Job ID = 1295204 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,493,128 reads read : 18,493,128 reads written : 18,493,128 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: 00:07:00 18493128 reads; of these: 18493128 (100.00%) were unpaired; of these: 1125023 (6.08%) aligned 0 times 13121015 (70.95%) aligned exactly 1 time 4247090 (22.97%) aligned >1 times 93.92% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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 8 files... [bam_rmdupse_core] 1482253 / 17368105 = 0.0853 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 12:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.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 12:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.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 12:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.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 12:58:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:58:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:58:30: 1000000 INFO @ Mon, 03 Jun 2019 12:58:32: 1000000 INFO @ Mon, 03 Jun 2019 12:58:33: 1000000 INFO @ Mon, 03 Jun 2019 12:58:38: 2000000 INFO @ Mon, 03 Jun 2019 12:58:41: 2000000 INFO @ Mon, 03 Jun 2019 12:58:43: 2000000 INFO @ Mon, 03 Jun 2019 12:58:45: 3000000 INFO @ Mon, 03 Jun 2019 12:58:50: 3000000 INFO @ Mon, 03 Jun 2019 12:58:53: 4000000 INFO @ Mon, 03 Jun 2019 12:58:54: 3000000 INFO @ Mon, 03 Jun 2019 12:58:59: 4000000 INFO @ Mon, 03 Jun 2019 12:59:01: 5000000 INFO @ Mon, 03 Jun 2019 12:59:04: 4000000 INFO @ Mon, 03 Jun 2019 12:59:08: 5000000 INFO @ Mon, 03 Jun 2019 12:59:08: 6000000 INFO @ Mon, 03 Jun 2019 12:59:14: 5000000 INFO @ Mon, 03 Jun 2019 12:59:16: 7000000 INFO @ Mon, 03 Jun 2019 12:59:17: 6000000 INFO @ Mon, 03 Jun 2019 12:59:24: 8000000 INFO @ Mon, 03 Jun 2019 12:59:25: 6000000 INFO @ Mon, 03 Jun 2019 12:59:26: 7000000 INFO @ Mon, 03 Jun 2019 12:59:31: 9000000 INFO @ Mon, 03 Jun 2019 12:59:34: 8000000 INFO @ Mon, 03 Jun 2019 12:59:35: 7000000 INFO @ Mon, 03 Jun 2019 12:59:39: 10000000 INFO @ Mon, 03 Jun 2019 12:59:43: 9000000 INFO @ Mon, 03 Jun 2019 12:59:45: 8000000 INFO @ Mon, 03 Jun 2019 12:59:47: 11000000 INFO @ Mon, 03 Jun 2019 12:59:51: 10000000 INFO @ Mon, 03 Jun 2019 12:59:54: 12000000 INFO @ Mon, 03 Jun 2019 12:59:55: 9000000 INFO @ Mon, 03 Jun 2019 13:00:00: 11000000 INFO @ Mon, 03 Jun 2019 13:00:02: 13000000 INFO @ Mon, 03 Jun 2019 13:00:05: 10000000 INFO @ Mon, 03 Jun 2019 13:00:08: 12000000 INFO @ Mon, 03 Jun 2019 13:00:11: 14000000 INFO @ Mon, 03 Jun 2019 13:00:16: 11000000 INFO @ Mon, 03 Jun 2019 13:00:17: 13000000 INFO @ Mon, 03 Jun 2019 13:00:19: 15000000 INFO @ Mon, 03 Jun 2019 13:00:26: 12000000 INFO @ Mon, 03 Jun 2019 13:00:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:00:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:00:26: #1 total tags in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:00:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:00:26: #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 13:00:26: #1 tags after filtering in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:00:26: #1 finished! INFO @ Mon, 03 Jun 2019 13:00:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:00:26: 14000000 INFO @ Mon, 03 Jun 2019 13:00:28: #2 number of paired peaks: 158 WARNING @ Mon, 03 Jun 2019 13:00:28: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Mon, 03 Jun 2019 13:00:28: start model_add_line... INFO @ Mon, 03 Jun 2019 13:00:28: start X-correlation... INFO @ Mon, 03 Jun 2019 13:00:28: end of X-cor INFO @ Mon, 03 Jun 2019 13:00:28: #2 finished! INFO @ Mon, 03 Jun 2019 13:00:28: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:00:28: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05_model.r WARNING @ Mon, 03 Jun 2019 13:00:28: #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 13:00:28: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:00:28: #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 13:00:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:00:35: 15000000 INFO @ Mon, 03 Jun 2019 13:00:37: 13000000 INFO @ Mon, 03 Jun 2019 13:00:43: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:00:43: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:00:43: #1 total tags in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:00:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:00:43: #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 13:00:43: #1 tags after filtering in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:00:43: #1 finished! INFO @ Mon, 03 Jun 2019 13:00:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:00:44: #2 number of paired peaks: 158 WARNING @ Mon, 03 Jun 2019 13:00:44: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Mon, 03 Jun 2019 13:00:44: start model_add_line... INFO @ Mon, 03 Jun 2019 13:00:44: start X-correlation... INFO @ Mon, 03 Jun 2019 13:00:44: end of X-cor INFO @ Mon, 03 Jun 2019 13:00:44: #2 finished! INFO @ Mon, 03 Jun 2019 13:00:44: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:00:44: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20_model.r WARNING @ Mon, 03 Jun 2019 13:00:44: #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 13:00:44: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:00:44: #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 13:00:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:00:47: 14000000 INFO @ Mon, 03 Jun 2019 13:00:57: 15000000 INFO @ Mon, 03 Jun 2019 13:01:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:01:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:01:06: #1 total tags in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:01:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:01:06: #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 13:01:07: #1 tags after filtering in treatment: 15885852 INFO @ Mon, 03 Jun 2019 13:01:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:01:07: #1 finished! INFO @ Mon, 03 Jun 2019 13:01:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:01:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:01:08: #2 number of paired peaks: 158 WARNING @ Mon, 03 Jun 2019 13:01:08: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Mon, 03 Jun 2019 13:01:08: start model_add_line... INFO @ Mon, 03 Jun 2019 13:01:08: start X-correlation... INFO @ Mon, 03 Jun 2019 13:01:08: end of X-cor INFO @ Mon, 03 Jun 2019 13:01:08: #2 finished! INFO @ Mon, 03 Jun 2019 13:01:08: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 13:01:08: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 13:01:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10_model.r WARNING @ Mon, 03 Jun 2019 13:01:08: #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 13:01:08: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 13:01:08: #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 13:01:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:01:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:01:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:01:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.05_summits.bed INFO @ Mon, 03 Jun 2019 13:01:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1994 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.20_summits.bed INFO @ Mon, 03 Jun 2019 13:01:45: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1076 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:01:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331385/SRX331385.10_summits.bed INFO @ Mon, 03 Jun 2019 13:02:09: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1589 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。