Job ID = 4178391 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,452,600 reads read : 17,452,600 reads written : 17,452,600 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 17452600 reads; of these: 17452600 (100.00%) were unpaired; of these: 2240579 (12.84%) aligned 0 times 13225712 (75.78%) aligned exactly 1 time 1986309 (11.38%) aligned >1 times 87.16% 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] 3632313 / 15212021 = 0.2388 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:32:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.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, 05 Dec 2019 12:32:30: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:30: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:32:41: 1000000 INFO @ Thu, 05 Dec 2019 12:32:54: 2000000 INFO @ Thu, 05 Dec 2019 12:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.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, 05 Dec 2019 12:32:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:32:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:06: 3000000 INFO @ Thu, 05 Dec 2019 12:33:09: 1000000 INFO @ Thu, 05 Dec 2019 12:33:18: 4000000 INFO @ Thu, 05 Dec 2019 12:33:20: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:33:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.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, 05 Dec 2019 12:33:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:30: 5000000 INFO @ Thu, 05 Dec 2019 12:33:31: 3000000 INFO @ Thu, 05 Dec 2019 12:33:39: 1000000 INFO @ Thu, 05 Dec 2019 12:33:42: 6000000 INFO @ Thu, 05 Dec 2019 12:33:43: 4000000 INFO @ Thu, 05 Dec 2019 12:33:49: 2000000 INFO @ Thu, 05 Dec 2019 12:33:54: 7000000 INFO @ Thu, 05 Dec 2019 12:33:54: 5000000 INFO @ Thu, 05 Dec 2019 12:34:00: 3000000 INFO @ Thu, 05 Dec 2019 12:34:05: 6000000 INFO @ Thu, 05 Dec 2019 12:34:05: 8000000 INFO @ Thu, 05 Dec 2019 12:34:10: 4000000 INFO @ Thu, 05 Dec 2019 12:34:16: 7000000 INFO @ Thu, 05 Dec 2019 12:34:17: 9000000 INFO @ Thu, 05 Dec 2019 12:34:21: 5000000 INFO @ Thu, 05 Dec 2019 12:34:26: 8000000 INFO @ Thu, 05 Dec 2019 12:34:30: 10000000 INFO @ Thu, 05 Dec 2019 12:34:31: 6000000 INFO @ Thu, 05 Dec 2019 12:34:37: 9000000 INFO @ Thu, 05 Dec 2019 12:34:42: 7000000 INFO @ Thu, 05 Dec 2019 12:34:42: 11000000 INFO @ Thu, 05 Dec 2019 12:34:47: 10000000 INFO @ Thu, 05 Dec 2019 12:34:49: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:49: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:49: #1 total tags in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:34:49: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:34:50: #1 tags after filtering in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:50: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:51: #2 number of paired peaks: 1161 INFO @ Thu, 05 Dec 2019 12:34:51: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:51: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:51: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:51: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:51: #2 predicted fragment length is 119 bps INFO @ Thu, 05 Dec 2019 12:34:51: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 05 Dec 2019 12:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05_model.r INFO @ Thu, 05 Dec 2019 12:34:51: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:52: 8000000 INFO @ Thu, 05 Dec 2019 12:34:58: 11000000 INFO @ Thu, 05 Dec 2019 12:35:03: 9000000 INFO @ Thu, 05 Dec 2019 12:35:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:04: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:04: #1 total tags in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:35:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:04: #1 tags after filtering in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:04: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:05: #2 number of paired peaks: 1161 INFO @ Thu, 05 Dec 2019 12:35:05: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:05: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:05: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:05: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:05: #2 predicted fragment length is 119 bps INFO @ Thu, 05 Dec 2019 12:35:05: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 05 Dec 2019 12:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10_model.r INFO @ Thu, 05 Dec 2019 12:35:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:13: 10000000 INFO @ Thu, 05 Dec 2019 12:35:22: 11000000 INFO @ Thu, 05 Dec 2019 12:35:27: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:27: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:27: #1 total tags in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:35:27: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:27: #1 tags after filtering in treatment: 11579708 INFO @ Thu, 05 Dec 2019 12:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:27: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:27: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:28: #2 number of paired peaks: 1161 INFO @ Thu, 05 Dec 2019 12:35:28: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:28: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:28: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:28: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:28: #2 predicted fragment length is 119 bps INFO @ Thu, 05 Dec 2019 12:35:28: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 05 Dec 2019 12:35:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20_model.r INFO @ Thu, 05 Dec 2019 12:35:28: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:29: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:35:46: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.05_summits.bed INFO @ Thu, 05 Dec 2019 12:36:00: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5526 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.10_summits.bed INFO @ Thu, 05 Dec 2019 12:36:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4202 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107869/SRX4107869.20_summits.bed INFO @ Thu, 05 Dec 2019 12:36:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2904 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。