Job ID = 1294011 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 47,460,072 reads read : 47,460,072 reads written : 47,460,072 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: 00:09:59 47460072 reads; of these: 47460072 (100.00%) were unpaired; of these: 26689148 (56.23%) aligned 0 times 14682933 (30.94%) aligned exactly 1 time 6087991 (12.83%) aligned >1 times 43.77% overall alignment rate Time searching: 00:09:59 Overall time: 00:09:59 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] 12154977 / 20770924 = 0.5852 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 04:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.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 04:20:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.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 04:20:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.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 04:20:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:20:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:20:43: 1000000 INFO @ Mon, 03 Jun 2019 04:20:43: 1000000 INFO @ Mon, 03 Jun 2019 04:20:44: 1000000 INFO @ Mon, 03 Jun 2019 04:20:53: 2000000 INFO @ Mon, 03 Jun 2019 04:20:54: 2000000 INFO @ Mon, 03 Jun 2019 04:20:56: 2000000 INFO @ Mon, 03 Jun 2019 04:21:02: 3000000 INFO @ Mon, 03 Jun 2019 04:21:03: 3000000 INFO @ Mon, 03 Jun 2019 04:21:07: 3000000 INFO @ Mon, 03 Jun 2019 04:21:12: 4000000 INFO @ Mon, 03 Jun 2019 04:21:13: 4000000 INFO @ Mon, 03 Jun 2019 04:21:18: 4000000 INFO @ Mon, 03 Jun 2019 04:21:21: 5000000 INFO @ Mon, 03 Jun 2019 04:21:22: 5000000 INFO @ Mon, 03 Jun 2019 04:21:29: 5000000 INFO @ Mon, 03 Jun 2019 04:21:30: 6000000 INFO @ Mon, 03 Jun 2019 04:21:32: 6000000 INFO @ Mon, 03 Jun 2019 04:21:40: 7000000 INFO @ Mon, 03 Jun 2019 04:21:40: 6000000 INFO @ Mon, 03 Jun 2019 04:21:41: 7000000 INFO @ Mon, 03 Jun 2019 04:21:49: 8000000 INFO @ Mon, 03 Jun 2019 04:21:50: 8000000 INFO @ Mon, 03 Jun 2019 04:21:51: 7000000 INFO @ Mon, 03 Jun 2019 04:21:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:21:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:21:55: #1 total tags in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:21:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:21:55: #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 04:21:55: #1 tags after filtering in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:21:55: #1 finished! INFO @ Mon, 03 Jun 2019 04:21:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:21:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:21:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:21:56: #1 total tags in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:21:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:21:56: #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 04:21:56: #2 number of paired peaks: 1509 INFO @ Mon, 03 Jun 2019 04:21:56: start model_add_line... INFO @ Mon, 03 Jun 2019 04:21:56: start X-correlation... INFO @ Mon, 03 Jun 2019 04:21:56: #1 tags after filtering in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:21:56: #1 finished! INFO @ Mon, 03 Jun 2019 04:21:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:21:56: end of X-cor INFO @ Mon, 03 Jun 2019 04:21:56: #2 finished! INFO @ Mon, 03 Jun 2019 04:21:56: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 04:21:56: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 04:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10_model.r WARNING @ Mon, 03 Jun 2019 04:21:56: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:21:56: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 04:21:56: #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 04:21:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:21:57: #2 number of paired peaks: 1509 INFO @ Mon, 03 Jun 2019 04:21:57: start model_add_line... INFO @ Mon, 03 Jun 2019 04:21:57: start X-correlation... INFO @ Mon, 03 Jun 2019 04:21:57: end of X-cor INFO @ Mon, 03 Jun 2019 04:21:57: #2 finished! INFO @ Mon, 03 Jun 2019 04:21:57: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 04:21:57: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 04:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05_model.r WARNING @ Mon, 03 Jun 2019 04:21:57: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:21:57: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 04:21:57: #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 04:21:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:22:02: 8000000 INFO @ Mon, 03 Jun 2019 04:22:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:22:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:22:08: #1 total tags in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:22:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:22:08: #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 04:22:08: #1 tags after filtering in treatment: 8615947 INFO @ Mon, 03 Jun 2019 04:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:22:08: #1 finished! INFO @ Mon, 03 Jun 2019 04:22:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:22:09: #2 number of paired peaks: 1509 INFO @ Mon, 03 Jun 2019 04:22:09: start model_add_line... INFO @ Mon, 03 Jun 2019 04:22:09: start X-correlation... INFO @ Mon, 03 Jun 2019 04:22:09: end of X-cor INFO @ Mon, 03 Jun 2019 04:22:09: #2 finished! INFO @ Mon, 03 Jun 2019 04:22:09: #2 predicted fragment length is 61 bps INFO @ Mon, 03 Jun 2019 04:22:09: #2 alternative fragment length(s) may be 61 bps INFO @ Mon, 03 Jun 2019 04:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20_model.r WARNING @ Mon, 03 Jun 2019 04:22:09: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:22:09: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Mon, 03 Jun 2019 04:22:09: #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 04:22:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:22:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:22:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.10_summits.bed INFO @ Mon, 03 Jun 2019 04:22:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2851 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:22:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.05_summits.bed INFO @ Mon, 03 Jun 2019 04:22:35: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5861 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX170983/SRX170983.20_summits.bed INFO @ Mon, 03 Jun 2019 04:22:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1349 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。