Job ID = 2590629 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,162,813 reads read : 25,162,813 reads written : 25,162,813 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198781.sra.cache’: 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: 00:10:09 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1369089 (5.44%) aligned 0 times 16619075 (66.05%) aligned exactly 1 time 7174649 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:10:09 Overall time: 00:10:09 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] 5652038 / 23793724 = 0.2375 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 23:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.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, 12 Aug 2019 23:04:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.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, 12 Aug 2019 23:04:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.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, 12 Aug 2019 23:04:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:04:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:04:06: 1000000 INFO @ Mon, 12 Aug 2019 23:04:08: 1000000 INFO @ Mon, 12 Aug 2019 23:04:09: 1000000 INFO @ Mon, 12 Aug 2019 23:04:13: 2000000 INFO @ Mon, 12 Aug 2019 23:04:14: 2000000 INFO @ Mon, 12 Aug 2019 23:04:16: 2000000 INFO @ Mon, 12 Aug 2019 23:04:19: 3000000 INFO @ Mon, 12 Aug 2019 23:04:21: 3000000 INFO @ Mon, 12 Aug 2019 23:04:22: 3000000 INFO @ Mon, 12 Aug 2019 23:04:26: 4000000 INFO @ Mon, 12 Aug 2019 23:04:28: 4000000 INFO @ Mon, 12 Aug 2019 23:04:29: 4000000 INFO @ Mon, 12 Aug 2019 23:04:32: 5000000 INFO @ Mon, 12 Aug 2019 23:04:35: 5000000 INFO @ Mon, 12 Aug 2019 23:04:36: 5000000 INFO @ Mon, 12 Aug 2019 23:04:38: 6000000 INFO @ Mon, 12 Aug 2019 23:04:44: 6000000 INFO @ Mon, 12 Aug 2019 23:04:45: 7000000 INFO @ Mon, 12 Aug 2019 23:04:46: 6000000 INFO @ Mon, 12 Aug 2019 23:04:51: 8000000 INFO @ Mon, 12 Aug 2019 23:04:53: 7000000 INFO @ Mon, 12 Aug 2019 23:04:55: 7000000 INFO @ Mon, 12 Aug 2019 23:04:57: 9000000 INFO @ Mon, 12 Aug 2019 23:05:02: 8000000 INFO @ Mon, 12 Aug 2019 23:05:04: 10000000 INFO @ Mon, 12 Aug 2019 23:05:04: 8000000 INFO @ Mon, 12 Aug 2019 23:05:10: 11000000 INFO @ Mon, 12 Aug 2019 23:05:11: 9000000 INFO @ Mon, 12 Aug 2019 23:05:13: 9000000 INFO @ Mon, 12 Aug 2019 23:05:17: 12000000 INFO @ Mon, 12 Aug 2019 23:05:20: 10000000 INFO @ Mon, 12 Aug 2019 23:05:21: 10000000 INFO @ Mon, 12 Aug 2019 23:05:23: 13000000 INFO @ Mon, 12 Aug 2019 23:05:29: 11000000 INFO @ Mon, 12 Aug 2019 23:05:29: 14000000 INFO @ Mon, 12 Aug 2019 23:05:30: 11000000 INFO @ Mon, 12 Aug 2019 23:05:36: 15000000 INFO @ Mon, 12 Aug 2019 23:05:38: 12000000 INFO @ Mon, 12 Aug 2019 23:05:39: 12000000 INFO @ Mon, 12 Aug 2019 23:05:42: 16000000 INFO @ Mon, 12 Aug 2019 23:05:47: 13000000 INFO @ Mon, 12 Aug 2019 23:05:48: 13000000 INFO @ Mon, 12 Aug 2019 23:05:48: 17000000 INFO @ Mon, 12 Aug 2019 23:05:55: 18000000 INFO @ Mon, 12 Aug 2019 23:05:55: 14000000 INFO @ Mon, 12 Aug 2019 23:05:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:05:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:05:56: #1 total tags in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:05:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:05:56: #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 23:05:56: #1 tags after filtering in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:05:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:05:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:05:57: 14000000 INFO @ Mon, 12 Aug 2019 23:05:58: #2 number of paired peaks: 113 WARNING @ Mon, 12 Aug 2019 23:05:58: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 12 Aug 2019 23:05:58: start model_add_line... INFO @ Mon, 12 Aug 2019 23:05:58: start X-correlation... INFO @ Mon, 12 Aug 2019 23:05:58: end of X-cor INFO @ Mon, 12 Aug 2019 23:05:58: #2 finished! INFO @ Mon, 12 Aug 2019 23:05:58: #2 predicted fragment length is 57 bps INFO @ Mon, 12 Aug 2019 23:05:58: #2 alternative fragment length(s) may be 3,10,57,102,105,212,481,512,537,570,593 bps INFO @ Mon, 12 Aug 2019 23:05:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05_model.r WARNING @ Mon, 12 Aug 2019 23:05:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:05:58: #2 You may need to consider one of the other alternative d(s): 3,10,57,102,105,212,481,512,537,570,593 WARNING @ Mon, 12 Aug 2019 23:05:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:05:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:05:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:04: 15000000 INFO @ Mon, 12 Aug 2019 23:06:06: 15000000 INFO @ Mon, 12 Aug 2019 23:06:13: 16000000 INFO @ Mon, 12 Aug 2019 23:06:15: 16000000 INFO @ Mon, 12 Aug 2019 23:06:22: 17000000 INFO @ Mon, 12 Aug 2019 23:06:24: 17000000 INFO @ Mon, 12 Aug 2019 23:06:30: 18000000 INFO @ Mon, 12 Aug 2019 23:06:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:32: #1 total tags in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:06:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:32: #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 23:06:32: 18000000 INFO @ Mon, 12 Aug 2019 23:06:32: #1 tags after filtering in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:06:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:06:33: #1 total tags in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:06:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:06:33: #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 23:06:34: #2 number of paired peaks: 113 WARNING @ Mon, 12 Aug 2019 23:06:34: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:34: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:34: #1 tags after filtering in treatment: 18141686 INFO @ Mon, 12 Aug 2019 23:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:06:34: #1 finished! INFO @ Mon, 12 Aug 2019 23:06:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:06:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:34: #2 predicted fragment length is 57 bps INFO @ Mon, 12 Aug 2019 23:06:34: #2 alternative fragment length(s) may be 3,10,57,102,105,212,481,512,537,570,593 bps INFO @ Mon, 12 Aug 2019 23:06:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10_model.r WARNING @ Mon, 12 Aug 2019 23:06:34: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:34: #2 You may need to consider one of the other alternative d(s): 3,10,57,102,105,212,481,512,537,570,593 WARNING @ Mon, 12 Aug 2019 23:06:34: #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 23:06:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:35: #2 number of paired peaks: 113 WARNING @ Mon, 12 Aug 2019 23:06:35: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Mon, 12 Aug 2019 23:06:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:06:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:06:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:06:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:06:35: #2 predicted fragment length is 57 bps INFO @ Mon, 12 Aug 2019 23:06:35: #2 alternative fragment length(s) may be 3,10,57,102,105,212,481,512,537,570,593 bps INFO @ Mon, 12 Aug 2019 23:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20_model.r WARNING @ Mon, 12 Aug 2019 23:06:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:06:35: #2 You may need to consider one of the other alternative d(s): 3,10,57,102,105,212,481,512,537,570,593 WARNING @ Mon, 12 Aug 2019 23:06:35: #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 23:06:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:06:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.05_summits.bed INFO @ Mon, 12 Aug 2019 23:07:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2358 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.10_summits.bed INFO @ Mon, 12 Aug 2019 23:07:46: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1192 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495276/SRX495276.20_summits.bed INFO @ Mon, 12 Aug 2019 23:07:47: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。