Job ID = 1293924 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,972,800 reads read : 13,972,800 reads written : 13,972,800 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:37 13972800 reads; of these: 13972800 (100.00%) were unpaired; of these: 4201478 (30.07%) aligned 0 times 6250549 (44.73%) aligned exactly 1 time 3520773 (25.20%) aligned >1 times 69.93% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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_rmdupse_core] 1561625 / 9771322 = 0.1598 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 03:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.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 03:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.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 03:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.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 03:20:56: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:20:56: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:21:04: 1000000 INFO @ Mon, 03 Jun 2019 03:21:05: 1000000 INFO @ Mon, 03 Jun 2019 03:21:05: 1000000 INFO @ Mon, 03 Jun 2019 03:21:12: 2000000 INFO @ Mon, 03 Jun 2019 03:21:13: 2000000 INFO @ Mon, 03 Jun 2019 03:21:14: 2000000 INFO @ Mon, 03 Jun 2019 03:21:20: 3000000 INFO @ Mon, 03 Jun 2019 03:21:22: 3000000 INFO @ Mon, 03 Jun 2019 03:21:22: 3000000 INFO @ Mon, 03 Jun 2019 03:21:28: 4000000 INFO @ Mon, 03 Jun 2019 03:21:30: 4000000 INFO @ Mon, 03 Jun 2019 03:21:30: 4000000 INFO @ Mon, 03 Jun 2019 03:21:36: 5000000 INFO @ Mon, 03 Jun 2019 03:21:39: 5000000 INFO @ Mon, 03 Jun 2019 03:21:39: 5000000 INFO @ Mon, 03 Jun 2019 03:21:45: 6000000 INFO @ Mon, 03 Jun 2019 03:21:47: 6000000 INFO @ Mon, 03 Jun 2019 03:21:48: 6000000 INFO @ Mon, 03 Jun 2019 03:21:53: 7000000 INFO @ Mon, 03 Jun 2019 03:21:56: 7000000 INFO @ Mon, 03 Jun 2019 03:21:57: 7000000 INFO @ Mon, 03 Jun 2019 03:22:01: 8000000 INFO @ Mon, 03 Jun 2019 03:22:03: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:22:03: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:22:03: #1 total tags in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:03: #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 03:22:03: #1 tags after filtering in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:03: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:04: #2 number of paired peaks: 1056 INFO @ Mon, 03 Jun 2019 03:22:04: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:04: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:04: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:04: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:04: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 03:22:04: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 03:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05_model.r WARNING @ Mon, 03 Jun 2019 03:22:04: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:22:04: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 03:22:04: #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 03:22:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:04: 8000000 INFO @ Mon, 03 Jun 2019 03:22:06: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:22:06: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:22:06: #1 total tags in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:06: #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 03:22:06: #1 tags after filtering in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:06: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:06: 8000000 INFO @ Mon, 03 Jun 2019 03:22:07: #2 number of paired peaks: 1056 INFO @ Mon, 03 Jun 2019 03:22:07: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:07: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:07: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:07: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:07: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 03:22:07: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 03:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10_model.r WARNING @ Mon, 03 Jun 2019 03:22:07: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:22:07: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 03:22:07: #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 03:22:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:08: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 03:22:08: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 03:22:08: #1 total tags in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:08: #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 03:22:08: #1 tags after filtering in treatment: 8209697 INFO @ Mon, 03 Jun 2019 03:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:08: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:09: #2 number of paired peaks: 1056 INFO @ Mon, 03 Jun 2019 03:22:09: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:09: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:09: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:09: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:09: #2 predicted fragment length is 48 bps INFO @ Mon, 03 Jun 2019 03:22:09: #2 alternative fragment length(s) may be 48 bps INFO @ Mon, 03 Jun 2019 03:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20_model.r WARNING @ Mon, 03 Jun 2019 03:22:09: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:22:09: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Mon, 03 Jun 2019 03:22:09: #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 03:22:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:22:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:22:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.05_summits.bed INFO @ Mon, 03 Jun 2019 03:22:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3843 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:22:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:22:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.10_summits.bed INFO @ Mon, 03 Jun 2019 03:22:42: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1642 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:22:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:22:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX149192/SRX149192.20_summits.bed INFO @ Mon, 03 Jun 2019 03:22:45: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。