Job ID = 1293177 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:20:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 41,191,721 reads read : 41,191,721 reads written : 41,191,721 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: 00:11:45 41191721 reads; of these: 41191721 (100.00%) were unpaired; of these: 6316131 (15.33%) aligned 0 times 22086826 (53.62%) aligned exactly 1 time 12788764 (31.05%) aligned >1 times 84.67% overall alignment rate Time searching: 00:11:45 Overall time: 00:11:45 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_sort_core] merging from 16 files... [bam_rmdupse_core] 9812854 / 34875590 = 0.2814 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 22:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.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 22:46:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:46:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.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 22:46:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:46:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:46:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.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 22:46:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:46:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:46:47: 1000000 INFO @ Sun, 02 Jun 2019 22:46:48: 1000000 INFO @ Sun, 02 Jun 2019 22:46:49: 1000000 INFO @ Sun, 02 Jun 2019 22:46:54: 2000000 INFO @ Sun, 02 Jun 2019 22:46:55: 2000000 INFO @ Sun, 02 Jun 2019 22:46:57: 2000000 INFO @ Sun, 02 Jun 2019 22:47:01: 3000000 INFO @ Sun, 02 Jun 2019 22:47:02: 3000000 INFO @ Sun, 02 Jun 2019 22:47:05: 3000000 INFO @ Sun, 02 Jun 2019 22:47:07: 4000000 INFO @ Sun, 02 Jun 2019 22:47:09: 4000000 INFO @ Sun, 02 Jun 2019 22:47:14: 4000000 INFO @ Sun, 02 Jun 2019 22:47:14: 5000000 INFO @ Sun, 02 Jun 2019 22:47:17: 5000000 INFO @ Sun, 02 Jun 2019 22:47:21: 6000000 INFO @ Sun, 02 Jun 2019 22:47:23: 5000000 INFO @ Sun, 02 Jun 2019 22:47:25: 6000000 INFO @ Sun, 02 Jun 2019 22:47:28: 7000000 INFO @ Sun, 02 Jun 2019 22:47:31: 6000000 INFO @ Sun, 02 Jun 2019 22:47:32: 7000000 INFO @ Sun, 02 Jun 2019 22:47:35: 8000000 INFO @ Sun, 02 Jun 2019 22:47:40: 8000000 INFO @ Sun, 02 Jun 2019 22:47:40: 7000000 INFO @ Sun, 02 Jun 2019 22:47:41: 9000000 INFO @ Sun, 02 Jun 2019 22:47:47: 9000000 INFO @ Sun, 02 Jun 2019 22:47:48: 10000000 INFO @ Sun, 02 Jun 2019 22:47:48: 8000000 INFO @ Sun, 02 Jun 2019 22:47:54: 10000000 INFO @ Sun, 02 Jun 2019 22:47:55: 11000000 INFO @ Sun, 02 Jun 2019 22:47:57: 9000000 INFO @ Sun, 02 Jun 2019 22:48:01: 12000000 INFO @ Sun, 02 Jun 2019 22:48:01: 11000000 INFO @ Sun, 02 Jun 2019 22:48:05: 10000000 INFO @ Sun, 02 Jun 2019 22:48:08: 13000000 INFO @ Sun, 02 Jun 2019 22:48:09: 12000000 INFO @ Sun, 02 Jun 2019 22:48:14: 11000000 INFO @ Sun, 02 Jun 2019 22:48:15: 14000000 INFO @ Sun, 02 Jun 2019 22:48:16: 13000000 INFO @ Sun, 02 Jun 2019 22:48:22: 15000000 INFO @ Sun, 02 Jun 2019 22:48:22: 12000000 INFO @ Sun, 02 Jun 2019 22:48:24: 14000000 INFO @ Sun, 02 Jun 2019 22:48:29: 16000000 INFO @ Sun, 02 Jun 2019 22:48:31: 13000000 INFO @ Sun, 02 Jun 2019 22:48:31: 15000000 INFO @ Sun, 02 Jun 2019 22:48:35: 17000000 INFO @ Sun, 02 Jun 2019 22:48:38: 16000000 INFO @ Sun, 02 Jun 2019 22:48:39: 14000000 INFO @ Sun, 02 Jun 2019 22:48:42: 18000000 INFO @ Sun, 02 Jun 2019 22:48:45: 17000000 INFO @ Sun, 02 Jun 2019 22:48:47: 15000000 INFO @ Sun, 02 Jun 2019 22:48:48: 19000000 INFO @ Sun, 02 Jun 2019 22:48:52: 18000000 INFO @ Sun, 02 Jun 2019 22:48:55: 20000000 INFO @ Sun, 02 Jun 2019 22:48:56: 16000000 INFO @ Sun, 02 Jun 2019 22:49:00: 19000000 INFO @ Sun, 02 Jun 2019 22:49:02: 21000000 INFO @ Sun, 02 Jun 2019 22:49:04: 17000000 INFO @ Sun, 02 Jun 2019 22:49:07: 20000000 INFO @ Sun, 02 Jun 2019 22:49:08: 22000000 INFO @ Sun, 02 Jun 2019 22:49:12: 18000000 INFO @ Sun, 02 Jun 2019 22:49:14: 21000000 INFO @ Sun, 02 Jun 2019 22:49:15: 23000000 INFO @ Sun, 02 Jun 2019 22:49:20: 19000000 INFO @ Sun, 02 Jun 2019 22:49:21: 22000000 INFO @ Sun, 02 Jun 2019 22:49:22: 24000000 INFO @ Sun, 02 Jun 2019 22:49:28: 23000000 INFO @ Sun, 02 Jun 2019 22:49:28: 20000000 INFO @ Sun, 02 Jun 2019 22:49:28: 25000000 INFO @ Sun, 02 Jun 2019 22:49:29: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:49:29: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:49:29: #1 total tags in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:49:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:49:29: #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 22:49:30: #1 tags after filtering in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:49:30: #1 finished! INFO @ Sun, 02 Jun 2019 22:49:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:49:32: #2 number of paired peaks: 704 WARNING @ Sun, 02 Jun 2019 22:49:32: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 02 Jun 2019 22:49:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:49:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:49:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:49:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:49:32: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:49:32: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 02 Jun 2019 22:49:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20_model.r WARNING @ Sun, 02 Jun 2019 22:49:32: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:49:32: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 02 Jun 2019 22:49:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:49:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:49:35: 24000000 INFO @ Sun, 02 Jun 2019 22:49:36: 21000000 INFO @ Sun, 02 Jun 2019 22:49:43: 25000000 INFO @ Sun, 02 Jun 2019 22:49:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:49:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:49:43: #1 total tags in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:49:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:49:43: #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 22:49:44: #1 tags after filtering in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:49:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:49:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:49:45: 22000000 INFO @ Sun, 02 Jun 2019 22:49:46: #2 number of paired peaks: 704 WARNING @ Sun, 02 Jun 2019 22:49:46: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 02 Jun 2019 22:49:46: start model_add_line... INFO @ Sun, 02 Jun 2019 22:49:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:49:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:49:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:49:46: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:49:46: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 02 Jun 2019 22:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10_model.r WARNING @ Sun, 02 Jun 2019 22:49:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:49:46: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 02 Jun 2019 22:49:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:49:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:49:52: 23000000 INFO @ Sun, 02 Jun 2019 22:50:00: 24000000 INFO @ Sun, 02 Jun 2019 22:50:09: 25000000 INFO @ Sun, 02 Jun 2019 22:50:09: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:50:09: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:50:09: #1 total tags in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:50:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:50:09: #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 22:50:10: #1 tags after filtering in treatment: 25062736 INFO @ Sun, 02 Jun 2019 22:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:50:10: #1 finished! INFO @ Sun, 02 Jun 2019 22:50:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:50:12: #2 number of paired peaks: 704 WARNING @ Sun, 02 Jun 2019 22:50:12: Fewer paired peaks (704) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 704 pairs to build model! INFO @ Sun, 02 Jun 2019 22:50:12: start model_add_line... INFO @ Sun, 02 Jun 2019 22:50:12: start X-correlation... INFO @ Sun, 02 Jun 2019 22:50:12: end of X-cor INFO @ Sun, 02 Jun 2019 22:50:12: #2 finished! INFO @ Sun, 02 Jun 2019 22:50:12: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 22:50:12: #2 alternative fragment length(s) may be 2 bps INFO @ Sun, 02 Jun 2019 22:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05_model.r WARNING @ Sun, 02 Jun 2019 22:50:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:50:12: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Sun, 02 Jun 2019 22:50:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:50:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:50:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:50:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.20_summits.bed INFO @ Sun, 02 Jun 2019 22:50:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.10_summits.bed INFO @ Sun, 02 Jun 2019 22:50:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:51:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402739/SRX5402739.05_summits.bed INFO @ Sun, 02 Jun 2019 22:51:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。