Job ID = 4303044 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,216,614 reads read : 24,216,614 reads written : 24,216,614 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198441.sra.cache’: 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: 00:07:45 24216614 reads; of these: 24216614 (100.00%) were unpaired; of these: 5371290 (22.18%) aligned 0 times 13973331 (57.70%) aligned exactly 1 time 4871993 (20.12%) aligned >1 times 77.82% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9022579 / 18845324 = 0.4788 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:49:18: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:18: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:27: 1000000 INFO @ Thu, 12 Dec 2019 00:49:38: 2000000 INFO @ Thu, 12 Dec 2019 00:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:49:48: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:48: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:48: 3000000 INFO @ Thu, 12 Dec 2019 00:49:58: 4000000 INFO @ Thu, 12 Dec 2019 00:49:58: 1000000 INFO @ Thu, 12 Dec 2019 00:50:08: 5000000 INFO @ Thu, 12 Dec 2019 00:50:09: 2000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:50:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 12 Dec 2019 00:50:17: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:17: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:18: 6000000 INFO @ Thu, 12 Dec 2019 00:50:18: 3000000 INFO @ Thu, 12 Dec 2019 00:50:27: 1000000 INFO @ Thu, 12 Dec 2019 00:50:28: 7000000 INFO @ Thu, 12 Dec 2019 00:50:28: 4000000 INFO @ Thu, 12 Dec 2019 00:50:36: 2000000 INFO @ Thu, 12 Dec 2019 00:50:37: 8000000 INFO @ Thu, 12 Dec 2019 00:50:37: 5000000 INFO @ Thu, 12 Dec 2019 00:50:46: 3000000 INFO @ Thu, 12 Dec 2019 00:50:46: 9000000 INFO @ Thu, 12 Dec 2019 00:50:47: 6000000 INFO @ Thu, 12 Dec 2019 00:50:53: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:50:53: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:50:53: #1 total tags in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:50:53: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:50:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:50:54: #1 tags after filtering in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:50:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:50:54: #1 finished! INFO @ Thu, 12 Dec 2019 00:50:54: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:50:54: 4000000 INFO @ Thu, 12 Dec 2019 00:50:55: #2 number of paired peaks: 1049 INFO @ Thu, 12 Dec 2019 00:50:55: start model_add_line... INFO @ Thu, 12 Dec 2019 00:50:55: start X-correlation... INFO @ Thu, 12 Dec 2019 00:50:55: end of X-cor INFO @ Thu, 12 Dec 2019 00:50:55: #2 finished! INFO @ Thu, 12 Dec 2019 00:50:55: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:50:55: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05_model.r INFO @ Thu, 12 Dec 2019 00:50:55: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:50:55: 7000000 INFO @ Thu, 12 Dec 2019 00:51:02: 5000000 INFO @ Thu, 12 Dec 2019 00:51:03: 8000000 INFO @ Thu, 12 Dec 2019 00:51:09: 6000000 INFO @ Thu, 12 Dec 2019 00:51:12: 9000000 INFO @ Thu, 12 Dec 2019 00:51:18: 7000000 INFO @ Thu, 12 Dec 2019 00:51:19: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:51:19: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:51:19: #1 total tags in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:51:19: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:51:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:51:20: #1 tags after filtering in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:51:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:51:20: #1 finished! INFO @ Thu, 12 Dec 2019 00:51:20: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:51:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:51:21: #2 number of paired peaks: 1049 INFO @ Thu, 12 Dec 2019 00:51:21: start model_add_line... INFO @ Thu, 12 Dec 2019 00:51:21: start X-correlation... INFO @ Thu, 12 Dec 2019 00:51:21: end of X-cor INFO @ Thu, 12 Dec 2019 00:51:21: #2 finished! INFO @ Thu, 12 Dec 2019 00:51:21: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:51:21: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10_model.r INFO @ Thu, 12 Dec 2019 00:51:21: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:51:28: 8000000 INFO @ Thu, 12 Dec 2019 00:51:30: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:51:42: 9000000 INFO @ Thu, 12 Dec 2019 00:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.05_summits.bed INFO @ Thu, 12 Dec 2019 00:51:53: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2284 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:51:54: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:51:54: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:51:54: #1 total tags in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:51:54: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:51:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:51:54: #1 tags after filtering in treatment: 9822745 INFO @ Thu, 12 Dec 2019 00:51:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:51:54: #1 finished! INFO @ Thu, 12 Dec 2019 00:51:54: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:51:56: #2 number of paired peaks: 1049 INFO @ Thu, 12 Dec 2019 00:51:56: start model_add_line... INFO @ Thu, 12 Dec 2019 00:51:56: start X-correlation... INFO @ Thu, 12 Dec 2019 00:51:56: end of X-cor INFO @ Thu, 12 Dec 2019 00:51:56: #2 finished! INFO @ Thu, 12 Dec 2019 00:51:56: #2 predicted fragment length is 129 bps INFO @ Thu, 12 Dec 2019 00:51:56: #2 alternative fragment length(s) may be 129 bps INFO @ Thu, 12 Dec 2019 00:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20_model.r INFO @ Thu, 12 Dec 2019 00:51:56: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:52:08: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:52:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.10_summits.bed INFO @ Thu, 12 Dec 2019 00:52:35: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (1610 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:52:47: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494909/SRX494909.20_summits.bed INFO @ Thu, 12 Dec 2019 00:53:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1046 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。