Job ID = 1291876 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,014,644 reads read : 64,029,288 reads written : 32,014,644 reads 0-length : 32,014,644 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: 00:00:01 Multiseed full-index search: 00:08:56 32014644 reads; of these: 32014644 (100.00%) were unpaired; of these: 637049 (1.99%) aligned 0 times 26437311 (82.58%) aligned exactly 1 time 4940284 (15.43%) aligned >1 times 98.01% overall alignment rate Time searching: 00:08:57 Overall time: 00:08:57 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] 4527281 / 31377595 = 0.1443 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 17:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.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 17:13:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:13:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.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 17:13:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:13:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.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 17:13:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:13:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:13:58: 1000000 INFO @ Sun, 02 Jun 2019 17:13:59: 1000000 INFO @ Sun, 02 Jun 2019 17:14:00: 1000000 INFO @ Sun, 02 Jun 2019 17:14:04: 2000000 INFO @ Sun, 02 Jun 2019 17:14:06: 2000000 INFO @ Sun, 02 Jun 2019 17:14:08: 2000000 INFO @ Sun, 02 Jun 2019 17:14:11: 3000000 INFO @ Sun, 02 Jun 2019 17:14:13: 3000000 INFO @ Sun, 02 Jun 2019 17:14:17: 3000000 INFO @ Sun, 02 Jun 2019 17:14:18: 4000000 INFO @ Sun, 02 Jun 2019 17:14:20: 4000000 INFO @ Sun, 02 Jun 2019 17:14:24: 5000000 INFO @ Sun, 02 Jun 2019 17:14:25: 4000000 INFO @ Sun, 02 Jun 2019 17:14:28: 5000000 INFO @ Sun, 02 Jun 2019 17:14:31: 6000000 INFO @ Sun, 02 Jun 2019 17:14:34: 5000000 INFO @ Sun, 02 Jun 2019 17:14:37: 6000000 INFO @ Sun, 02 Jun 2019 17:14:38: 7000000 INFO @ Sun, 02 Jun 2019 17:14:43: 6000000 INFO @ Sun, 02 Jun 2019 17:14:44: 7000000 INFO @ Sun, 02 Jun 2019 17:14:45: 8000000 INFO @ Sun, 02 Jun 2019 17:14:52: 8000000 INFO @ Sun, 02 Jun 2019 17:14:52: 7000000 INFO @ Sun, 02 Jun 2019 17:14:52: 9000000 INFO @ Sun, 02 Jun 2019 17:14:59: 10000000 INFO @ Sun, 02 Jun 2019 17:14:59: 9000000 INFO @ Sun, 02 Jun 2019 17:15:01: 8000000 INFO @ Sun, 02 Jun 2019 17:15:06: 11000000 INFO @ Sun, 02 Jun 2019 17:15:06: 10000000 INFO @ Sun, 02 Jun 2019 17:15:09: 9000000 INFO @ Sun, 02 Jun 2019 17:15:12: 12000000 INFO @ Sun, 02 Jun 2019 17:15:13: 11000000 INFO @ Sun, 02 Jun 2019 17:15:18: 10000000 INFO @ Sun, 02 Jun 2019 17:15:19: 13000000 INFO @ Sun, 02 Jun 2019 17:15:21: 12000000 INFO @ Sun, 02 Jun 2019 17:15:26: 11000000 INFO @ Sun, 02 Jun 2019 17:15:26: 14000000 INFO @ Sun, 02 Jun 2019 17:15:28: 13000000 INFO @ Sun, 02 Jun 2019 17:15:33: 15000000 INFO @ Sun, 02 Jun 2019 17:15:34: 12000000 INFO @ Sun, 02 Jun 2019 17:15:35: 14000000 INFO @ Sun, 02 Jun 2019 17:15:40: 16000000 INFO @ Sun, 02 Jun 2019 17:15:42: 15000000 INFO @ Sun, 02 Jun 2019 17:15:43: 13000000 INFO @ Sun, 02 Jun 2019 17:15:47: 17000000 INFO @ Sun, 02 Jun 2019 17:15:49: 16000000 INFO @ Sun, 02 Jun 2019 17:15:51: 14000000 INFO @ Sun, 02 Jun 2019 17:15:54: 18000000 INFO @ Sun, 02 Jun 2019 17:15:56: 17000000 INFO @ Sun, 02 Jun 2019 17:15:59: 15000000 INFO @ Sun, 02 Jun 2019 17:16:00: 19000000 INFO @ Sun, 02 Jun 2019 17:16:04: 18000000 INFO @ Sun, 02 Jun 2019 17:16:07: 20000000 INFO @ Sun, 02 Jun 2019 17:16:07: 16000000 INFO @ Sun, 02 Jun 2019 17:16:11: 19000000 INFO @ Sun, 02 Jun 2019 17:16:14: 21000000 INFO @ Sun, 02 Jun 2019 17:16:16: 17000000 INFO @ Sun, 02 Jun 2019 17:16:18: 20000000 INFO @ Sun, 02 Jun 2019 17:16:21: 22000000 INFO @ Sun, 02 Jun 2019 17:16:24: 18000000 INFO @ Sun, 02 Jun 2019 17:16:25: 21000000 INFO @ Sun, 02 Jun 2019 17:16:28: 23000000 INFO @ Sun, 02 Jun 2019 17:16:32: 19000000 INFO @ Sun, 02 Jun 2019 17:16:32: 22000000 INFO @ Sun, 02 Jun 2019 17:16:35: 24000000 INFO @ Sun, 02 Jun 2019 17:16:39: 23000000 INFO @ Sun, 02 Jun 2019 17:16:40: 20000000 INFO @ Sun, 02 Jun 2019 17:16:42: 25000000 INFO @ Sun, 02 Jun 2019 17:16:46: 24000000 INFO @ Sun, 02 Jun 2019 17:16:48: 21000000 INFO @ Sun, 02 Jun 2019 17:16:48: 26000000 INFO @ Sun, 02 Jun 2019 17:16:53: 25000000 INFO @ Sun, 02 Jun 2019 17:16:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:16:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:16:54: #1 total tags in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:16:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:16:54: #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 17:16:55: #1 tags after filtering in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:16:55: #1 finished! INFO @ Sun, 02 Jun 2019 17:16:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:16:56: 22000000 INFO @ Sun, 02 Jun 2019 17:16:57: #2 number of paired peaks: 108 WARNING @ Sun, 02 Jun 2019 17:16:57: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 02 Jun 2019 17:16:57: start model_add_line... INFO @ Sun, 02 Jun 2019 17:16:57: start X-correlation... INFO @ Sun, 02 Jun 2019 17:16:57: end of X-cor INFO @ Sun, 02 Jun 2019 17:16:57: #2 finished! INFO @ Sun, 02 Jun 2019 17:16:57: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:16:57: #2 alternative fragment length(s) may be 1,47,447,509,579 bps INFO @ Sun, 02 Jun 2019 17:16:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05_model.r WARNING @ Sun, 02 Jun 2019 17:16:57: #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 17:16:57: #2 You may need to consider one of the other alternative d(s): 1,47,447,509,579 WARNING @ Sun, 02 Jun 2019 17:16:57: #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 17:16:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:16:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:01: 26000000 INFO @ Sun, 02 Jun 2019 17:17:05: 23000000 INFO @ Sun, 02 Jun 2019 17:17:08: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:08: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:08: #1 total tags in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:17:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:08: #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 17:17:09: #1 tags after filtering in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:09: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:11: #2 number of paired peaks: 108 WARNING @ Sun, 02 Jun 2019 17:17:11: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 02 Jun 2019 17:17:11: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:11: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:11: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:11: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:11: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:17:11: #2 alternative fragment length(s) may be 1,47,447,509,579 bps INFO @ Sun, 02 Jun 2019 17:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10_model.r WARNING @ Sun, 02 Jun 2019 17:17:11: #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 17:17:11: #2 You may need to consider one of the other alternative d(s): 1,47,447,509,579 WARNING @ Sun, 02 Jun 2019 17:17:11: #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 17:17:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:13: 24000000 INFO @ Sun, 02 Jun 2019 17:17:21: 25000000 INFO @ Sun, 02 Jun 2019 17:17:29: 26000000 INFO @ Sun, 02 Jun 2019 17:17:36: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:17:36: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:17:36: #1 total tags in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:17:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:17:36: #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 17:17:37: #1 tags after filtering in treatment: 26850314 INFO @ Sun, 02 Jun 2019 17:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:17:37: #1 finished! INFO @ Sun, 02 Jun 2019 17:17:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:17:39: #2 number of paired peaks: 108 WARNING @ Sun, 02 Jun 2019 17:17:39: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Sun, 02 Jun 2019 17:17:39: start model_add_line... INFO @ Sun, 02 Jun 2019 17:17:39: start X-correlation... INFO @ Sun, 02 Jun 2019 17:17:39: end of X-cor INFO @ Sun, 02 Jun 2019 17:17:39: #2 finished! INFO @ Sun, 02 Jun 2019 17:17:39: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 17:17:39: #2 alternative fragment length(s) may be 1,47,447,509,579 bps INFO @ Sun, 02 Jun 2019 17:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20_model.r WARNING @ Sun, 02 Jun 2019 17:17:39: #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 17:17:39: #2 You may need to consider one of the other alternative d(s): 1,47,447,509,579 WARNING @ Sun, 02 Jun 2019 17:17:39: #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 17:17:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:17:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:18:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.05_summits.bed INFO @ Sun, 02 Jun 2019 17:18:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.10_summits.bed INFO @ Sun, 02 Jun 2019 17:18:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:18:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:18:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:18:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:18:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737087/SRX2737087.20_summits.bed INFO @ Sun, 02 Jun 2019 17:18:56: Done! pass1 - making usageList (0 chroms): 2 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。