Job ID = 1293910 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 55,746,252 reads read : 55,746,252 reads written : 55,746,252 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: 00:13:00 55746252 reads; of these: 55746252 (100.00%) were unpaired; of these: 12397437 (22.24%) aligned 0 times 32562344 (58.41%) aligned exactly 1 time 10786471 (19.35%) aligned >1 times 77.76% overall alignment rate Time searching: 00:13:00 Overall time: 00:13:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9162513 / 43348815 = 0.2114 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, 03 Jun 2019 03:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 03:31:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 03:31:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 03:31:48: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:31:48: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:31:56: 1000000 INFO @ Mon, 03 Jun 2019 03:31:57: 1000000 INFO @ Mon, 03 Jun 2019 03:31:57: 1000000 INFO @ Mon, 03 Jun 2019 03:32:03: 2000000 INFO @ Mon, 03 Jun 2019 03:32:06: 2000000 INFO @ Mon, 03 Jun 2019 03:32:06: 2000000 INFO @ Mon, 03 Jun 2019 03:32:10: 3000000 INFO @ Mon, 03 Jun 2019 03:32:14: 3000000 INFO @ Mon, 03 Jun 2019 03:32:14: 3000000 INFO @ Mon, 03 Jun 2019 03:32:18: 4000000 INFO @ Mon, 03 Jun 2019 03:32:23: 4000000 INFO @ Mon, 03 Jun 2019 03:32:23: 4000000 INFO @ Mon, 03 Jun 2019 03:32:25: 5000000 INFO @ Mon, 03 Jun 2019 03:32:31: 5000000 INFO @ Mon, 03 Jun 2019 03:32:31: 5000000 INFO @ Mon, 03 Jun 2019 03:32:32: 6000000 INFO @ Mon, 03 Jun 2019 03:32:39: 7000000 INFO @ Mon, 03 Jun 2019 03:32:39: 6000000 INFO @ Mon, 03 Jun 2019 03:32:39: 6000000 INFO @ Mon, 03 Jun 2019 03:32:46: 8000000 INFO @ Mon, 03 Jun 2019 03:32:47: 7000000 INFO @ Mon, 03 Jun 2019 03:32:47: 7000000 INFO @ Mon, 03 Jun 2019 03:32:53: 9000000 INFO @ Mon, 03 Jun 2019 03:32:55: 8000000 INFO @ Mon, 03 Jun 2019 03:32:56: 8000000 INFO @ Mon, 03 Jun 2019 03:33:00: 10000000 INFO @ Mon, 03 Jun 2019 03:33:03: 9000000 INFO @ Mon, 03 Jun 2019 03:33:04: 9000000 INFO @ Mon, 03 Jun 2019 03:33:07: 11000000 INFO @ Mon, 03 Jun 2019 03:33:11: 10000000 INFO @ Mon, 03 Jun 2019 03:33:12: 10000000 INFO @ Mon, 03 Jun 2019 03:33:14: 12000000 INFO @ Mon, 03 Jun 2019 03:33:20: 11000000 INFO @ Mon, 03 Jun 2019 03:33:20: 11000000 INFO @ Mon, 03 Jun 2019 03:33:21: 13000000 INFO @ Mon, 03 Jun 2019 03:33:28: 12000000 INFO @ Mon, 03 Jun 2019 03:33:28: 14000000 INFO @ Mon, 03 Jun 2019 03:33:28: 12000000 INFO @ Mon, 03 Jun 2019 03:33:35: 15000000 INFO @ Mon, 03 Jun 2019 03:33:36: 13000000 INFO @ Mon, 03 Jun 2019 03:33:36: 13000000 INFO @ Mon, 03 Jun 2019 03:33:42: 16000000 INFO @ Mon, 03 Jun 2019 03:33:44: 14000000 INFO @ Mon, 03 Jun 2019 03:33:44: 14000000 INFO @ Mon, 03 Jun 2019 03:33:49: 17000000 INFO @ Mon, 03 Jun 2019 03:33:52: 15000000 INFO @ Mon, 03 Jun 2019 03:33:53: 15000000 INFO @ Mon, 03 Jun 2019 03:33:57: 18000000 INFO @ Mon, 03 Jun 2019 03:34:00: 16000000 INFO @ Mon, 03 Jun 2019 03:34:01: 16000000 INFO @ Mon, 03 Jun 2019 03:34:05: 19000000 INFO @ Mon, 03 Jun 2019 03:34:08: 17000000 INFO @ Mon, 03 Jun 2019 03:34:09: 17000000 INFO @ Mon, 03 Jun 2019 03:34:12: 20000000 INFO @ Mon, 03 Jun 2019 03:34:17: 18000000 INFO @ Mon, 03 Jun 2019 03:34:17: 18000000 INFO @ Mon, 03 Jun 2019 03:34:19: 21000000 INFO @ Mon, 03 Jun 2019 03:34:25: 19000000 INFO @ Mon, 03 Jun 2019 03:34:26: 19000000 INFO @ Mon, 03 Jun 2019 03:34:26: 22000000 INFO @ Mon, 03 Jun 2019 03:34:33: 20000000 INFO @ Mon, 03 Jun 2019 03:34:33: 23000000 INFO @ Mon, 03 Jun 2019 03:34:34: 20000000 INFO @ Mon, 03 Jun 2019 03:34:41: 24000000 INFO @ Mon, 03 Jun 2019 03:34:41: 21000000 INFO @ Mon, 03 Jun 2019 03:34:42: 21000000 INFO @ Mon, 03 Jun 2019 03:34:48: 25000000 INFO @ Mon, 03 Jun 2019 03:34:49: 22000000 INFO @ Mon, 03 Jun 2019 03:34:50: 22000000 INFO @ Mon, 03 Jun 2019 03:34:55: 26000000 INFO @ Mon, 03 Jun 2019 03:34:57: 23000000 INFO @ Mon, 03 Jun 2019 03:34:59: 23000000 INFO @ Mon, 03 Jun 2019 03:35:03: 27000000 INFO @ Mon, 03 Jun 2019 03:35:06: 24000000 INFO @ Mon, 03 Jun 2019 03:35:07: 24000000 INFO @ Mon, 03 Jun 2019 03:35:10: 28000000 INFO @ Mon, 03 Jun 2019 03:35:14: 25000000 INFO @ Mon, 03 Jun 2019 03:35:15: 25000000 INFO @ Mon, 03 Jun 2019 03:35:18: 29000000 INFO @ Mon, 03 Jun 2019 03:35:22: 26000000 INFO @ Mon, 03 Jun 2019 03:35:23: 26000000 INFO @ Mon, 03 Jun 2019 03:35:25: 30000000 INFO @ Mon, 03 Jun 2019 03:35:30: 27000000 INFO @ Mon, 03 Jun 2019 03:35:31: 27000000 INFO @ Mon, 03 Jun 2019 03:35:32: 31000000 INFO @ Mon, 03 Jun 2019 03:35:38: 28000000 INFO @ Mon, 03 Jun 2019 03:35:39: 32000000 INFO @ Mon, 03 Jun 2019 03:35:40: 28000000 INFO @ Mon, 03 Jun 2019 03:35:46: 29000000 INFO @ Mon, 03 Jun 2019 03:35:46: 33000000 INFO @ Mon, 03 Jun 2019 03:35:48: 29000000 INFO @ Mon, 03 Jun 2019 03:35:53: 34000000 INFO @ Mon, 03 Jun 2019 03:35:54: 30000000 INFO @ Mon, 03 Jun 2019 03:35:55: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:35:55: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:35:55: #1 total tags in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:35:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:35:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:35:56: #1 tags after filtering in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:35:56: #1 finished! INFO @ Mon, 03 Jun 2019 03:35:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:35:56: 30000000 INFO @ Mon, 03 Jun 2019 03:35:58: #2 number of paired peaks: 218 WARNING @ Mon, 03 Jun 2019 03:35:58: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 03 Jun 2019 03:35:58: start model_add_line... INFO @ Mon, 03 Jun 2019 03:35:59: start X-correlation... INFO @ Mon, 03 Jun 2019 03:35:59: end of X-cor INFO @ Mon, 03 Jun 2019 03:35:59: #2 finished! INFO @ Mon, 03 Jun 2019 03:35:59: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:35:59: #2 alternative fragment length(s) may be 1,25,592,597 bps INFO @ Mon, 03 Jun 2019 03:35:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20_model.r WARNING @ Mon, 03 Jun 2019 03:35:59: #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, 03 Jun 2019 03:35:59: #2 You may need to consider one of the other alternative d(s): 1,25,592,597 WARNING @ Mon, 03 Jun 2019 03:35:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:35:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:35:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:36:02: 31000000 INFO @ Mon, 03 Jun 2019 03:36:04: 31000000 INFO @ Mon, 03 Jun 2019 03:36:10: 32000000 INFO @ Mon, 03 Jun 2019 03:36:12: 32000000 INFO @ Mon, 03 Jun 2019 03:36:17: 33000000 INFO @ Mon, 03 Jun 2019 03:36:20: 33000000 INFO @ Mon, 03 Jun 2019 03:36:25: 34000000 INFO @ Mon, 03 Jun 2019 03:36:27: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:36:27: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:36:27: #1 total tags in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:36:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:36:27: #1 tags after filtering in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:27: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:36:28: 34000000 INFO @ Mon, 03 Jun 2019 03:36:30: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 03:36:30: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 03:36:30: #1 total tags in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:36:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:36:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:36:30: #2 number of paired peaks: 218 WARNING @ Mon, 03 Jun 2019 03:36:30: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 03 Jun 2019 03:36:30: start model_add_line... INFO @ Mon, 03 Jun 2019 03:36:30: #1 tags after filtering in treatment: 34186302 INFO @ Mon, 03 Jun 2019 03:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:36:30: #1 finished! INFO @ Mon, 03 Jun 2019 03:36:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:36:31: start X-correlation... INFO @ Mon, 03 Jun 2019 03:36:31: end of X-cor INFO @ Mon, 03 Jun 2019 03:36:31: #2 finished! INFO @ Mon, 03 Jun 2019 03:36:31: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:36:31: #2 alternative fragment length(s) may be 1,25,592,597 bps INFO @ Mon, 03 Jun 2019 03:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05_model.r WARNING @ Mon, 03 Jun 2019 03:36:31: #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, 03 Jun 2019 03:36:31: #2 You may need to consider one of the other alternative d(s): 1,25,592,597 WARNING @ Mon, 03 Jun 2019 03:36:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:36:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:36:33: #2 number of paired peaks: 218 WARNING @ Mon, 03 Jun 2019 03:36:33: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Mon, 03 Jun 2019 03:36:33: start model_add_line... INFO @ Mon, 03 Jun 2019 03:36:33: start X-correlation... INFO @ Mon, 03 Jun 2019 03:36:33: end of X-cor INFO @ Mon, 03 Jun 2019 03:36:33: #2 finished! INFO @ Mon, 03 Jun 2019 03:36:33: #2 predicted fragment length is 1 bps INFO @ Mon, 03 Jun 2019 03:36:33: #2 alternative fragment length(s) may be 1,25,592,597 bps INFO @ Mon, 03 Jun 2019 03:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10_model.r WARNING @ Mon, 03 Jun 2019 03:36:33: #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, 03 Jun 2019 03:36:33: #2 You may need to consider one of the other alternative d(s): 1,25,592,597 WARNING @ Mon, 03 Jun 2019 03:36:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 03:36:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:37:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:37:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.20_summits.bed INFO @ Mon, 03 Jun 2019 03:37:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:37:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.05_summits.bed INFO @ Mon, 03 Jun 2019 03:38:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147004/SRX147004.10_summits.bed INFO @ Mon, 03 Jun 2019 03:38:14: 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。