Job ID = 1292527 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:15:33 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T10:15:33 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-1/SRR1163607/SRR1163607.1' 2019-06-02T10:15:44 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1163607' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T10:15:44 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) *** Error in `/home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump': malloc(): smallbin double linked list corrupted: 0x00007fffc8002db0 *** ======= Backtrace: ========= /lib64/libc.so.6(+0x7f5e4)[0x7ffff736b5e4] /lib64/libc.so.6(+0x82d00)[0x7ffff736ed00] /lib64/libc.so.6(__libc_malloc+0x4c)[0x7ffff737184c] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x492c20] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x46fa1a] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x470057] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x47300b] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump(KConfigMake+0xad)[0x474d8d] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x455b3c] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x43c1e1] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x43b0f5] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x40fade] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x411d62] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x415045] /home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump[0x51a6ea] /lib64/libpthread.so.0(+0x7e25)[0x7ffff79c2e25] /lib64/libc.so.6(clone+0x6d)[0x7ffff73eabad] ======= Memory map: ======== 00400000-006c5000 r-xp 00000000 bd0:3f89c 144116276061639710 /lustre7/home/lustre4/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump.2.9.6 008c5000-008d3000 rw-p 002c5000 bd0:3f89c 144116276061639710 /lustre7/home/lustre4/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump.2.9.6 008d3000-00b5c000 rw-p 00000000 00:00 0 [heap] 7fffc8000000-7fffc8021000 rw-p 00000000 00:00 0 7fffc8021000-7fffcc000000 ---p 00000000 00:00 0 7fffcc000000-7fffcc021000 rw-p 00000000 00:00 0 7fffcc021000-7fffd0000000 ---p 00000000 00:00 0 7fffd0000000-7fffd0051000 rw-p 00000000 00:00 0 7fffd0051000-7fffd4000000 ---p 00000000 00:00 0 7fffd57ff000-7fffd5800000 ---p 00000000 00:00 0 7fffd5800000-7fffd8000000 rw-p 00000000 00:00 0 7fffd8000000-7fffd8041000 rw-p 00000000 00:00 0 7fffd8041000-7fffdc000000 ---p 00000000 00:00 0 7fffdc000000-7fffdc047000 rw-p 00000000 00:00 0 7fffdc047000-7fffe0000000 ---p 00000000 00:00 0 7fffe0000000-7fffe0043000 rw-p 00000000 00:00 0 7fffe0044000-7fffe4000000 ---p 00000000 00:00 0 7fffe57ff000-7fffe5800000 ---p 00000000 00:00 0 7fffe5800000-7fffe8000000 rw-p 00000000 00:00 0 7fffe8000000-7fffe8045000 rw-p 00000000 00:00 0 7fffe8045000-7fffec000000 ---p 00000000 00:00 0 7fffeca9f000-7fffecab4000 r-xp 00000000 103:06 6443908675 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffecab4000-7fffeccb3000 ---p 00015000 103:06 6443908675 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffeccb3000-7fffeccb4000 r--p 00014000 103:06 6443908675 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffeccb4000-7fffeccb5000 rw-p 00015000 103:06 6443908675 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffeccb5000-7fffeccb6000 ---p 00000000 00:00 0 7fffeccb6000-7fffef4b6000 rw-p 00000000 00:00 0 7fffef4b6000-7fffef4b7000 ---p 00000000 00:00 0 7fffef4b7000-7ffff1cb7000 rw-p 00000000 00:00 0 7ffff1cb7000-7ffff1cb8000 ---p 00000000 00:00 0 7ffff1cb8000-7ffff44b8000 rw-p 00000000 00:00 0 7ffff44b8000-7ffff44b9000 ---p 00000000 00:00 0 7ffff44b9000-7ffff6cb9000 rw-p 00000000 00:00 0 7ffff6cb9000-7ffff6ccf000 r-xp 00000000 103:06 6447349671 /usr/lib64/libresolv-2.17.so 7ffff6ccf000-7ffff6ece000 ---p 00016000 103:06 6447349671 /usr/lib64/libresolv-2.17.so 7ffff6ece000-7ffff6ecf000 r--p 00015000 103:06 6447349671 /usr/lib64/libresolv-2.17.so 7ffff6ecf000-7ffff6ed0000 rw-p 00016000 103:06 6447349671 /usr/lib64/libresolv-2.17.so 7ffff6ed0000-7ffff6ed2000 rw-p 00000000 00:00 0 7ffff6ed2000-7ffff6ed7000 r-xp 00000000 103:06 6447216851 /usr/lib64/libnss_dns-2.17.so 7ffff6ed7000-7ffff70d7000 ---p 00005000 103:06 6447216851 /usr/lib64/libnss_dns-2.17.so 7ffff70d7000-7ffff70d8000 r--p 00005000 103:06 6447216851 /usr/lib64/libnss_dns-2.17.so 7ffff70d8000-7ffff70d9000 rw-p 00006000 103:06 6447216851 /usr/lib64/libnss_dns-2.17.so 7ffff70d9000-7ffff70e5000 r-xp 00000000 103:06 6447216852 /usr/lib64/libnss_files-2.17.so 7ffff70e5000-7ffff72e4000 ---p 0000c000 103:06 6447216852 /usr/lib64/libnss_files-2.17.so 7ffff72e4000-7ffff72e5000 r--p 0000b000 103:06 6447216852 /usr/lib64/libnss_files-2.17.so 7ffff72e5000-7ffff72e6000 rw-p 0000c000 103:06 6447216852 /usr/lib64/libnss_files-2.17.so 7ffff72e6000-7ffff72ec000 rw-p 00000000 00:00 0 7ffff72ec000-7ffff74af000 r-xp 00000000 103:06 6446818461 /usr/lib64/libc-2.17.so 7ffff74af000-7ffff76ae000 ---p 001c3000 103:06 6446818461 /usr/lib64/libc-2.17.so 7ffff76ae000-7ffff76b2000 r--p 001c2000 103:06 6446818461 /usr/lib64/libc-2.17.so 7ffff76b2000-7ffff76b4000 rw-p 001c6000 103:06 6446818461 /usr/lib64/libc-2.17.so 7ffff76b4000-7ffff76b9000 rw-p 00000000 00:00 0 7ffff76b9000-7ffff77ba000 r-xp 00000000 103:06 6447192066 /usr/lib64/libm-2.17.so 7ffff77ba000-7ffff79b9000 ---p 00101000 103:06 6447192066 /usr/lib64/libm-2.17.so 7ffff79b9000-7ffff79ba000 r--p 00100000 103:06 6447192066 /usr/lib64/libm-2.17.so 7ffff79ba000-7ffff79bb000 rw-p 00101000 103:06 6447192066 /usr/lib64/libm-2.17.so 7ffff79bb000-7ffff79d2000 r-xp 00000000 103:06 6447349656 /usr/lib64/libpthread-2.17.so 7ffff79d2000-7ffff7bd1000 ---p 00017000 103:06 6447349656 /usr/lib64/libpthread-2.17.so 7ffff7bd1000-7ffff7bd2000 r--p 00016000 103:06 6447349656 /usr/lib64/libpthread-2.17.so 7ffff7bd2000-7ffff7bd3000 rw-p 00017000 103:06 6447349656 /usr/lib64/libpthread-2.17.so 7ffff7bd3000-7ffff7bd7000 rw-p 00000000 00:00 0 7ffff7bd7000-7ffff7bd9000 r-xp 00000000 103:06 6446911791 /usr/lib64/libdl-2.17.so 7ffff7bd9000-7ffff7dd9000 ---p 00002000 103:06 6446911791 /usr/lib64/libdl-2.17.so 7ffff7dd9000-7ffff7dda000 r--p 00002000 103:06 6446911791 /usr/lib64/libdl-2.17.so 7ffff7dda000-7ffff7ddb000 rw-p 00003000 103:06 6446911791 /usr/lib64/libdl-2.17.so 7ffff7ddb000-7ffff7dfd000 r-xp 00000000 103:06 6446187793 /usr/lib64/ld-2.17.so 7ffff7fdc000-7ffff7fe1000 rw-p 00000000 00:00 0 7ffff7ff8000-7ffff7ffa000 rw-p 00000000 00:00 0 7ffff7ffa000-7ffff7ffc000 r-xp 00000000 00:00 0 [vdso] 7ffff7ffc000-7ffff7ffd000 r--p 00021000 103:06 6446187793 /usr/lib64/ld-2.17.so 7ffff7ffd000-7ffff7ffe000 rw-p 00022000 103:06 6446187793 /usr/lib64/ld-2.17.so 7ffff7ffe000-7ffff7fff000 rw-p 00000000 00:00 0 7ffffffdc000-7ffffffff000 rw-p 00000000 00:00 0 [stack] ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] 2019-06-02T10:16:56 fasterq-dump.2.9.6 fatal: SIGNAL - 6 spots read : 9,182,496 reads read : 9,182,496 reads written : 9,182,496 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:53 9182496 reads; of these: 9182496 (100.00%) were unpaired; of these: 487341 (5.31%) aligned 0 times 7902316 (86.06%) aligned exactly 1 time 792839 (8.63%) aligned >1 times 94.69% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 6574559 / 8695155 = 0.7561 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 19:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:22:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:22:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 02 Jun 2019 19:22:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:13: 1000000 INFO @ Sun, 02 Jun 2019 19:22:14: 1000000 INFO @ Sun, 02 Jun 2019 19:22:14: 1000000 INFO @ Sun, 02 Jun 2019 19:22:25: 2000000 INFO @ Sun, 02 Jun 2019 19:22:25: 2000000 INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:22:26: #1 total tags in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:22:26: #1 tags after filtering in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:26: 2000000 INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:22:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:22:26: #1 total tags in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:22:26: #1 tags after filtering in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:26: #2 number of paired peaks: 6664 INFO @ Sun, 02 Jun 2019 19:22:26: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:26: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:26: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:26: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:26: #2 predicted fragment length is 308 bps INFO @ Sun, 02 Jun 2019 19:22:26: #2 alternative fragment length(s) may be 308 bps INFO @ Sun, 02 Jun 2019 19:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10_model.r INFO @ Sun, 02 Jun 2019 19:22:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:27: #2 number of paired peaks: 6664 INFO @ Sun, 02 Jun 2019 19:22:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:27: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:27: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:27: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:27: #2 predicted fragment length is 308 bps INFO @ Sun, 02 Jun 2019 19:22:27: #2 alternative fragment length(s) may be 308 bps INFO @ Sun, 02 Jun 2019 19:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20_model.r INFO @ Sun, 02 Jun 2019 19:22:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:27: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:22:27: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:22:27: #1 total tags in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:22:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:22:27: #1 tags after filtering in treatment: 2120596 INFO @ Sun, 02 Jun 2019 19:22:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:22:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:22:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:22:27: #2 number of paired peaks: 6664 INFO @ Sun, 02 Jun 2019 19:22:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:22:27: start X-correlation... INFO @ Sun, 02 Jun 2019 19:22:27: end of X-cor INFO @ Sun, 02 Jun 2019 19:22:27: #2 finished! INFO @ Sun, 02 Jun 2019 19:22:27: #2 predicted fragment length is 308 bps INFO @ Sun, 02 Jun 2019 19:22:27: #2 alternative fragment length(s) may be 308 bps INFO @ Sun, 02 Jun 2019 19:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05_model.r INFO @ Sun, 02 Jun 2019 19:22:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:22:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 19:22:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.20_summits.bed INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:39: Done! INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.10_summits.bed INFO @ Sun, 02 Jun 2019 19:22:39: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2655 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3475 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466541/SRX466541.05_summits.bed INFO @ Sun, 02 Jun 2019 19:22:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4111 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。