Job ID = 1293570 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,187,983 reads read : 34,187,983 reads written : 34,187,983 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: 00:09:29 34187983 reads; of these: 34187983 (100.00%) were unpaired; of these: 13904121 (40.67%) aligned 0 times 14903958 (43.59%) aligned exactly 1 time 5379904 (15.74%) aligned >1 times 59.33% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 11016139 / 20283862 = 0.5431 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 01:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.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 01:09:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:09:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.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 01:09:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:09:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.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 01:09:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:09:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:09:49: 1000000 INFO @ Mon, 03 Jun 2019 01:09:49: 1000000 INFO @ Mon, 03 Jun 2019 01:09:50: 1000000 INFO @ Mon, 03 Jun 2019 01:09:59: 2000000 INFO @ Mon, 03 Jun 2019 01:10:00: 2000000 INFO @ Mon, 03 Jun 2019 01:10:00: 2000000 INFO @ Mon, 03 Jun 2019 01:10:08: 3000000 INFO @ Mon, 03 Jun 2019 01:10:10: 3000000 INFO @ Mon, 03 Jun 2019 01:10:10: 3000000 INFO @ Mon, 03 Jun 2019 01:10:17: 4000000 INFO @ Mon, 03 Jun 2019 01:10:20: 4000000 INFO @ Mon, 03 Jun 2019 01:10:20: 4000000 INFO @ Mon, 03 Jun 2019 01:10:27: 5000000 INFO @ Mon, 03 Jun 2019 01:10:30: 5000000 INFO @ Mon, 03 Jun 2019 01:10:30: 5000000 INFO @ Mon, 03 Jun 2019 01:10:36: 6000000 INFO @ Mon, 03 Jun 2019 01:10:40: 6000000 INFO @ Mon, 03 Jun 2019 01:10:40: 6000000 INFO @ Mon, 03 Jun 2019 01:10:46: 7000000 INFO @ Mon, 03 Jun 2019 01:10:50: 7000000 INFO @ Mon, 03 Jun 2019 01:10:50: 7000000 INFO @ Mon, 03 Jun 2019 01:10:55: 8000000 INFO @ Mon, 03 Jun 2019 01:11:00: 8000000 INFO @ Mon, 03 Jun 2019 01:11:00: 8000000 INFO @ Mon, 03 Jun 2019 01:11:04: 9000000 INFO @ Mon, 03 Jun 2019 01:11:07: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:11:07: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:11:07: #1 total tags in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:11:07: #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 01:11:07: #1 tags after filtering in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:11:07: #1 finished! INFO @ Mon, 03 Jun 2019 01:11:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:11:08: #2 number of paired peaks: 148 WARNING @ Mon, 03 Jun 2019 01:11:08: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 03 Jun 2019 01:11:08: start model_add_line... INFO @ Mon, 03 Jun 2019 01:11:08: start X-correlation... INFO @ Mon, 03 Jun 2019 01:11:08: end of X-cor INFO @ Mon, 03 Jun 2019 01:11:08: #2 finished! INFO @ Mon, 03 Jun 2019 01:11:08: #2 predicted fragment length is 83 bps INFO @ Mon, 03 Jun 2019 01:11:08: #2 alternative fragment length(s) may be 83 bps INFO @ Mon, 03 Jun 2019 01:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10_model.r INFO @ Mon, 03 Jun 2019 01:11:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:11:10: 9000000 INFO @ Mon, 03 Jun 2019 01:11:10: 9000000 INFO @ Mon, 03 Jun 2019 01:11:13: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:11:13: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:11:13: #1 total tags in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:11:13: #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 01:11:13: #1 tag size is determined as 41 bps INFO @ Mon, 03 Jun 2019 01:11:13: #1 tag size = 41 INFO @ Mon, 03 Jun 2019 01:11:13: #1 total tags in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:11:13: #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 01:11:13: #1 tags after filtering in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:11:13: #1 finished! INFO @ Mon, 03 Jun 2019 01:11:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:11:13: #1 tags after filtering in treatment: 9267723 INFO @ Mon, 03 Jun 2019 01:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:11:13: #1 finished! INFO @ Mon, 03 Jun 2019 01:11:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:11:14: #2 number of paired peaks: 148 WARNING @ Mon, 03 Jun 2019 01:11:14: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 03 Jun 2019 01:11:14: start model_add_line... INFO @ Mon, 03 Jun 2019 01:11:14: start X-correlation... INFO @ Mon, 03 Jun 2019 01:11:14: #2 number of paired peaks: 148 WARNING @ Mon, 03 Jun 2019 01:11:14: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Mon, 03 Jun 2019 01:11:14: start model_add_line... INFO @ Mon, 03 Jun 2019 01:11:14: end of X-cor INFO @ Mon, 03 Jun 2019 01:11:14: #2 finished! INFO @ Mon, 03 Jun 2019 01:11:14: #2 predicted fragment length is 83 bps INFO @ Mon, 03 Jun 2019 01:11:14: #2 alternative fragment length(s) may be 83 bps INFO @ Mon, 03 Jun 2019 01:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20_model.r INFO @ Mon, 03 Jun 2019 01:11:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:11:14: start X-correlation... INFO @ Mon, 03 Jun 2019 01:11:14: end of X-cor INFO @ Mon, 03 Jun 2019 01:11:14: #2 finished! INFO @ Mon, 03 Jun 2019 01:11:14: #2 predicted fragment length is 83 bps INFO @ Mon, 03 Jun 2019 01:11:14: #2 alternative fragment length(s) may be 83 bps INFO @ Mon, 03 Jun 2019 01:11:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05_model.r INFO @ Mon, 03 Jun 2019 01:11:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:11:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:11:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:11:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:11:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.10_summits.bed INFO @ Mon, 03 Jun 2019 01:11:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1490 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.20_summits.bed INFO @ Mon, 03 Jun 2019 01:11:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX101476/SRX101476.05_summits.bed INFO @ Mon, 03 Jun 2019 01:11:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6301 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。