Job ID = 1292521 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:05:43 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171806 (0.56%) aligned 0 times 25273690 (82.09%) aligned exactly 1 time 5342653 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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 8 files... [bam_rmdupse_core] 4710870 / 30616343 = 0.1539 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 19:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.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 19:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.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 19:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.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 19:39:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:39:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:39:25: 1000000 INFO @ Sun, 02 Jun 2019 19:39:25: 1000000 INFO @ Sun, 02 Jun 2019 19:39:26: 1000000 INFO @ Sun, 02 Jun 2019 19:39:32: 2000000 INFO @ Sun, 02 Jun 2019 19:39:33: 2000000 INFO @ Sun, 02 Jun 2019 19:39:34: 2000000 INFO @ Sun, 02 Jun 2019 19:39:39: 3000000 INFO @ Sun, 02 Jun 2019 19:39:41: 3000000 INFO @ Sun, 02 Jun 2019 19:39:41: 3000000 INFO @ Sun, 02 Jun 2019 19:39:46: 4000000 INFO @ Sun, 02 Jun 2019 19:39:48: 4000000 INFO @ Sun, 02 Jun 2019 19:39:49: 4000000 INFO @ Sun, 02 Jun 2019 19:39:53: 5000000 INFO @ Sun, 02 Jun 2019 19:39:56: 5000000 INFO @ Sun, 02 Jun 2019 19:39:57: 5000000 INFO @ Sun, 02 Jun 2019 19:40:00: 6000000 INFO @ Sun, 02 Jun 2019 19:40:04: 6000000 INFO @ Sun, 02 Jun 2019 19:40:05: 6000000 INFO @ Sun, 02 Jun 2019 19:40:07: 7000000 INFO @ Sun, 02 Jun 2019 19:40:11: 7000000 INFO @ Sun, 02 Jun 2019 19:40:13: 7000000 INFO @ Sun, 02 Jun 2019 19:40:14: 8000000 INFO @ Sun, 02 Jun 2019 19:40:19: 8000000 INFO @ Sun, 02 Jun 2019 19:40:21: 8000000 INFO @ Sun, 02 Jun 2019 19:40:22: 9000000 INFO @ Sun, 02 Jun 2019 19:40:27: 9000000 INFO @ Sun, 02 Jun 2019 19:40:29: 10000000 INFO @ Sun, 02 Jun 2019 19:40:29: 9000000 INFO @ Sun, 02 Jun 2019 19:40:34: 10000000 INFO @ Sun, 02 Jun 2019 19:40:36: 11000000 INFO @ Sun, 02 Jun 2019 19:40:37: 10000000 INFO @ Sun, 02 Jun 2019 19:40:42: 11000000 INFO @ Sun, 02 Jun 2019 19:40:43: 12000000 INFO @ Sun, 02 Jun 2019 19:40:44: 11000000 INFO @ Sun, 02 Jun 2019 19:40:50: 13000000 INFO @ Sun, 02 Jun 2019 19:40:50: 12000000 INFO @ Sun, 02 Jun 2019 19:40:52: 12000000 INFO @ Sun, 02 Jun 2019 19:40:57: 14000000 INFO @ Sun, 02 Jun 2019 19:40:58: 13000000 INFO @ Sun, 02 Jun 2019 19:41:01: 13000000 INFO @ Sun, 02 Jun 2019 19:41:05: 15000000 INFO @ Sun, 02 Jun 2019 19:41:06: 14000000 INFO @ Sun, 02 Jun 2019 19:41:09: 14000000 INFO @ Sun, 02 Jun 2019 19:41:13: 16000000 INFO @ Sun, 02 Jun 2019 19:41:14: 15000000 INFO @ Sun, 02 Jun 2019 19:41:17: 15000000 INFO @ Sun, 02 Jun 2019 19:41:20: 17000000 INFO @ Sun, 02 Jun 2019 19:41:22: 16000000 INFO @ Sun, 02 Jun 2019 19:41:25: 16000000 INFO @ Sun, 02 Jun 2019 19:41:27: 18000000 INFO @ Sun, 02 Jun 2019 19:41:30: 17000000 INFO @ Sun, 02 Jun 2019 19:41:33: 17000000 INFO @ Sun, 02 Jun 2019 19:41:34: 19000000 INFO @ Sun, 02 Jun 2019 19:41:37: 18000000 INFO @ Sun, 02 Jun 2019 19:41:41: 20000000 INFO @ Sun, 02 Jun 2019 19:41:41: 18000000 INFO @ Sun, 02 Jun 2019 19:41:45: 19000000 INFO @ Sun, 02 Jun 2019 19:41:48: 21000000 INFO @ Sun, 02 Jun 2019 19:41:49: 19000000 INFO @ Sun, 02 Jun 2019 19:41:53: 20000000 INFO @ Sun, 02 Jun 2019 19:41:55: 22000000 INFO @ Sun, 02 Jun 2019 19:41:57: 20000000 INFO @ Sun, 02 Jun 2019 19:42:00: 21000000 INFO @ Sun, 02 Jun 2019 19:42:02: 23000000 INFO @ Sun, 02 Jun 2019 19:42:05: 21000000 INFO @ Sun, 02 Jun 2019 19:42:08: 22000000 INFO @ Sun, 02 Jun 2019 19:42:09: 24000000 INFO @ Sun, 02 Jun 2019 19:42:13: 22000000 INFO @ Sun, 02 Jun 2019 19:42:15: 23000000 INFO @ Sun, 02 Jun 2019 19:42:16: 25000000 INFO @ Sun, 02 Jun 2019 19:42:21: 23000000 INFO @ Sun, 02 Jun 2019 19:42:23: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:42:23: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:42:23: #1 total tags in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:42:23: #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 19:42:23: 24000000 INFO @ Sun, 02 Jun 2019 19:42:23: #1 tags after filtering in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:42:23: #1 finished! INFO @ Sun, 02 Jun 2019 19:42:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:42:25: #2 number of paired peaks: 152 WARNING @ Sun, 02 Jun 2019 19:42:25: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sun, 02 Jun 2019 19:42:25: start model_add_line... INFO @ Sun, 02 Jun 2019 19:42:26: start X-correlation... INFO @ Sun, 02 Jun 2019 19:42:26: end of X-cor INFO @ Sun, 02 Jun 2019 19:42:26: #2 finished! INFO @ Sun, 02 Jun 2019 19:42:26: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:42:26: #2 alternative fragment length(s) may be 1,31,411,490,576,584 bps INFO @ Sun, 02 Jun 2019 19:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10_model.r WARNING @ Sun, 02 Jun 2019 19:42:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:42:26: #2 You may need to consider one of the other alternative d(s): 1,31,411,490,576,584 WARNING @ Sun, 02 Jun 2019 19:42:26: #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 19:42:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:42:28: 24000000 INFO @ Sun, 02 Jun 2019 19:42:31: 25000000 INFO @ Sun, 02 Jun 2019 19:42:37: 25000000 INFO @ Sun, 02 Jun 2019 19:42:38: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:42:38: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:42:38: #1 total tags in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:42:38: #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 19:42:38: #1 tags after filtering in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:42:38: #1 finished! INFO @ Sun, 02 Jun 2019 19:42:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:42:40: #2 number of paired peaks: 152 WARNING @ Sun, 02 Jun 2019 19:42:40: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sun, 02 Jun 2019 19:42:40: start model_add_line... INFO @ Sun, 02 Jun 2019 19:42:41: start X-correlation... INFO @ Sun, 02 Jun 2019 19:42:41: end of X-cor INFO @ Sun, 02 Jun 2019 19:42:41: #2 finished! INFO @ Sun, 02 Jun 2019 19:42:41: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:42:41: #2 alternative fragment length(s) may be 1,31,411,490,576,584 bps INFO @ Sun, 02 Jun 2019 19:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20_model.r WARNING @ Sun, 02 Jun 2019 19:42:41: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:42:41: #2 You may need to consider one of the other alternative d(s): 1,31,411,490,576,584 WARNING @ Sun, 02 Jun 2019 19:42:41: #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 19:42:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:42:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:42:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:42:44: #1 total tags in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:42:44: #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 19:42:44: #1 tags after filtering in treatment: 25905473 INFO @ Sun, 02 Jun 2019 19:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:42:44: #1 finished! INFO @ Sun, 02 Jun 2019 19:42:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:42:47: #2 number of paired peaks: 152 WARNING @ Sun, 02 Jun 2019 19:42:47: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sun, 02 Jun 2019 19:42:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:42:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:42:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:42:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:42:47: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:42:47: #2 alternative fragment length(s) may be 1,31,411,490,576,584 bps INFO @ Sun, 02 Jun 2019 19:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05_model.r WARNING @ Sun, 02 Jun 2019 19:42:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:42:47: #2 You may need to consider one of the other alternative d(s): 1,31,411,490,576,584 WARNING @ Sun, 02 Jun 2019 19:42:47: #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 19:42:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:43:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:43:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:43:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.10_summits.bed INFO @ Sun, 02 Jun 2019 19:43:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.20_summits.bed INFO @ Sun, 02 Jun 2019 19:43:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466535/SRX466535.05_summits.bed INFO @ Sun, 02 Jun 2019 19:44:01: Done! pass1 - making usageList (0 chroms): 0 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。