Job ID = 1293681 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,395,688 reads read : 18,791,376 reads written : 9,395,688 reads 0-length : 9,395,688 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: 00:07:22 9395688 reads; of these: 9395688 (100.00%) were unpaired; of these: 415961 (4.43%) aligned 0 times 8291781 (88.25%) aligned exactly 1 time 687946 (7.32%) aligned >1 times 95.57% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 3094585 / 8979727 = 0.3446 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 01:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.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 01:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.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 01:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.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 01:57:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:57:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:57:36: 1000000 INFO @ Mon, 03 Jun 2019 01:57:37: 1000000 INFO @ Mon, 03 Jun 2019 01:57:40: 1000000 INFO @ Mon, 03 Jun 2019 01:57:46: 2000000 INFO @ Mon, 03 Jun 2019 01:57:49: 2000000 INFO @ Mon, 03 Jun 2019 01:57:55: 2000000 INFO @ Mon, 03 Jun 2019 01:57:57: 3000000 INFO @ Mon, 03 Jun 2019 01:58:01: 3000000 INFO @ Mon, 03 Jun 2019 01:58:08: 4000000 INFO @ Mon, 03 Jun 2019 01:58:09: 3000000 INFO @ Mon, 03 Jun 2019 01:58:12: 4000000 INFO @ Mon, 03 Jun 2019 01:58:18: 5000000 INFO @ Mon, 03 Jun 2019 01:58:24: 4000000 INFO @ Mon, 03 Jun 2019 01:58:24: 5000000 INFO @ Mon, 03 Jun 2019 01:58:28: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 01:58:28: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 01:58:28: #1 total tags in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:58:28: #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 01:58:28: #1 tags after filtering in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:58:28: #1 finished! INFO @ Mon, 03 Jun 2019 01:58:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:58:29: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 01:58:29: start model_add_line... INFO @ Mon, 03 Jun 2019 01:58:29: start X-correlation... INFO @ Mon, 03 Jun 2019 01:58:29: end of X-cor INFO @ Mon, 03 Jun 2019 01:58:29: #2 finished! INFO @ Mon, 03 Jun 2019 01:58:29: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 01:58:29: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 01:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05_model.r WARNING @ Mon, 03 Jun 2019 01:58:29: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:58:29: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Mon, 03 Jun 2019 01:58:29: #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 01:58:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:58:35: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 01:58:35: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 01:58:35: #1 total tags in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:58:35: #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 01:58:35: #1 tags after filtering in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:58:35: #1 finished! INFO @ Mon, 03 Jun 2019 01:58:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:58:36: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 01:58:36: start model_add_line... INFO @ Mon, 03 Jun 2019 01:58:36: start X-correlation... INFO @ Mon, 03 Jun 2019 01:58:36: end of X-cor INFO @ Mon, 03 Jun 2019 01:58:36: #2 finished! INFO @ Mon, 03 Jun 2019 01:58:36: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 01:58:36: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 01:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20_model.r WARNING @ Mon, 03 Jun 2019 01:58:36: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:58:36: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Mon, 03 Jun 2019 01:58:36: #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 01:58:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:58:38: 5000000 INFO @ Mon, 03 Jun 2019 01:58:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:58:50: #1 tag size is determined as 145 bps INFO @ Mon, 03 Jun 2019 01:58:50: #1 tag size = 145 INFO @ Mon, 03 Jun 2019 01:58:50: #1 total tags in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:58:50: #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 01:58:50: #1 tags after filtering in treatment: 5885142 INFO @ Mon, 03 Jun 2019 01:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:58:50: #1 finished! INFO @ Mon, 03 Jun 2019 01:58:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:58:51: #2 number of paired peaks: 3223 INFO @ Mon, 03 Jun 2019 01:58:51: start model_add_line... INFO @ Mon, 03 Jun 2019 01:58:51: start X-correlation... INFO @ Mon, 03 Jun 2019 01:58:51: end of X-cor INFO @ Mon, 03 Jun 2019 01:58:51: #2 finished! INFO @ Mon, 03 Jun 2019 01:58:51: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 01:58:51: #2 alternative fragment length(s) may be 168 bps INFO @ Mon, 03 Jun 2019 01:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10_model.r WARNING @ Mon, 03 Jun 2019 01:58:51: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 01:58:51: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Mon, 03 Jun 2019 01:58:51: #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 01:58:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:58:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.05_summits.bed INFO @ Mon, 03 Jun 2019 01:59:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10039 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.20_summits.bed INFO @ Mon, 03 Jun 2019 01:59:06: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2477 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:59:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091592/SRX1091592.10_summits.bed INFO @ Mon, 03 Jun 2019 01:59:22: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5272 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。