Job ID = 2589381 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,216,640 reads read : 36,216,640 reads written : 36,216,640 rm: cannot remove ‘[DSE]RR*’: 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: 00:09:40 36216640 reads; of these: 36216640 (100.00%) were unpaired; of these: 431305 (1.19%) aligned 0 times 30081805 (83.06%) aligned exactly 1 time 5703530 (15.75%) aligned >1 times 98.81% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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] 8491066 / 35785335 = 0.2373 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 @ Mon, 12 Aug 2019 18:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.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 @ Mon, 12 Aug 2019 18:12:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:12:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.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 @ Mon, 12 Aug 2019 18:12:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:12:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.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 @ Mon, 12 Aug 2019 18:12:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:12:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:00: 1000000 INFO @ Mon, 12 Aug 2019 18:13:01: 1000000 INFO @ Mon, 12 Aug 2019 18:13:01: 1000000 INFO @ Mon, 12 Aug 2019 18:13:07: 2000000 INFO @ Mon, 12 Aug 2019 18:13:08: 2000000 INFO @ Mon, 12 Aug 2019 18:13:08: 2000000 INFO @ Mon, 12 Aug 2019 18:13:14: 3000000 INFO @ Mon, 12 Aug 2019 18:13:14: 3000000 INFO @ Mon, 12 Aug 2019 18:13:15: 3000000 INFO @ Mon, 12 Aug 2019 18:13:21: 4000000 INFO @ Mon, 12 Aug 2019 18:13:21: 4000000 INFO @ Mon, 12 Aug 2019 18:13:22: 4000000 INFO @ Mon, 12 Aug 2019 18:13:27: 5000000 INFO @ Mon, 12 Aug 2019 18:13:28: 5000000 INFO @ Mon, 12 Aug 2019 18:13:29: 5000000 INFO @ Mon, 12 Aug 2019 18:13:34: 6000000 INFO @ Mon, 12 Aug 2019 18:13:35: 6000000 INFO @ Mon, 12 Aug 2019 18:13:36: 6000000 INFO @ Mon, 12 Aug 2019 18:13:41: 7000000 INFO @ Mon, 12 Aug 2019 18:13:42: 7000000 INFO @ Mon, 12 Aug 2019 18:13:43: 7000000 INFO @ Mon, 12 Aug 2019 18:13:47: 8000000 INFO @ Mon, 12 Aug 2019 18:13:49: 8000000 INFO @ Mon, 12 Aug 2019 18:13:50: 8000000 INFO @ Mon, 12 Aug 2019 18:13:54: 9000000 INFO @ Mon, 12 Aug 2019 18:13:55: 9000000 INFO @ Mon, 12 Aug 2019 18:13:57: 9000000 INFO @ Mon, 12 Aug 2019 18:14:00: 10000000 INFO @ Mon, 12 Aug 2019 18:14:02: 10000000 INFO @ Mon, 12 Aug 2019 18:14:04: 10000000 INFO @ Mon, 12 Aug 2019 18:14:07: 11000000 INFO @ Mon, 12 Aug 2019 18:14:09: 11000000 INFO @ Mon, 12 Aug 2019 18:14:11: 11000000 INFO @ Mon, 12 Aug 2019 18:14:13: 12000000 INFO @ Mon, 12 Aug 2019 18:14:16: 12000000 INFO @ Mon, 12 Aug 2019 18:14:17: 12000000 INFO @ Mon, 12 Aug 2019 18:14:20: 13000000 INFO @ Mon, 12 Aug 2019 18:14:23: 13000000 INFO @ Mon, 12 Aug 2019 18:14:25: 13000000 INFO @ Mon, 12 Aug 2019 18:14:26: 14000000 INFO @ Mon, 12 Aug 2019 18:14:30: 14000000 INFO @ Mon, 12 Aug 2019 18:14:33: 15000000 INFO @ Mon, 12 Aug 2019 18:14:33: 14000000 INFO @ Mon, 12 Aug 2019 18:14:37: 15000000 INFO @ Mon, 12 Aug 2019 18:14:39: 16000000 INFO @ Mon, 12 Aug 2019 18:14:41: 15000000 INFO @ Mon, 12 Aug 2019 18:14:44: 16000000 INFO @ Mon, 12 Aug 2019 18:14:46: 17000000 INFO @ Mon, 12 Aug 2019 18:14:48: 16000000 INFO @ Mon, 12 Aug 2019 18:14:51: 17000000 INFO @ Mon, 12 Aug 2019 18:14:52: 18000000 INFO @ Mon, 12 Aug 2019 18:14:56: 17000000 INFO @ Mon, 12 Aug 2019 18:14:58: 18000000 INFO @ Mon, 12 Aug 2019 18:14:59: 19000000 INFO @ Mon, 12 Aug 2019 18:15:04: 18000000 INFO @ Mon, 12 Aug 2019 18:15:05: 19000000 INFO @ Mon, 12 Aug 2019 18:15:05: 20000000 INFO @ Mon, 12 Aug 2019 18:15:11: 20000000 INFO @ Mon, 12 Aug 2019 18:15:12: 21000000 INFO @ Mon, 12 Aug 2019 18:15:12: 19000000 INFO @ Mon, 12 Aug 2019 18:15:18: 22000000 INFO @ Mon, 12 Aug 2019 18:15:18: 21000000 INFO @ Mon, 12 Aug 2019 18:15:19: 20000000 INFO @ Mon, 12 Aug 2019 18:15:25: 23000000 INFO @ Mon, 12 Aug 2019 18:15:25: 22000000 INFO @ Mon, 12 Aug 2019 18:15:27: 21000000 INFO @ Mon, 12 Aug 2019 18:15:31: 24000000 INFO @ Mon, 12 Aug 2019 18:15:32: 23000000 INFO @ Mon, 12 Aug 2019 18:15:35: 22000000 INFO @ Mon, 12 Aug 2019 18:15:37: 25000000 INFO @ Mon, 12 Aug 2019 18:15:39: 24000000 INFO @ Mon, 12 Aug 2019 18:15:43: 23000000 INFO @ Mon, 12 Aug 2019 18:15:44: 26000000 INFO @ Mon, 12 Aug 2019 18:15:46: 25000000 INFO @ Mon, 12 Aug 2019 18:15:50: 27000000 INFO @ Mon, 12 Aug 2019 18:15:50: 24000000 INFO @ Mon, 12 Aug 2019 18:15:53: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:15:53: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:15:53: #1 total tags in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:15:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:15:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:15:53: 26000000 INFO @ Mon, 12 Aug 2019 18:15:53: #1 tags after filtering in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:15:53: #1 finished! INFO @ Mon, 12 Aug 2019 18:15:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:15:55: #2 number of paired peaks: 121 WARNING @ Mon, 12 Aug 2019 18:15:55: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 12 Aug 2019 18:15:55: start model_add_line... INFO @ Mon, 12 Aug 2019 18:15:56: start X-correlation... INFO @ Mon, 12 Aug 2019 18:15:56: end of X-cor INFO @ Mon, 12 Aug 2019 18:15:56: #2 finished! INFO @ Mon, 12 Aug 2019 18:15:56: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:15:56: #2 alternative fragment length(s) may be 1,13,49,131,148,208,225,282,431,452,465,533,598 bps INFO @ Mon, 12 Aug 2019 18:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20_model.r WARNING @ Mon, 12 Aug 2019 18:15:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:15:56: #2 You may need to consider one of the other alternative d(s): 1,13,49,131,148,208,225,282,431,452,465,533,598 WARNING @ Mon, 12 Aug 2019 18:15:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:15:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:15:58: 25000000 INFO @ Mon, 12 Aug 2019 18:16:00: 27000000 INFO @ Mon, 12 Aug 2019 18:16:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:16:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:16:02: #1 total tags in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:16:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:16:02: #1 tags after filtering in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:02: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:05: #2 number of paired peaks: 121 WARNING @ Mon, 12 Aug 2019 18:16:05: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:05: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:05: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:05: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:05: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:05: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:16:05: #2 alternative fragment length(s) may be 1,13,49,131,148,208,225,282,431,452,465,533,598 bps INFO @ Mon, 12 Aug 2019 18:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05_model.r WARNING @ Mon, 12 Aug 2019 18:16:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:16:05: #2 You may need to consider one of the other alternative d(s): 1,13,49,131,148,208,225,282,431,452,465,533,598 WARNING @ Mon, 12 Aug 2019 18:16:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:16:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:06: 26000000 INFO @ Mon, 12 Aug 2019 18:16:14: 27000000 INFO @ Mon, 12 Aug 2019 18:16:16: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:16:16: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:16:16: #1 total tags in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:16:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:16:17: #1 tags after filtering in treatment: 27294269 INFO @ Mon, 12 Aug 2019 18:16:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:17: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:19: #2 number of paired peaks: 121 WARNING @ Mon, 12 Aug 2019 18:16:19: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:19: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:19: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:19: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:19: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:19: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 18:16:19: #2 alternative fragment length(s) may be 1,13,49,131,148,208,225,282,431,452,465,533,598 bps INFO @ Mon, 12 Aug 2019 18:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10_model.r WARNING @ Mon, 12 Aug 2019 18:16:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:16:19: #2 You may need to consider one of the other alternative d(s): 1,13,49,131,148,208,225,282,431,452,465,533,598 WARNING @ Mon, 12 Aug 2019 18:16:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:16:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.20_summits.bed INFO @ Mon, 12 Aug 2019 18:17:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:17:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.05_summits.bed INFO @ Mon, 12 Aug 2019 18:17:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:17:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:17:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:17:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1078732/SRX1078732.10_summits.bed INFO @ Mon, 12 Aug 2019 18:17:36: 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。