 00000000 00:00 0 7f038be44000-7f038be59000 r-xp 00000000 103:01 12582995 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f038be59000-7f038c058000 ---p 00015000 103:01 12582995 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f038c058000-7f038c059000 r--p 00014000 103:01 12582995 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f038c059000-7f038c05a000 rw-p 00015000 103:01 12582995 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7f038c05a000-7f038c07f000 r-xp 00000000 103:01 12608612 /usr/lib64/libgomp.so.1.0.0 7f038c07f000-7f038c27e000 ---p 00025000 103:01 12608612 /usr/lib64/libgomp.so.1.0.0 7f038c27e000-7f038c27f000 r--p 00024000 103:01 12608612 /usr/lib64/libgomp.so.1.0.0 7f038c27f000-7f038c280000 rw-p 00025000 103:01 12608612 /usr/lib64/libgomp.so.1.0.0 7f038c280000-7f038c381000 r-xp 00000000 103:01 12583940 /usr/lib64/libm-2.17.so 7f038c381000-7f038c580000 ---p 00101000 103:01 12583940 /usr/lib64/libm-2.17.so 7f038c580000-7f038c581000 r--p 00100000 103:01 12583940 /usr/lib64/libm-2.17.so 7f038c581000-7f038c582000 rw-p 00101000 103:01 12583940 /usr/lib64/libm-2.17.so 7f038c582000-7f038c66b000 r-xp 00000000 103:01 12584007 /usr/lib64/libstdc++.so.6.0.19 7f038c66b000-7f038c86b000 ---p 000e9000 103:01 12584007 /usr/lib64/libstdc++.so.6.0.19 7f038c86b000-7f038c873000 r--p 000e9000 103:01 12584007 /usr/lib64/libstdc++.so.6.0.19 7f038c873000-7f038c875000 rw-p 000f1000 103:01 12584007 /usr/lib64/libstdc++.so.6.0.19 7f038c875000-7f038c88a000 rw-p 00000000 00:00 0 7f038c88a000-7f038c89f000 r-xp 00000000 103:01 12629245 /usr/lib64/libz.so.1.2.7 7f038c89f000-7f038ca9e000 ---p 00015000 103:01 12629245 /usr/lib64/libz.so.1.2.7 7f038ca9e000-7f038ca9f000 r--p 00014000 103:01 12629245 /usr/lib64/libz.so.1.2.7 7f038ca9f000-7f038caa0000 rw-p 00015000 103:01 12629245 /usr/lib64/libz.so.1.2.7 7f038caa0000-7f038cac2000 r-xp 00000000 103:01 12583924 /usr/lib64/ld-2.17.so 7f038cafc000-7f038ccb5000 rw-p 00000000 00:00 0 7f038ccbe000-7f038ccc1000 rw-p 00000000 00:00 0 7f038ccc1000-7f038ccc2000 r--p 00021000 103:01 12583924 /usr/lib64/ld-2.17.so 7f038ccc2000-7f038ccc3000 rw-p 00022000 103:01 12583924 /usr/lib64/ld-2.17.so 7f038ccc3000-7f038ccc4000 rw-p 00000000 00:00 0 7ffdc1cb2000-7ffdc1cd3000 rw-p 00000000 00:00 0 [stack] 7ffdc1d13000-7ffdc1d15000 r-xp 00000000 00:00 0 [vdso] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]

barcoded_fastqs.zip STAR_index.zip

alexdobin commented 1 year ago

Hi @yagam-fluent

please try the latest release: https://github.com/alexdobin/STAR/releases/tag/2.7.10b both the dynamic and static executables in Linux_x86_64 and Linux_x86_64_static.