Job ID = 1293471 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 208,558,541 reads read : 208,558,541 reads written : 208,558,541 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: 01:00:18 208558541 reads; of these: 208558541 (100.00%) were unpaired; of these: 127935891 (61.34%) aligned 0 times 53165067 (25.49%) aligned exactly 1 time 27457583 (13.17%) aligned >1 times 38.66% overall alignment rate Time searching: 01:00:18 Overall time: 01:00:18 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 36 files... [bam_rmdupse_core] 66635100 / 80622650 = 0.8265 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 02:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.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 02:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.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 02:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.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 02:48:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:48:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:48:11: 1000000 INFO @ Mon, 03 Jun 2019 02:48:11: 1000000 INFO @ Mon, 03 Jun 2019 02:48:13: 1000000 INFO @ Mon, 03 Jun 2019 02:48:19: 2000000 INFO @ Mon, 03 Jun 2019 02:48:19: 2000000 INFO @ Mon, 03 Jun 2019 02:48:23: 2000000 INFO @ Mon, 03 Jun 2019 02:48:26: 3000000 INFO @ Mon, 03 Jun 2019 02:48:26: 3000000 INFO @ Mon, 03 Jun 2019 02:48:33: 3000000 INFO @ Mon, 03 Jun 2019 02:48:34: 4000000 INFO @ Mon, 03 Jun 2019 02:48:34: 4000000 INFO @ Mon, 03 Jun 2019 02:48:42: 4000000 INFO @ Mon, 03 Jun 2019 02:48:42: 5000000 INFO @ Mon, 03 Jun 2019 02:48:42: 5000000 INFO @ Mon, 03 Jun 2019 02:48:51: 6000000 INFO @ Mon, 03 Jun 2019 02:48:51: 6000000 INFO @ Mon, 03 Jun 2019 02:48:52: 5000000 INFO @ Mon, 03 Jun 2019 02:48:59: 7000000 INFO @ Mon, 03 Jun 2019 02:48:59: 7000000 INFO @ Mon, 03 Jun 2019 02:49:02: 6000000 INFO @ Mon, 03 Jun 2019 02:49:08: 8000000 INFO @ Mon, 03 Jun 2019 02:49:08: 8000000 INFO @ Mon, 03 Jun 2019 02:49:12: 7000000 INFO @ Mon, 03 Jun 2019 02:49:16: 9000000 INFO @ Mon, 03 Jun 2019 02:49:16: 9000000 INFO @ Mon, 03 Jun 2019 02:49:22: 8000000 INFO @ Mon, 03 Jun 2019 02:49:25: 10000000 INFO @ Mon, 03 Jun 2019 02:49:25: 10000000 INFO @ Mon, 03 Jun 2019 02:49:32: 9000000 INFO @ Mon, 03 Jun 2019 02:49:33: 11000000 INFO @ Mon, 03 Jun 2019 02:49:33: 11000000 INFO @ Mon, 03 Jun 2019 02:49:42: 12000000 INFO @ Mon, 03 Jun 2019 02:49:42: 12000000 INFO @ Mon, 03 Jun 2019 02:49:43: 10000000 INFO @ Mon, 03 Jun 2019 02:49:50: 13000000 INFO @ Mon, 03 Jun 2019 02:49:50: 13000000 INFO @ Mon, 03 Jun 2019 02:49:53: 11000000 INFO @ Mon, 03 Jun 2019 02:49:59: #1 tag size is determined as 52 bps INFO @ Mon, 03 Jun 2019 02:49:59: #1 tag size = 52 INFO @ Mon, 03 Jun 2019 02:49:59: #1 total tags in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:49:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:49:59: #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 02:49:59: #1 tag size is determined as 52 bps INFO @ Mon, 03 Jun 2019 02:49:59: #1 tag size = 52 INFO @ Mon, 03 Jun 2019 02:49:59: #1 total tags in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:49:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:49:59: #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 02:49:59: #1 tags after filtering in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:49:59: #1 finished! INFO @ Mon, 03 Jun 2019 02:49:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:49:59: #1 tags after filtering in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:49:59: #1 finished! INFO @ Mon, 03 Jun 2019 02:49:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:50:01: #2 number of paired peaks: 3999 INFO @ Mon, 03 Jun 2019 02:50:01: start model_add_line... INFO @ Mon, 03 Jun 2019 02:50:01: #2 number of paired peaks: 3999 INFO @ Mon, 03 Jun 2019 02:50:01: start model_add_line... INFO @ Mon, 03 Jun 2019 02:50:01: start X-correlation... INFO @ Mon, 03 Jun 2019 02:50:01: start X-correlation... INFO @ Mon, 03 Jun 2019 02:50:01: end of X-cor INFO @ Mon, 03 Jun 2019 02:50:01: #2 finished! INFO @ Mon, 03 Jun 2019 02:50:01: #2 predicted fragment length is 31 bps INFO @ Mon, 03 Jun 2019 02:50:01: #2 alternative fragment length(s) may be 31 bps INFO @ Mon, 03 Jun 2019 02:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10_model.r INFO @ Mon, 03 Jun 2019 02:50:01: end of X-cor INFO @ Mon, 03 Jun 2019 02:50:01: #2 finished! INFO @ Mon, 03 Jun 2019 02:50:01: #2 predicted fragment length is 31 bps INFO @ Mon, 03 Jun 2019 02:50:01: #2 alternative fragment length(s) may be 31 bps INFO @ Mon, 03 Jun 2019 02:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20_model.r WARNING @ Mon, 03 Jun 2019 02:50:01: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:50:01: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Mon, 03 Jun 2019 02:50:01: #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 02:50:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:50:01: #3 Pre-compute pvalue-qvalue table... WARNING @ Mon, 03 Jun 2019 02:50:01: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:50:01: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Mon, 03 Jun 2019 02:50:01: #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 02:50:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:50:02: 12000000 INFO @ Mon, 03 Jun 2019 02:50:13: 13000000 INFO @ Mon, 03 Jun 2019 02:50:24: #1 tag size is determined as 52 bps INFO @ Mon, 03 Jun 2019 02:50:24: #1 tag size = 52 INFO @ Mon, 03 Jun 2019 02:50:24: #1 total tags in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:50:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:50:24: #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 02:50:24: #1 tags after filtering in treatment: 13987550 INFO @ Mon, 03 Jun 2019 02:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:50:24: #1 finished! INFO @ Mon, 03 Jun 2019 02:50:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:50:26: #2 number of paired peaks: 3999 INFO @ Mon, 03 Jun 2019 02:50:26: start model_add_line... INFO @ Mon, 03 Jun 2019 02:50:26: start X-correlation... INFO @ Mon, 03 Jun 2019 02:50:26: end of X-cor INFO @ Mon, 03 Jun 2019 02:50:26: #2 finished! INFO @ Mon, 03 Jun 2019 02:50:26: #2 predicted fragment length is 31 bps INFO @ Mon, 03 Jun 2019 02:50:26: #2 alternative fragment length(s) may be 31 bps INFO @ Mon, 03 Jun 2019 02:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05_model.r WARNING @ Mon, 03 Jun 2019 02:50:26: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:50:26: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Mon, 03 Jun 2019 02:50:26: #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 02:50:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:50:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:50:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.10_summits.bed INFO @ Mon, 03 Jun 2019 02:50:55: Done! INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.20_summits.bed INFO @ Mon, 03 Jun 2019 02:50:55: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8258 records, 4 fields): 14 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2333 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:51:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX321071/ERX321071.05_summits.bed INFO @ Mon, 03 Jun 2019 02:51:21: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11515 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。