Job ID = 1294906 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,133,552 reads read : 17,133,552 reads written : 17,133,552 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: 00:08:35 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 669253 (3.91%) aligned 0 times 11145730 (65.05%) aligned exactly 1 time 5318569 (31.04%) aligned >1 times 96.09% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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 8 files... [bam_rmdupse_core] 2379039 / 16464299 = 0.1445 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 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:58:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.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 10:58:54: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:58:54: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:59:02: 1000000 INFO @ Mon, 03 Jun 2019 10:59:04: 1000000 INFO @ Mon, 03 Jun 2019 10:59:06: 1000000 INFO @ Mon, 03 Jun 2019 10:59:10: 2000000 INFO @ Mon, 03 Jun 2019 10:59:12: 2000000 INFO @ Mon, 03 Jun 2019 10:59:16: 2000000 INFO @ Mon, 03 Jun 2019 10:59:18: 3000000 INFO @ Mon, 03 Jun 2019 10:59:21: 3000000 INFO @ Mon, 03 Jun 2019 10:59:25: 4000000 INFO @ Mon, 03 Jun 2019 10:59:26: 3000000 INFO @ Mon, 03 Jun 2019 10:59:29: 4000000 INFO @ Mon, 03 Jun 2019 10:59:33: 5000000 INFO @ Mon, 03 Jun 2019 10:59:36: 4000000 INFO @ Mon, 03 Jun 2019 10:59:37: 5000000 INFO @ Mon, 03 Jun 2019 10:59:40: 6000000 INFO @ Mon, 03 Jun 2019 10:59:46: 5000000 INFO @ Mon, 03 Jun 2019 10:59:46: 6000000 INFO @ Mon, 03 Jun 2019 10:59:48: 7000000 INFO @ Mon, 03 Jun 2019 10:59:54: 7000000 INFO @ Mon, 03 Jun 2019 10:59:56: 8000000 INFO @ Mon, 03 Jun 2019 10:59:56: 6000000 INFO @ Mon, 03 Jun 2019 11:00:03: 8000000 INFO @ Mon, 03 Jun 2019 11:00:04: 9000000 INFO @ Mon, 03 Jun 2019 11:00:07: 7000000 INFO @ Mon, 03 Jun 2019 11:00:12: 10000000 INFO @ Mon, 03 Jun 2019 11:00:12: 9000000 INFO @ Mon, 03 Jun 2019 11:00:18: 8000000 INFO @ Mon, 03 Jun 2019 11:00:20: 11000000 INFO @ Mon, 03 Jun 2019 11:00:22: 10000000 INFO @ Mon, 03 Jun 2019 11:00:28: 12000000 INFO @ Mon, 03 Jun 2019 11:00:28: 9000000 INFO @ Mon, 03 Jun 2019 11:00:31: 11000000 INFO @ Mon, 03 Jun 2019 11:00:35: 13000000 INFO @ Mon, 03 Jun 2019 11:00:39: 10000000 INFO @ Mon, 03 Jun 2019 11:00:40: 12000000 INFO @ Mon, 03 Jun 2019 11:00:44: 14000000 INFO @ Mon, 03 Jun 2019 11:00:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:45: #1 total tags in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:00:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:45: #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 11:00:45: #1 tags after filtering in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:45: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:00:47: #2 number of paired peaks: 349 WARNING @ Mon, 03 Jun 2019 11:00:47: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 03 Jun 2019 11:00:47: start model_add_line... INFO @ Mon, 03 Jun 2019 11:00:47: start X-correlation... INFO @ Mon, 03 Jun 2019 11:00:47: end of X-cor INFO @ Mon, 03 Jun 2019 11:00:47: #2 finished! INFO @ Mon, 03 Jun 2019 11:00:47: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:00:47: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:00:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10_model.r WARNING @ Mon, 03 Jun 2019 11:00:47: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:00:47: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:00:47: #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 11:00:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:00:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:00:48: 13000000 INFO @ Mon, 03 Jun 2019 11:00:49: 11000000 INFO @ Mon, 03 Jun 2019 11:00:57: 14000000 INFO @ Mon, 03 Jun 2019 11:00:58: 12000000 INFO @ Mon, 03 Jun 2019 11:00:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:00:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:00:58: #1 total tags in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:00:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:00:58: #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 11:00:58: #1 tags after filtering in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:00:58: #1 finished! INFO @ Mon, 03 Jun 2019 11:00:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #2 number of paired peaks: 349 WARNING @ Mon, 03 Jun 2019 11:01:00: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 03 Jun 2019 11:01:00: start model_add_line... INFO @ Mon, 03 Jun 2019 11:01:00: start X-correlation... INFO @ Mon, 03 Jun 2019 11:01:00: end of X-cor INFO @ Mon, 03 Jun 2019 11:01:00: #2 finished! INFO @ Mon, 03 Jun 2019 11:01:00: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20_model.r WARNING @ Mon, 03 Jun 2019 11:01:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:01:00: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:01:00: #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 11:01:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:01:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:01:08: 13000000 INFO @ Mon, 03 Jun 2019 11:01:18: 14000000 INFO @ Mon, 03 Jun 2019 11:01:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:01:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:01:18: #1 total tags in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:01:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:01:18: #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 11:01:19: #1 tags after filtering in treatment: 14085260 INFO @ Mon, 03 Jun 2019 11:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:01:19: #1 finished! INFO @ Mon, 03 Jun 2019 11:01:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:01:20: #2 number of paired peaks: 349 WARNING @ Mon, 03 Jun 2019 11:01:20: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Mon, 03 Jun 2019 11:01:20: start model_add_line... INFO @ Mon, 03 Jun 2019 11:01:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:01:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:01:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:01:20: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 11:01:20: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 11:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05_model.r WARNING @ Mon, 03 Jun 2019 11:01:20: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:01:20: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 11:01:20: #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 11:01:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:01:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.10_summits.bed INFO @ Mon, 03 Jun 2019 11:01:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.20_summits.bed INFO @ Mon, 03 Jun 2019 11:01:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1500 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:01:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287980/SRX287980.05_summits.bed INFO @ Mon, 03 Jun 2019 11:02:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2169 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。