Job ID = 2011927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,245,399 reads read : 36,245,399 reads written : 36,245,399 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1284641.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: 00:05:49 36245399 reads; of these: 36245399 (100.00%) were unpaired; of these: 12694561 (35.02%) aligned 0 times 12547691 (34.62%) aligned exactly 1 time 11003147 (30.36%) aligned >1 times 64.98% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 21964644 / 23550838 = 0.9326 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 @ Sat, 06 Jul 2019 03:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 03:33:48: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:33:48: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:33:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 03:33:49: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:33:49: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 06 Jul 2019 03:33:50: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:33:50: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:33:56: 1000000 INFO @ Sat, 06 Jul 2019 03:33:58: 1000000 INFO @ Sat, 06 Jul 2019 03:33:59: 1000000 INFO @ Sat, 06 Jul 2019 03:34:00: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:00: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:00: #1 total tags in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:00: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:00: #1 tags after filtering in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:00: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:00: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:00: #2 number of paired peaks: 1360 INFO @ Sat, 06 Jul 2019 03:34:00: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:01: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:01: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:01: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:01: #2 predicted fragment length is 108 bps INFO @ Sat, 06 Jul 2019 03:34:01: #2 alternative fragment length(s) may be 2,108 bps INFO @ Sat, 06 Jul 2019 03:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10_model.r INFO @ Sat, 06 Jul 2019 03:34:01: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 03:34:04: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:04: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:04: #1 total tags in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:04: #1 tags after filtering in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:04: #1 tag size is determined as 50 bps INFO @ Sat, 06 Jul 2019 03:34:04: #1 tag size = 50 INFO @ Sat, 06 Jul 2019 03:34:04: #1 total tags in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:04: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:34:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:34:04: #1 tags after filtering in treatment: 1586194 INFO @ Sat, 06 Jul 2019 03:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 03:34:04: #1 finished! INFO @ Sat, 06 Jul 2019 03:34:04: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:34:04: #2 number of paired peaks: 1360 INFO @ Sat, 06 Jul 2019 03:34:04: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:04: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:04: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:04: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:04: #2 predicted fragment length is 108 bps INFO @ Sat, 06 Jul 2019 03:34:04: #2 alternative fragment length(s) may be 2,108 bps INFO @ Sat, 06 Jul 2019 03:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05_model.r INFO @ Sat, 06 Jul 2019 03:34:04: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:34:04: #2 number of paired peaks: 1360 INFO @ Sat, 06 Jul 2019 03:34:04: start model_add_line... INFO @ Sat, 06 Jul 2019 03:34:04: start X-correlation... INFO @ Sat, 06 Jul 2019 03:34:04: end of X-cor INFO @ Sat, 06 Jul 2019 03:34:04: #2 finished! INFO @ Sat, 06 Jul 2019 03:34:04: #2 predicted fragment length is 108 bps INFO @ Sat, 06 Jul 2019 03:34:04: #2 alternative fragment length(s) may be 2,108 bps INFO @ Sat, 06 Jul 2019 03:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20_model.r INFO @ Sat, 06 Jul 2019 03:34:04: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:34:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 03:34:08: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:34:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.10_summits.bed INFO @ Sat, 06 Jul 2019 03:34:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (549 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:34:12: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:12: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.20_summits.bed INFO @ Sat, 06 Jul 2019 03:34:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 4 millis INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX541154/SRX541154.05_summits.bed INFO @ Sat, 06 Jul 2019 03:34:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling