Job ID = 4178222 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,109,239 reads read : 14,109,239 reads written : 14,109,239 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: 00:02:26 14109239 reads; of these: 14109239 (100.00%) were unpaired; of these: 2180303 (15.45%) aligned 0 times 10644783 (75.45%) aligned exactly 1 time 1284153 (9.10%) aligned >1 times 84.55% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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] 2733707 / 11928936 = 0.2292 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.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 12:29:29: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:29: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:37: 1000000 INFO @ Thu, 05 Dec 2019 12:29:46: 2000000 INFO @ Thu, 05 Dec 2019 12:29:54: 3000000 INFO @ Thu, 05 Dec 2019 12:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.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 12:29:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:03: 4000000 INFO @ Thu, 05 Dec 2019 12:30:07: 1000000 INFO @ Thu, 05 Dec 2019 12:30:12: 5000000 INFO @ Thu, 05 Dec 2019 12:30:17: 2000000 INFO @ Thu, 05 Dec 2019 12:30:21: 6000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:30:26: 3000000 INFO @ Thu, 05 Dec 2019 12:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.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 12:30:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:30: 7000000 INFO @ Thu, 05 Dec 2019 12:30:35: 4000000 INFO @ Thu, 05 Dec 2019 12:30:35: 1000000 INFO @ Thu, 05 Dec 2019 12:30:39: 8000000 INFO @ Thu, 05 Dec 2019 12:30:42: 2000000 INFO @ Thu, 05 Dec 2019 12:30:44: 5000000 INFO @ Thu, 05 Dec 2019 12:30:48: 9000000 INFO @ Thu, 05 Dec 2019 12:30:49: 3000000 INFO @ Thu, 05 Dec 2019 12:30:50: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:30:50: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:30:50: #1 total tags in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:30:50: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:50: #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 12:30:50: #1 tags after filtering in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:30:50: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:50: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:50: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:52: #2 number of paired peaks: 6173 INFO @ Thu, 05 Dec 2019 12:30:52: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:52: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:52: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:52: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:52: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Dec 2019 12:30:52: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 05 Dec 2019 12:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05_model.r INFO @ Thu, 05 Dec 2019 12:30:52: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:53: 6000000 INFO @ Thu, 05 Dec 2019 12:30:56: 4000000 INFO @ Thu, 05 Dec 2019 12:31:01: 7000000 INFO @ Thu, 05 Dec 2019 12:31:03: 5000000 INFO @ Thu, 05 Dec 2019 12:31:09: 8000000 INFO @ Thu, 05 Dec 2019 12:31:10: 6000000 INFO @ Thu, 05 Dec 2019 12:31:17: 7000000 INFO @ Thu, 05 Dec 2019 12:31:18: 9000000 INFO @ Thu, 05 Dec 2019 12:31:19: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:31:19: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:31:19: #1 total tags in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:31:19: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:19: #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 12:31:20: #1 tags after filtering in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:20: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:20: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:21: #2 number of paired peaks: 6173 INFO @ Thu, 05 Dec 2019 12:31:21: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:21: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:21: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:21: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:21: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Dec 2019 12:31:21: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 05 Dec 2019 12:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10_model.r INFO @ Thu, 05 Dec 2019 12:31:22: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:25: 8000000 INFO @ Thu, 05 Dec 2019 12:31:25: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:31: 9000000 INFO @ Thu, 05 Dec 2019 12:31:33: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:31:33: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:31:33: #1 total tags in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:31:33: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:33: #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 12:31:33: #1 tags after filtering in treatment: 9195229 INFO @ Thu, 05 Dec 2019 12:31:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:33: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:33: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:34: #2 number of paired peaks: 6173 INFO @ Thu, 05 Dec 2019 12:31:34: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:34: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:34: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:34: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:34: #2 predicted fragment length is 141 bps INFO @ Thu, 05 Dec 2019 12:31:34: #2 alternative fragment length(s) may be 141 bps INFO @ Thu, 05 Dec 2019 12:31:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20_model.r INFO @ Thu, 05 Dec 2019 12:31:34: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.05_summits.bed INFO @ Thu, 05 Dec 2019 12:31:41: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (6884 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:31:55: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:04: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.10_summits.bed INFO @ Thu, 05 Dec 2019 12:32:09: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (5562 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107862/SRX4107862.20_summits.bed INFO @ Thu, 05 Dec 2019 12:32:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4527 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。