Job ID = 1294210 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,417,081 reads read : 41,417,081 reads written : 41,417,081 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: 00:27:39 41417081 reads; of these: 41417081 (100.00%) were unpaired; of these: 691164 (1.67%) aligned 0 times 12205955 (29.47%) aligned exactly 1 time 28519962 (68.86%) aligned >1 times 98.33% overall alignment rate Time searching: 00:27:39 Overall time: 00:27:39 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 20 files... [bam_rmdupse_core] 12270511 / 40725917 = 0.3013 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 06:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.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 06:11:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.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 06:11:21: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:21: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.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 06:11:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:30: 1000000 INFO @ Mon, 03 Jun 2019 06:11:31: 1000000 INFO @ Mon, 03 Jun 2019 06:11:32: 1000000 INFO @ Mon, 03 Jun 2019 06:11:38: 2000000 INFO @ Mon, 03 Jun 2019 06:11:41: 2000000 INFO @ Mon, 03 Jun 2019 06:11:42: 2000000 INFO @ Mon, 03 Jun 2019 06:11:46: 3000000 INFO @ Mon, 03 Jun 2019 06:11:50: 3000000 INFO @ Mon, 03 Jun 2019 06:11:51: 3000000 INFO @ Mon, 03 Jun 2019 06:11:54: 4000000 INFO @ Mon, 03 Jun 2019 06:11:59: 4000000 INFO @ Mon, 03 Jun 2019 06:12:00: 4000000 INFO @ Mon, 03 Jun 2019 06:12:02: 5000000 INFO @ Mon, 03 Jun 2019 06:12:09: 5000000 INFO @ Mon, 03 Jun 2019 06:12:09: 5000000 INFO @ Mon, 03 Jun 2019 06:12:10: 6000000 INFO @ Mon, 03 Jun 2019 06:12:18: 6000000 INFO @ Mon, 03 Jun 2019 06:12:18: 7000000 INFO @ Mon, 03 Jun 2019 06:12:19: 6000000 INFO @ Mon, 03 Jun 2019 06:12:25: 8000000 INFO @ Mon, 03 Jun 2019 06:12:27: 7000000 INFO @ Mon, 03 Jun 2019 06:12:28: 7000000 INFO @ Mon, 03 Jun 2019 06:12:32: 9000000 INFO @ Mon, 03 Jun 2019 06:12:36: 8000000 INFO @ Mon, 03 Jun 2019 06:12:37: 8000000 INFO @ Mon, 03 Jun 2019 06:12:40: 10000000 INFO @ Mon, 03 Jun 2019 06:12:45: 9000000 INFO @ Mon, 03 Jun 2019 06:12:46: 9000000 INFO @ Mon, 03 Jun 2019 06:12:47: 11000000 INFO @ Mon, 03 Jun 2019 06:12:54: 12000000 INFO @ Mon, 03 Jun 2019 06:12:54: 10000000 INFO @ Mon, 03 Jun 2019 06:12:55: 10000000 INFO @ Mon, 03 Jun 2019 06:13:01: 13000000 INFO @ Mon, 03 Jun 2019 06:13:04: 11000000 INFO @ Mon, 03 Jun 2019 06:13:04: 11000000 INFO @ Mon, 03 Jun 2019 06:13:09: 14000000 INFO @ Mon, 03 Jun 2019 06:13:13: 12000000 INFO @ Mon, 03 Jun 2019 06:13:14: 12000000 INFO @ Mon, 03 Jun 2019 06:13:16: 15000000 INFO @ Mon, 03 Jun 2019 06:13:22: 13000000 INFO @ Mon, 03 Jun 2019 06:13:23: 13000000 INFO @ Mon, 03 Jun 2019 06:13:23: 16000000 INFO @ Mon, 03 Jun 2019 06:13:30: 17000000 INFO @ Mon, 03 Jun 2019 06:13:32: 14000000 INFO @ Mon, 03 Jun 2019 06:13:32: 14000000 INFO @ Mon, 03 Jun 2019 06:13:38: 18000000 INFO @ Mon, 03 Jun 2019 06:13:41: 15000000 INFO @ Mon, 03 Jun 2019 06:13:42: 15000000 INFO @ Mon, 03 Jun 2019 06:13:45: 19000000 INFO @ Mon, 03 Jun 2019 06:13:50: 16000000 INFO @ Mon, 03 Jun 2019 06:13:51: 16000000 INFO @ Mon, 03 Jun 2019 06:13:53: 20000000 INFO @ Mon, 03 Jun 2019 06:13:59: 17000000 INFO @ Mon, 03 Jun 2019 06:14:00: 17000000 INFO @ Mon, 03 Jun 2019 06:14:00: 21000000 INFO @ Mon, 03 Jun 2019 06:14:07: 22000000 INFO @ Mon, 03 Jun 2019 06:14:08: 18000000 INFO @ Mon, 03 Jun 2019 06:14:08: 18000000 INFO @ Mon, 03 Jun 2019 06:14:14: 23000000 INFO @ Mon, 03 Jun 2019 06:14:18: 19000000 INFO @ Mon, 03 Jun 2019 06:14:18: 19000000 INFO @ Mon, 03 Jun 2019 06:14:21: 24000000 INFO @ Mon, 03 Jun 2019 06:14:28: 20000000 INFO @ Mon, 03 Jun 2019 06:14:28: 20000000 INFO @ Mon, 03 Jun 2019 06:14:29: 25000000 INFO @ Mon, 03 Jun 2019 06:14:36: 26000000 INFO @ Mon, 03 Jun 2019 06:14:37: 21000000 INFO @ Mon, 03 Jun 2019 06:14:37: 21000000 INFO @ Mon, 03 Jun 2019 06:14:44: 27000000 INFO @ Mon, 03 Jun 2019 06:14:46: 22000000 INFO @ Mon, 03 Jun 2019 06:14:48: 22000000 INFO @ Mon, 03 Jun 2019 06:14:51: 28000000 INFO @ Mon, 03 Jun 2019 06:14:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:14:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:14:55: #1 total tags in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:14:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:14:55: #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 06:14:55: 23000000 INFO @ Mon, 03 Jun 2019 06:14:56: #1 tags after filtering in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:14:56: #1 finished! INFO @ Mon, 03 Jun 2019 06:14:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:14:57: 23000000 INFO @ Mon, 03 Jun 2019 06:14:58: #2 number of paired peaks: 708 WARNING @ Mon, 03 Jun 2019 06:14:58: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Mon, 03 Jun 2019 06:14:58: start model_add_line... INFO @ Mon, 03 Jun 2019 06:14:58: start X-correlation... INFO @ Mon, 03 Jun 2019 06:14:58: end of X-cor INFO @ Mon, 03 Jun 2019 06:14:58: #2 finished! INFO @ Mon, 03 Jun 2019 06:14:58: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 06:14:58: #2 alternative fragment length(s) may be 2,28,40 bps INFO @ Mon, 03 Jun 2019 06:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05_model.r WARNING @ Mon, 03 Jun 2019 06:14:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:14:58: #2 You may need to consider one of the other alternative d(s): 2,28,40 WARNING @ Mon, 03 Jun 2019 06:14:58: #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 06:14:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:15:04: 24000000 INFO @ Mon, 03 Jun 2019 06:15:06: 24000000 INFO @ Mon, 03 Jun 2019 06:15:13: 25000000 INFO @ Mon, 03 Jun 2019 06:15:15: 25000000 INFO @ Mon, 03 Jun 2019 06:15:22: 26000000 INFO @ Mon, 03 Jun 2019 06:15:24: 26000000 INFO @ Mon, 03 Jun 2019 06:15:32: 27000000 INFO @ Mon, 03 Jun 2019 06:15:33: 27000000 INFO @ Mon, 03 Jun 2019 06:15:41: 28000000 INFO @ Mon, 03 Jun 2019 06:15:43: 28000000 INFO @ Mon, 03 Jun 2019 06:15:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:15:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:15:45: #1 total tags in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:15:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:15:45: #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 06:15:46: #1 tags after filtering in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:15:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:15:46: #1 finished! INFO @ Mon, 03 Jun 2019 06:15:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:15:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:15:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:15:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:15:47: #1 total tags in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:15:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:15:47: #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 06:15:48: #1 tags after filtering in treatment: 28455406 INFO @ Mon, 03 Jun 2019 06:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:15:48: #1 finished! INFO @ Mon, 03 Jun 2019 06:15:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:15:48: #2 number of paired peaks: 708 WARNING @ Mon, 03 Jun 2019 06:15:48: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Mon, 03 Jun 2019 06:15:48: start model_add_line... INFO @ Mon, 03 Jun 2019 06:15:49: start X-correlation... INFO @ Mon, 03 Jun 2019 06:15:49: end of X-cor INFO @ Mon, 03 Jun 2019 06:15:49: #2 finished! INFO @ Mon, 03 Jun 2019 06:15:49: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 06:15:49: #2 alternative fragment length(s) may be 2,28,40 bps INFO @ Mon, 03 Jun 2019 06:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10_model.r WARNING @ Mon, 03 Jun 2019 06:15:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:15:49: #2 You may need to consider one of the other alternative d(s): 2,28,40 WARNING @ Mon, 03 Jun 2019 06:15:49: #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 06:15:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:15:50: #2 number of paired peaks: 708 WARNING @ Mon, 03 Jun 2019 06:15:50: Fewer paired peaks (708) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 708 pairs to build model! INFO @ Mon, 03 Jun 2019 06:15:50: start model_add_line... INFO @ Mon, 03 Jun 2019 06:15:50: start X-correlation... INFO @ Mon, 03 Jun 2019 06:15:50: end of X-cor INFO @ Mon, 03 Jun 2019 06:15:50: #2 finished! INFO @ Mon, 03 Jun 2019 06:15:50: #2 predicted fragment length is 2 bps INFO @ Mon, 03 Jun 2019 06:15:50: #2 alternative fragment length(s) may be 2,28,40 bps INFO @ Mon, 03 Jun 2019 06:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20_model.r WARNING @ Mon, 03 Jun 2019 06:15:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:15:50: #2 You may need to consider one of the other alternative d(s): 2,28,40 WARNING @ Mon, 03 Jun 2019 06:15:50: #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 06:15:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:15:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.05_summits.bed INFO @ Mon, 03 Jun 2019 06:16:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:16:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:16:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:17:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:17:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:17:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.10_summits.bed INFO @ Mon, 03 Jun 2019 06:17:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201887/SRX201887.20_summits.bed INFO @ Mon, 03 Jun 2019 06:17:09: 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。