Job ID = 4178268 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,335,185 reads read : 16,335,185 reads written : 16,335,185 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: 00:03:14 16335185 reads; of these: 16335185 (100.00%) were unpaired; of these: 7026650 (43.02%) aligned 0 times 7434566 (45.51%) aligned exactly 1 time 1873969 (11.47%) aligned >1 times 56.98% overall alignment rate Time searching: 00:03:14 Overall time: 00:03:14 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_rmdupse_core] 1356933 / 9308535 = 0.1458 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:30:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.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 12:30:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:36: 1000000 INFO @ Thu, 05 Dec 2019 12:30:46: 2000000 INFO @ Thu, 05 Dec 2019 12:30:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.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 12:30:53: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:53: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:56: 3000000 INFO @ Thu, 05 Dec 2019 12:31:02: 1000000 INFO @ Thu, 05 Dec 2019 12:31:07: 4000000 INFO @ Thu, 05 Dec 2019 12:31:11: 2000000 INFO @ Thu, 05 Dec 2019 12:31:18: 5000000 INFO @ Thu, 05 Dec 2019 12:31:19: 3000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.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 12:31:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:31:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:31:28: 4000000 INFO @ Thu, 05 Dec 2019 12:31:30: 6000000 INFO @ Thu, 05 Dec 2019 12:31:38: 5000000 INFO @ Thu, 05 Dec 2019 12:31:39: 1000000 INFO @ Thu, 05 Dec 2019 12:31:42: 7000000 INFO @ Thu, 05 Dec 2019 12:31:47: 6000000 INFO @ Thu, 05 Dec 2019 12:31:49: 2000000 INFO @ Thu, 05 Dec 2019 12:31:52: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:31:52: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:31:52: #1 total tags in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:31:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:52: #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 12:31:52: #1 tags after filtering in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:52: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:52: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:53: #2 number of paired peaks: 2243 INFO @ Thu, 05 Dec 2019 12:31:53: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:53: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:53: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:53: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:53: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 12:31:53: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 05 Dec 2019 12:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05_model.r INFO @ Thu, 05 Dec 2019 12:31:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:55: 7000000 INFO @ Thu, 05 Dec 2019 12:32:00: 3000000 INFO @ Thu, 05 Dec 2019 12:32:04: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:32:04: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:32:04: #1 total tags in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:32:04: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:04: #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 12:32:04: #1 tags after filtering in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:32:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:32:04: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:04: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:05: #2 number of paired peaks: 2243 INFO @ Thu, 05 Dec 2019 12:32:05: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:05: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:05: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:05: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:05: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 12:32:05: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 05 Dec 2019 12:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10_model.r INFO @ Thu, 05 Dec 2019 12:32:05: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:10: 4000000 INFO @ Thu, 05 Dec 2019 12:32:19: 5000000 INFO @ Thu, 05 Dec 2019 12:32:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:29: 6000000 INFO @ Thu, 05 Dec 2019 12:32:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.05_summits.bed INFO @ Thu, 05 Dec 2019 12:32:32: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (6929 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:39: 7000000 INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.10_summits.bed INFO @ Thu, 05 Dec 2019 12:32:44: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3814 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:48: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:32:48: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:32:48: #1 total tags in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:32:48: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:48: #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 12:32:48: #1 tags after filtering in treatment: 7951602 INFO @ Thu, 05 Dec 2019 12:32:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:32:48: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:48: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:49: #2 number of paired peaks: 2243 INFO @ Thu, 05 Dec 2019 12:32:49: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:49: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:49: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:49: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:49: #2 predicted fragment length is 144 bps INFO @ Thu, 05 Dec 2019 12:32:49: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 05 Dec 2019 12:32:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20_model.r INFO @ Thu, 05 Dec 2019 12:32:49: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:16: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107867/SRX4107867.20_summits.bed INFO @ Thu, 05 Dec 2019 12:33:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1692 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。