Job ID = 2640821 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... *** Error in `/home/okishinya/chipatlas/bin/sratoolkit.2.9.6-1-ubuntu64/bin/fasterq-dump': malloc(): smallbin double linked list corrupted: 0x00007fffcc002db0 *** ======= 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] 7fffc4000000-7fffc4021000 rw-p 00000000 00:00 0 7fffc4021000-7fffc8000000 ---p 00000000 00:00 0 7fffcc000000-7fffcc021000 rw-p 00000000 00:00 0 7fffcc021000-7fffd0000000 ---p 00000000 00:00 0 7fffd0000000-7fffd002e000 rw-p 00000000 00:00 0 7fffd002e000-7fffd4000000 ---p 00000000 00:00 0 7fffd57ff000-7fffd5800000 ---p 00000000 00:00 0 7fffd5800000-7fffd8000000 rw-p 00000000 00:00 0 7fffd8000000-7fffd802d000 rw-p 00000000 00:00 0 7fffd802d000-7fffdc000000 ---p 00000000 00:00 0 7fffdd7ff000-7fffdd800000 ---p 00000000 00:00 0 7fffdd800000-7fffe0000000 rw-p 00000000 00:00 0 7fffe0000000-7fffe002b000 rw-p 00000000 00:00 0 7fffe002b000-7fffe4000000 ---p 00000000 00:00 0 7fffe4000000-7fffe402f000 rw-p 00000000 00:00 0 7fffe402f000-7fffe8000000 ---p 00000000 00:00 0 7fffe8000000-7fffe8035000 rw-p 00000000 00:00 0 7fffe8035000-7fffec000000 ---p 00000000 00:00 0 7fffeca9f000-7fffecab4000 r-xp 00000000 103:06 6443013666 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffecab4000-7fffeccb3000 ---p 00015000 103:06 6443013666 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffeccb3000-7fffeccb4000 r--p 00014000 103:06 6443013666 /usr/lib64/libgcc_s-4.8.5-20150702.so.1 7fffeccb4000-7fffeccb5000 rw-p 00015000 103:06 6443013666 /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 6447902301 /usr/lib64/libresolv-2.17.so 7ffff6ccf000-7ffff6ece000 ---p 00016000 103:06 6447902301 /usr/lib64/libresolv-2.17.so 7ffff6ece000-7ffff6ecf000 r--p 00015000 103:06 6447902301 /usr/lib64/libresolv-2.17.so 7ffff6ecf000-7ffff6ed0000 rw-p 00016000 103:06 6447902301 /usr/lib64/libresolv-2.17.so 7ffff6ed0000-7ffff6ed2000 rw-p 00000000 00:00 0 7ffff6ed2000-7ffff6ed7000 r-xp 00000000 103:06 6447859977 /usr/lib64/libnss_dns-2.17.so 7ffff6ed7000-7ffff70d7000 ---p 00005000 103:06 6447859977 /usr/lib64/libnss_dns-2.17.so 7ffff70d7000-7ffff70d8000 r--p 00005000 103:06 6447859977 /usr/lib64/libnss_dns-2.17.so 7ffff70d8000-7ffff70d9000 rw-p 00006000 103:06 6447859977 /usr/lib64/libnss_dns-2.17.so 7ffff70d9000-7ffff70e5000 r-xp 00000000 103:06 6447859978 /usr/lib64/libnss_files-2.17.so 7ffff70e5000-7ffff72e4000 ---p 0000c000 103:06 6447859978 /usr/lib64/libnss_files-2.17.so 7ffff72e4000-7ffff72e5000 r--p 0000b000 103:06 6447859978 /usr/lib64/libnss_files-2.17.so 7ffff72e5000-7ffff72e6000 rw-p 0000c000 103:06 6447859978 /usr/lib64/libnss_files-2.17.so 7ffff72e6000-7ffff72ec000 rw-p 00000000 00:00 0 7ffff72ec000-7ffff74af000 r-xp 00000000 103:06 6447751511 /usr/lib64/libc-2.17.so 7ffff74af000-7ffff76ae000 ---p 001c3000 103:06 6447751511 /usr/lib64/libc-2.17.so 7ffff76ae000-7ffff76b2000 r--p 001c2000 103:06 6447751511 /usr/lib64/libc-2.17.so 7ffff76b2000-7ffff76b4000 rw-p 001c6000 103:06 6447751511 /usr/lib64/libc-2.17.so 7ffff76b4000-7ffff76b9000 rw-p 00000000 00:00 0 7ffff76b9000-7ffff77ba000 r-xp 00000000 103:06 6447831864 /usr/lib64/libm-2.17.so 7ffff77ba000-7ffff79b9000 ---p 00101000 103:06 6447831864 /usr/lib64/libm-2.17.so 7ffff79b9000-7ffff79ba000 r--p 00100000 103:06 6447831864 /usr/lib64/libm-2.17.so 7ffff79ba000-7ffff79bb000 rw-p 00101000 103:06 6447831864 /usr/lib64/libm-2.17.so 7ffff79bb000-7ffff79d2000 r-xp 00000000 103:06 6447902286 /usr/lib64/libpthread-2.17.so 7ffff79d2000-7ffff7bd1000 ---p 00017000 103:06 6447902286 /usr/lib64/libpthread-2.17.so 7ffff7bd1000-7ffff7bd2000 r--p 00016000 103:06 6447902286 /usr/lib64/libpthread-2.17.so 7ffff7bd2000-7ffff7bd3000 rw-p 00017000 103:06 6447902286 /usr/lib64/libpthread-2.17.so 7ffff7bd3000-7ffff7bd7000 rw-p 00000000 00:00 0 7ffff7bd7000-7ffff7bd9000 r-xp 00000000 103:06 6447778185 /usr/lib64/libdl-2.17.so 7ffff7bd9000-7ffff7dd9000 ---p 00002000 103:06 6447778185 /usr/lib64/libdl-2.17.so 7ffff7dd9000-7ffff7dda000 r--p 00002000 103:06 6447778185 /usr/lib64/libdl-2.17.so 7ffff7dda000-7ffff7ddb000 rw-p 00003000 103:06 6447778185 /usr/lib64/libdl-2.17.so 7ffff7ddb000-7ffff7dfd000 r-xp 00000000 103:06 6447740304 /usr/lib64/ld-2.17.so 7ffff7fdb000-7ffff7fe0000 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 6447740304 /usr/lib64/ld-2.17.so 7ffff7ffd000-7ffff7ffe000 rw-p 00022000 103:06 6447740304 /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] 2019-08-24T10:18:34 fasterq-dump.2.9.6 fatal: SIGNAL - 6 spots read : 3,550,149 reads read : 3,550,149 reads written : 3,550,149 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR6322051.sra.cache’: 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: 00:00:41 3550149 reads; of these: 3550149 (100.00%) were unpaired; of these: 106101 (2.99%) aligned 0 times 3164813 (89.15%) aligned exactly 1 time 279235 (7.87%) aligned >1 times 97.01% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 363773 / 3444048 = 0.1056 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:22:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:22: 1000000 INFO @ Sat, 24 Aug 2019 19:22:31: 2000000 INFO @ Sat, 24 Aug 2019 19:22:40: 3000000 INFO @ Sat, 24 Aug 2019 19:22:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:22:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:22:40: #1 total tags in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:22:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:40: #1 tags after filtering in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:22:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:41: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:22:41: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:22:41: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:22:43: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:43: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:52: 1000000 INFO @ Sat, 24 Aug 2019 19:23:01: 2000000 INFO @ Sat, 24 Aug 2019 19:23:10: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:23:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:23:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:23:11: #1 total tags in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:23:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:23:11: #1 tags after filtering in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:23:11: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:11: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:23:11: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:23:11: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:23:13: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:23:13: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:23:21: 1000000 INFO @ Sat, 24 Aug 2019 19:23:30: 2000000 INFO @ Sat, 24 Aug 2019 19:23:39: 3000000 INFO @ Sat, 24 Aug 2019 19:23:40: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 19:23:40: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 19:23:40: #1 total tags in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:23:40: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:23:40: #1 tags after filtering in treatment: 3080275 INFO @ Sat, 24 Aug 2019 19:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:23:40: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:40: #2 number of paired peaks: 30 WARNING @ Sat, 24 Aug 2019 19:23:40: Too few paired peaks (30) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 19:23:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX3421874/SRX3421874.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。