Job ID = 2589990 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,369,021 reads read : 22,369,021 reads written : 22,369,021 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:49 22369021 reads; of these: 22369021 (100.00%) were unpaired; of these: 4354316 (19.47%) aligned 0 times 14558539 (65.08%) aligned exactly 1 time 3456166 (15.45%) aligned >1 times 80.53% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 8070949 / 18014705 = 0.4480 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, 12 Aug 2019 19:08:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.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 @ Mon, 12 Aug 2019 19:08:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.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 @ Mon, 12 Aug 2019 19:08:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.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 @ Mon, 12 Aug 2019 19:08:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:08:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:08:55: 1000000 INFO @ Mon, 12 Aug 2019 19:08:56: 1000000 INFO @ Mon, 12 Aug 2019 19:08:56: 1000000 INFO @ Mon, 12 Aug 2019 19:09:03: 2000000 INFO @ Mon, 12 Aug 2019 19:09:04: 2000000 INFO @ Mon, 12 Aug 2019 19:09:05: 2000000 INFO @ Mon, 12 Aug 2019 19:09:11: 3000000 INFO @ Mon, 12 Aug 2019 19:09:12: 3000000 INFO @ Mon, 12 Aug 2019 19:09:15: 3000000 INFO @ Mon, 12 Aug 2019 19:09:20: 4000000 INFO @ Mon, 12 Aug 2019 19:09:21: 4000000 INFO @ Mon, 12 Aug 2019 19:09:24: 4000000 INFO @ Mon, 12 Aug 2019 19:09:27: 5000000 INFO @ Mon, 12 Aug 2019 19:09:29: 5000000 INFO @ Mon, 12 Aug 2019 19:09:33: 5000000 INFO @ Mon, 12 Aug 2019 19:09:35: 6000000 INFO @ Mon, 12 Aug 2019 19:09:36: 6000000 INFO @ Mon, 12 Aug 2019 19:09:42: 6000000 INFO @ Mon, 12 Aug 2019 19:09:43: 7000000 INFO @ Mon, 12 Aug 2019 19:09:44: 7000000 INFO @ Mon, 12 Aug 2019 19:09:50: 8000000 INFO @ Mon, 12 Aug 2019 19:09:51: 7000000 INFO @ Mon, 12 Aug 2019 19:09:52: 8000000 INFO @ Mon, 12 Aug 2019 19:09:58: 9000000 INFO @ Mon, 12 Aug 2019 19:09:59: 9000000 INFO @ Mon, 12 Aug 2019 19:09:59: 8000000 INFO @ Mon, 12 Aug 2019 19:10:05: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:10:05: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:10:05: #1 total tags in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:10:06: #1 tags after filtering in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:06: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:07: #2 number of paired peaks: 1155 INFO @ Mon, 12 Aug 2019 19:10:07: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:07: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:10:07: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:10:07: #1 total tags in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:10:07: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:07: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:07: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:07: #2 predicted fragment length is 184 bps INFO @ Mon, 12 Aug 2019 19:10:07: #2 alternative fragment length(s) may be 3,184 bps INFO @ Mon, 12 Aug 2019 19:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10_model.r INFO @ Mon, 12 Aug 2019 19:10:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:07: #1 tags after filtering in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:07: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:08: #2 number of paired peaks: 1155 INFO @ Mon, 12 Aug 2019 19:10:08: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:08: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:08: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:08: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:08: #2 predicted fragment length is 184 bps INFO @ Mon, 12 Aug 2019 19:10:08: #2 alternative fragment length(s) may be 3,184 bps INFO @ Mon, 12 Aug 2019 19:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20_model.r INFO @ Mon, 12 Aug 2019 19:10:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:08: 9000000 INFO @ Mon, 12 Aug 2019 19:10:16: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 19:10:16: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 19:10:16: #1 total tags in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:10:16: #1 tags after filtering in treatment: 9943756 INFO @ Mon, 12 Aug 2019 19:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:17: #2 number of paired peaks: 1155 INFO @ Mon, 12 Aug 2019 19:10:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:17: #2 predicted fragment length is 184 bps INFO @ Mon, 12 Aug 2019 19:10:17: #2 alternative fragment length(s) may be 3,184 bps INFO @ Mon, 12 Aug 2019 19:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05_model.r INFO @ Mon, 12 Aug 2019 19:10:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.10_summits.bed INFO @ Mon, 12 Aug 2019 19:10:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:10:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:10:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:10:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.20_summits.bed INFO @ Mon, 12 Aug 2019 19:10:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466576/SRX466576.05_summits.bed INFO @ Mon, 12 Aug 2019 19:11:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1101 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。