Job ID = 2590948 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,958,465 reads read : 71,916,930 reads written : 35,958,465 reads 0-length : 35,958,465 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: 00:17:45 35958465 reads; of these: 35958465 (100.00%) were unpaired; of these: 1050867 (2.92%) aligned 0 times 17711330 (49.25%) aligned exactly 1 time 17196268 (47.82%) aligned >1 times 97.08% overall alignment rate Time searching: 00:17:45 Overall time: 00:17:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 9456735 / 34907598 = 0.2709 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 @ Tue, 13 Aug 2019 00:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.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 @ Tue, 13 Aug 2019 00:33:22: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:22: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.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 @ Tue, 13 Aug 2019 00:33:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.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 @ Tue, 13 Aug 2019 00:33:24: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:33:24: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:33:31: 1000000 INFO @ Tue, 13 Aug 2019 00:33:32: 1000000 INFO @ Tue, 13 Aug 2019 00:33:34: 1000000 INFO @ Tue, 13 Aug 2019 00:33:40: 2000000 INFO @ Tue, 13 Aug 2019 00:33:41: 2000000 INFO @ Tue, 13 Aug 2019 00:33:45: 2000000 INFO @ Tue, 13 Aug 2019 00:33:49: 3000000 INFO @ Tue, 13 Aug 2019 00:33:49: 3000000 INFO @ Tue, 13 Aug 2019 00:33:55: 3000000 INFO @ Tue, 13 Aug 2019 00:33:57: 4000000 INFO @ Tue, 13 Aug 2019 00:33:58: 4000000 INFO @ Tue, 13 Aug 2019 00:34:05: 4000000 INFO @ Tue, 13 Aug 2019 00:34:06: 5000000 INFO @ Tue, 13 Aug 2019 00:34:07: 5000000 INFO @ Tue, 13 Aug 2019 00:34:15: 6000000 INFO @ Tue, 13 Aug 2019 00:34:15: 5000000 INFO @ Tue, 13 Aug 2019 00:34:16: 6000000 INFO @ Tue, 13 Aug 2019 00:34:24: 7000000 INFO @ Tue, 13 Aug 2019 00:34:25: 7000000 INFO @ Tue, 13 Aug 2019 00:34:25: 6000000 INFO @ Tue, 13 Aug 2019 00:34:32: 8000000 INFO @ Tue, 13 Aug 2019 00:34:33: 8000000 INFO @ Tue, 13 Aug 2019 00:34:36: 7000000 INFO @ Tue, 13 Aug 2019 00:34:41: 9000000 INFO @ Tue, 13 Aug 2019 00:34:42: 9000000 INFO @ Tue, 13 Aug 2019 00:34:46: 8000000 INFO @ Tue, 13 Aug 2019 00:34:50: 10000000 INFO @ Tue, 13 Aug 2019 00:34:50: 10000000 INFO @ Tue, 13 Aug 2019 00:34:56: 9000000 INFO @ Tue, 13 Aug 2019 00:34:58: 11000000 INFO @ Tue, 13 Aug 2019 00:34:59: 11000000 INFO @ Tue, 13 Aug 2019 00:35:05: 10000000 INFO @ Tue, 13 Aug 2019 00:35:07: 12000000 INFO @ Tue, 13 Aug 2019 00:35:08: 12000000 INFO @ Tue, 13 Aug 2019 00:35:16: 11000000 INFO @ Tue, 13 Aug 2019 00:35:16: 13000000 INFO @ Tue, 13 Aug 2019 00:35:17: 13000000 INFO @ Tue, 13 Aug 2019 00:35:25: 14000000 INFO @ Tue, 13 Aug 2019 00:35:26: 14000000 INFO @ Tue, 13 Aug 2019 00:35:26: 12000000 INFO @ Tue, 13 Aug 2019 00:35:34: 15000000 INFO @ Tue, 13 Aug 2019 00:35:34: 15000000 INFO @ Tue, 13 Aug 2019 00:35:36: 13000000 INFO @ Tue, 13 Aug 2019 00:35:42: 16000000 INFO @ Tue, 13 Aug 2019 00:35:43: 16000000 INFO @ Tue, 13 Aug 2019 00:35:46: 14000000 INFO @ Tue, 13 Aug 2019 00:35:50: 17000000 INFO @ Tue, 13 Aug 2019 00:35:52: 17000000 INFO @ Tue, 13 Aug 2019 00:35:57: 15000000 INFO @ Tue, 13 Aug 2019 00:35:58: 18000000 INFO @ Tue, 13 Aug 2019 00:36:00: 18000000 INFO @ Tue, 13 Aug 2019 00:36:05: 19000000 INFO @ Tue, 13 Aug 2019 00:36:07: 16000000 INFO @ Tue, 13 Aug 2019 00:36:09: 19000000 INFO @ Tue, 13 Aug 2019 00:36:13: 20000000 INFO @ Tue, 13 Aug 2019 00:36:17: 17000000 INFO @ Tue, 13 Aug 2019 00:36:17: 20000000 INFO @ Tue, 13 Aug 2019 00:36:20: 21000000 INFO @ Tue, 13 Aug 2019 00:36:25: 21000000 INFO @ Tue, 13 Aug 2019 00:36:27: 18000000 INFO @ Tue, 13 Aug 2019 00:36:28: 22000000 INFO @ Tue, 13 Aug 2019 00:36:34: 22000000 INFO @ Tue, 13 Aug 2019 00:36:35: 23000000 INFO @ Tue, 13 Aug 2019 00:36:37: 19000000 INFO @ Tue, 13 Aug 2019 00:36:42: 23000000 INFO @ Tue, 13 Aug 2019 00:36:43: 24000000 INFO @ Tue, 13 Aug 2019 00:36:48: 20000000 INFO @ Tue, 13 Aug 2019 00:36:51: 25000000 INFO @ Tue, 13 Aug 2019 00:36:51: 24000000 INFO @ Tue, 13 Aug 2019 00:36:54: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:36:54: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:36:54: #1 total tags in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:36:54: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:36:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:36:55: #1 tags after filtering in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:36:55: #1 finished! INFO @ Tue, 13 Aug 2019 00:36:55: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:36:57: #2 number of paired peaks: 318 WARNING @ Tue, 13 Aug 2019 00:36:57: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 13 Aug 2019 00:36:57: start model_add_line... INFO @ Tue, 13 Aug 2019 00:36:57: start X-correlation... INFO @ Tue, 13 Aug 2019 00:36:57: end of X-cor INFO @ Tue, 13 Aug 2019 00:36:57: #2 finished! INFO @ Tue, 13 Aug 2019 00:36:57: #2 predicted fragment length is 2 bps INFO @ Tue, 13 Aug 2019 00:36:57: #2 alternative fragment length(s) may be 2,20,37 bps INFO @ Tue, 13 Aug 2019 00:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05_model.r WARNING @ Tue, 13 Aug 2019 00:36:57: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:36:57: #2 You may need to consider one of the other alternative d(s): 2,20,37 WARNING @ Tue, 13 Aug 2019 00:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:36:57: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:36:58: 21000000 INFO @ Tue, 13 Aug 2019 00:36:59: 25000000 INFO @ Tue, 13 Aug 2019 00:37:03: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:37:03: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:37:03: #1 total tags in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:37:03: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:37:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:37:04: #1 tags after filtering in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:37:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:37:04: #1 finished! INFO @ Tue, 13 Aug 2019 00:37:04: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:37:06: #2 number of paired peaks: 318 WARNING @ Tue, 13 Aug 2019 00:37:06: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 13 Aug 2019 00:37:06: start model_add_line... INFO @ Tue, 13 Aug 2019 00:37:06: start X-correlation... INFO @ Tue, 13 Aug 2019 00:37:06: end of X-cor INFO @ Tue, 13 Aug 2019 00:37:06: #2 finished! INFO @ Tue, 13 Aug 2019 00:37:06: #2 predicted fragment length is 2 bps INFO @ Tue, 13 Aug 2019 00:37:06: #2 alternative fragment length(s) may be 2,20,37 bps INFO @ Tue, 13 Aug 2019 00:37:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10_model.r WARNING @ Tue, 13 Aug 2019 00:37:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:37:06: #2 You may need to consider one of the other alternative d(s): 2,20,37 WARNING @ Tue, 13 Aug 2019 00:37:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:37:06: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:37:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:37:08: 22000000 INFO @ Tue, 13 Aug 2019 00:37:17: 23000000 INFO @ Tue, 13 Aug 2019 00:37:27: 24000000 INFO @ Tue, 13 Aug 2019 00:37:37: 25000000 INFO @ Tue, 13 Aug 2019 00:37:41: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:37:41: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:37:41: #1 total tags in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:37:41: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:37:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:37:41: #1 tags after filtering in treatment: 25450863 INFO @ Tue, 13 Aug 2019 00:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:37:41: #1 finished! INFO @ Tue, 13 Aug 2019 00:37:41: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:37:44: #2 number of paired peaks: 318 WARNING @ Tue, 13 Aug 2019 00:37:44: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 13 Aug 2019 00:37:44: start model_add_line... INFO @ Tue, 13 Aug 2019 00:37:44: start X-correlation... INFO @ Tue, 13 Aug 2019 00:37:44: end of X-cor INFO @ Tue, 13 Aug 2019 00:37:44: #2 finished! INFO @ Tue, 13 Aug 2019 00:37:44: #2 predicted fragment length is 2 bps INFO @ Tue, 13 Aug 2019 00:37:44: #2 alternative fragment length(s) may be 2,20,37 bps INFO @ Tue, 13 Aug 2019 00:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20_model.r WARNING @ Tue, 13 Aug 2019 00:37:44: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:37:44: #2 You may need to consider one of the other alternative d(s): 2,20,37 WARNING @ Tue, 13 Aug 2019 00:37:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:37:44: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:37:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:37:53: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:38:02: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.05_summits.bed INFO @ Tue, 13 Aug 2019 00:38:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:38:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:38:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:38:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.10_summits.bed INFO @ Tue, 13 Aug 2019 00:38:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:38:40: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:39:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:39:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:39:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5661486/SRX5661486.20_summits.bed INFO @ Tue, 13 Aug 2019 00:39:06: 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。