Job ID = 1295031 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,810,407 reads read : 26,810,407 reads written : 26,810,407 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: 00:08:52 26810407 reads; of these: 26810407 (100.00%) were unpaired; of these: 1216972 (4.54%) aligned 0 times 20080031 (74.90%) aligned exactly 1 time 5513404 (20.56%) aligned >1 times 95.46% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 4648669 / 25593435 = 0.1816 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 11:48:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.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 11:48:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.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 11:48:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.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 11:48:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:48:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:48:58: 1000000 INFO @ Mon, 03 Jun 2019 11:48:59: 1000000 INFO @ Mon, 03 Jun 2019 11:49:00: 1000000 INFO @ Mon, 03 Jun 2019 11:49:06: 2000000 INFO @ Mon, 03 Jun 2019 11:49:08: 2000000 INFO @ Mon, 03 Jun 2019 11:49:09: 2000000 INFO @ Mon, 03 Jun 2019 11:49:14: 3000000 INFO @ Mon, 03 Jun 2019 11:49:16: 3000000 INFO @ Mon, 03 Jun 2019 11:49:17: 3000000 INFO @ Mon, 03 Jun 2019 11:49:22: 4000000 INFO @ Mon, 03 Jun 2019 11:49:25: 4000000 INFO @ Mon, 03 Jun 2019 11:49:26: 4000000 INFO @ Mon, 03 Jun 2019 11:49:31: 5000000 INFO @ Mon, 03 Jun 2019 11:49:34: 5000000 INFO @ Mon, 03 Jun 2019 11:49:35: 5000000 INFO @ Mon, 03 Jun 2019 11:49:39: 6000000 INFO @ Mon, 03 Jun 2019 11:49:42: 6000000 INFO @ Mon, 03 Jun 2019 11:49:43: 6000000 INFO @ Mon, 03 Jun 2019 11:49:46: 7000000 INFO @ Mon, 03 Jun 2019 11:49:50: 7000000 INFO @ Mon, 03 Jun 2019 11:49:52: 7000000 INFO @ Mon, 03 Jun 2019 11:49:54: 8000000 INFO @ Mon, 03 Jun 2019 11:49:58: 8000000 INFO @ Mon, 03 Jun 2019 11:50:01: 8000000 INFO @ Mon, 03 Jun 2019 11:50:02: 9000000 INFO @ Mon, 03 Jun 2019 11:50:07: 9000000 INFO @ Mon, 03 Jun 2019 11:50:09: 9000000 INFO @ Mon, 03 Jun 2019 11:50:10: 10000000 INFO @ Mon, 03 Jun 2019 11:50:16: 10000000 INFO @ Mon, 03 Jun 2019 11:50:18: 11000000 INFO @ Mon, 03 Jun 2019 11:50:18: 10000000 INFO @ Mon, 03 Jun 2019 11:50:24: 11000000 INFO @ Mon, 03 Jun 2019 11:50:25: 12000000 INFO @ Mon, 03 Jun 2019 11:50:26: 11000000 INFO @ Mon, 03 Jun 2019 11:50:32: 12000000 INFO @ Mon, 03 Jun 2019 11:50:33: 13000000 INFO @ Mon, 03 Jun 2019 11:50:35: 12000000 INFO @ Mon, 03 Jun 2019 11:50:40: 13000000 INFO @ Mon, 03 Jun 2019 11:50:41: 14000000 INFO @ Mon, 03 Jun 2019 11:50:43: 13000000 INFO @ Mon, 03 Jun 2019 11:50:48: 14000000 INFO @ Mon, 03 Jun 2019 11:50:49: 15000000 INFO @ Mon, 03 Jun 2019 11:50:52: 14000000 INFO @ Mon, 03 Jun 2019 11:50:56: 15000000 INFO @ Mon, 03 Jun 2019 11:50:57: 16000000 INFO @ Mon, 03 Jun 2019 11:51:01: 15000000 INFO @ Mon, 03 Jun 2019 11:51:04: 16000000 INFO @ Mon, 03 Jun 2019 11:51:05: 17000000 INFO @ Mon, 03 Jun 2019 11:51:09: 16000000 INFO @ Mon, 03 Jun 2019 11:51:12: 17000000 INFO @ Mon, 03 Jun 2019 11:51:13: 18000000 INFO @ Mon, 03 Jun 2019 11:51:18: 17000000 INFO @ Mon, 03 Jun 2019 11:51:21: 18000000 INFO @ Mon, 03 Jun 2019 11:51:21: 19000000 INFO @ Mon, 03 Jun 2019 11:51:26: 18000000 INFO @ Mon, 03 Jun 2019 11:51:29: 20000000 INFO @ Mon, 03 Jun 2019 11:51:30: 19000000 INFO @ Mon, 03 Jun 2019 11:51:35: 19000000 INFO @ Mon, 03 Jun 2019 11:51:37: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:51:37: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:51:37: #1 total tags in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:51:37: #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 11:51:37: #1 tags after filtering in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:51:37: #1 finished! INFO @ Mon, 03 Jun 2019 11:51:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:51:38: 20000000 INFO @ Mon, 03 Jun 2019 11:51:39: #2 number of paired peaks: 892 WARNING @ Mon, 03 Jun 2019 11:51:39: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Mon, 03 Jun 2019 11:51:39: start model_add_line... INFO @ Mon, 03 Jun 2019 11:51:39: start X-correlation... INFO @ Mon, 03 Jun 2019 11:51:39: end of X-cor INFO @ Mon, 03 Jun 2019 11:51:39: #2 finished! INFO @ Mon, 03 Jun 2019 11:51:39: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 11:51:39: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 11:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20_model.r INFO @ Mon, 03 Jun 2019 11:51:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:51:43: 20000000 INFO @ Mon, 03 Jun 2019 11:51:45: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:51:45: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:51:45: #1 total tags in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:51:45: #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 11:51:46: #1 tags after filtering in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:51:46: #1 finished! INFO @ Mon, 03 Jun 2019 11:51:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:51:48: #2 number of paired peaks: 892 WARNING @ Mon, 03 Jun 2019 11:51:48: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Mon, 03 Jun 2019 11:51:48: start model_add_line... INFO @ Mon, 03 Jun 2019 11:51:48: start X-correlation... INFO @ Mon, 03 Jun 2019 11:51:48: end of X-cor INFO @ Mon, 03 Jun 2019 11:51:48: #2 finished! INFO @ Mon, 03 Jun 2019 11:51:48: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 11:51:48: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 11:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10_model.r INFO @ Mon, 03 Jun 2019 11:51:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:51:51: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:51:51: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:51:51: #1 total tags in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:51:51: #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 11:51:51: #1 tags after filtering in treatment: 20944766 INFO @ Mon, 03 Jun 2019 11:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:51:51: #1 finished! INFO @ Mon, 03 Jun 2019 11:51:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:51:53: #2 number of paired peaks: 892 WARNING @ Mon, 03 Jun 2019 11:51:53: Fewer paired peaks (892) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 892 pairs to build model! INFO @ Mon, 03 Jun 2019 11:51:53: start model_add_line... INFO @ Mon, 03 Jun 2019 11:51:54: start X-correlation... INFO @ Mon, 03 Jun 2019 11:51:54: end of X-cor INFO @ Mon, 03 Jun 2019 11:51:54: #2 finished! INFO @ Mon, 03 Jun 2019 11:51:54: #2 predicted fragment length is 171 bps INFO @ Mon, 03 Jun 2019 11:51:54: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 03 Jun 2019 11:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05_model.r INFO @ Mon, 03 Jun 2019 11:51:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:52:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:52:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:52:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:53:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.20_summits.bed INFO @ Mon, 03 Jun 2019 11:53:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4639 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.10_summits.bed INFO @ Mon, 03 Jun 2019 11:53:19: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7125 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX306197/SRX306197.05_summits.bed INFO @ Mon, 03 Jun 2019 11:53:27: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9985 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。