Job ID = 2589545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,839,888 reads read : 6,839,888 reads written : 6,839,888 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR702398.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: 00:00:55 6839888 reads; of these: 6839888 (100.00%) were unpaired; of these: 2817634 (41.19%) aligned 0 times 3486125 (50.97%) aligned exactly 1 time 536129 (7.84%) aligned >1 times 58.81% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 481880 / 4022254 = 0.1198 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 17:56:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.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 17:56:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.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 17:56:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.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 17:56:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:56:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:56:49: 1000000 INFO @ Mon, 12 Aug 2019 17:56:49: 1000000 INFO @ Mon, 12 Aug 2019 17:56:50: 1000000 INFO @ Mon, 12 Aug 2019 17:56:57: 2000000 INFO @ Mon, 12 Aug 2019 17:56:57: 2000000 INFO @ Mon, 12 Aug 2019 17:56:57: 2000000 INFO @ Mon, 12 Aug 2019 17:57:04: 3000000 INFO @ Mon, 12 Aug 2019 17:57:05: 3000000 INFO @ Mon, 12 Aug 2019 17:57:05: 3000000 INFO @ Mon, 12 Aug 2019 17:57:07: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:07: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:07: #1 total tags in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:07: #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 17:57:07: #1 tags after filtering in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:07: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:08: #2 number of paired peaks: 1084 INFO @ Mon, 12 Aug 2019 17:57:08: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:08: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:08: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:08: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:08: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:57:08: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10_model.r INFO @ Mon, 12 Aug 2019 17:57:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:08: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:08: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:08: #1 total tags in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:08: #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 17:57:08: #1 tags after filtering in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:08: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:09: #2 number of paired peaks: 1084 INFO @ Mon, 12 Aug 2019 17:57:09: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:09: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:57:09: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20_model.r INFO @ Mon, 12 Aug 2019 17:57:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:57:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:57:09: #1 total tags in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:57:09: #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 17:57:09: #1 tags after filtering in treatment: 3540374 INFO @ Mon, 12 Aug 2019 17:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:57:09: #1 finished! INFO @ Mon, 12 Aug 2019 17:57:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:57:10: #2 number of paired peaks: 1084 INFO @ Mon, 12 Aug 2019 17:57:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:57:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:57:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:57:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:57:10: #2 predicted fragment length is 166 bps INFO @ Mon, 12 Aug 2019 17:57:10: #2 alternative fragment length(s) may be 166 bps INFO @ Mon, 12 Aug 2019 17:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05_model.r INFO @ Mon, 12 Aug 2019 17:57:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:57:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.10_summits.bed INFO @ Mon, 12 Aug 2019 17:57:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1732 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.20_summits.bed INFO @ Mon, 12 Aug 2019 17:57:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (718 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX233695/SRX233695.05_summits.bed INFO @ Mon, 12 Aug 2019 17:57:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3352 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。