Job ID = 2010560 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,861,239 reads read : 11,722,478 reads written : 11,722,478 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: 00:05:25 5861239 reads; of these: 5861239 (100.00%) were paired; of these: 824448 (14.07%) aligned concordantly 0 times 3596713 (61.36%) aligned concordantly exactly 1 time 1440078 (24.57%) aligned concordantly >1 times ---- 824448 pairs aligned concordantly 0 times; of these: 44686 (5.42%) aligned discordantly 1 time ---- 779762 pairs aligned 0 times concordantly or discordantly; of these: 1559524 mates make up the pairs; of these: 1363873 (87.45%) aligned 0 times 97467 (6.25%) aligned exactly 1 time 98184 (6.30%) aligned >1 times 88.37% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 415205 / 5074752 = 0.0818 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 @ Fri, 05 Jul 2019 23:14:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.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 @ Fri, 05 Jul 2019 23:14:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:14:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.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 @ Fri, 05 Jul 2019 23:14:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:14:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.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 @ Fri, 05 Jul 2019 23:14:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:14:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:14:11: 1000000 INFO @ Fri, 05 Jul 2019 23:14:11: 1000000 INFO @ Fri, 05 Jul 2019 23:14:12: 1000000 INFO @ Fri, 05 Jul 2019 23:14:17: 2000000 INFO @ Fri, 05 Jul 2019 23:14:18: 2000000 INFO @ Fri, 05 Jul 2019 23:14:19: 2000000 INFO @ Fri, 05 Jul 2019 23:14:24: 3000000 INFO @ Fri, 05 Jul 2019 23:14:25: 3000000 INFO @ Fri, 05 Jul 2019 23:14:25: 3000000 INFO @ Fri, 05 Jul 2019 23:14:30: 4000000 INFO @ Fri, 05 Jul 2019 23:14:31: 4000000 INFO @ Fri, 05 Jul 2019 23:14:32: 4000000 INFO @ Fri, 05 Jul 2019 23:14:37: 5000000 INFO @ Fri, 05 Jul 2019 23:14:37: 5000000 INFO @ Fri, 05 Jul 2019 23:14:38: 5000000 INFO @ Fri, 05 Jul 2019 23:14:43: 6000000 INFO @ Fri, 05 Jul 2019 23:14:44: 6000000 INFO @ Fri, 05 Jul 2019 23:14:45: 6000000 INFO @ Fri, 05 Jul 2019 23:14:49: 7000000 INFO @ Fri, 05 Jul 2019 23:14:50: 7000000 INFO @ Fri, 05 Jul 2019 23:14:51: 7000000 INFO @ Fri, 05 Jul 2019 23:14:55: 8000000 INFO @ Fri, 05 Jul 2019 23:14:57: 8000000 INFO @ Fri, 05 Jul 2019 23:14:58: 8000000 INFO @ Fri, 05 Jul 2019 23:15:01: 9000000 INFO @ Fri, 05 Jul 2019 23:15:03: 9000000 INFO @ Fri, 05 Jul 2019 23:15:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:15:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:15:04: #1 total tags in treatment: 4622188 INFO @ Fri, 05 Jul 2019 23:15:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:15:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:15:04: #1 tags after filtering in treatment: 2128176 INFO @ Fri, 05 Jul 2019 23:15:04: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 05 Jul 2019 23:15:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:15:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:15:04: 9000000 INFO @ Fri, 05 Jul 2019 23:15:05: #2 number of paired peaks: 1384 INFO @ Fri, 05 Jul 2019 23:15:05: start model_add_line... INFO @ Fri, 05 Jul 2019 23:15:05: start X-correlation... INFO @ Fri, 05 Jul 2019 23:15:05: end of X-cor INFO @ Fri, 05 Jul 2019 23:15:05: #2 finished! INFO @ Fri, 05 Jul 2019 23:15:05: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:15:05: #2 alternative fragment length(s) may be 0,148,193,226 bps INFO @ Fri, 05 Jul 2019 23:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20_model.r INFO @ Fri, 05 Jul 2019 23:15:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:15:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:15:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:15:07: #1 total tags in treatment: 4622188 INFO @ Fri, 05 Jul 2019 23:15:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:15:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:15:07: #1 tags after filtering in treatment: 2128176 INFO @ Fri, 05 Jul 2019 23:15:07: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 05 Jul 2019 23:15:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:15:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:15:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:15:07: #2 number of paired peaks: 1384 INFO @ Fri, 05 Jul 2019 23:15:07: start model_add_line... INFO @ Fri, 05 Jul 2019 23:15:07: start X-correlation... INFO @ Fri, 05 Jul 2019 23:15:07: end of X-cor INFO @ Fri, 05 Jul 2019 23:15:07: #2 finished! INFO @ Fri, 05 Jul 2019 23:15:07: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:15:07: #2 alternative fragment length(s) may be 0,148,193,226 bps INFO @ Fri, 05 Jul 2019 23:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05_model.r INFO @ Fri, 05 Jul 2019 23:15:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:15:08: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:15:08: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:15:08: #1 total tags in treatment: 4622188 INFO @ Fri, 05 Jul 2019 23:15:08: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:15:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:15:08: #1 tags after filtering in treatment: 2128176 INFO @ Fri, 05 Jul 2019 23:15:08: #1 Redundant rate of treatment: 0.54 INFO @ Fri, 05 Jul 2019 23:15:08: #1 finished! INFO @ Fri, 05 Jul 2019 23:15:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:15:08: #2 number of paired peaks: 1384 INFO @ Fri, 05 Jul 2019 23:15:08: start model_add_line... INFO @ Fri, 05 Jul 2019 23:15:09: start X-correlation... INFO @ Fri, 05 Jul 2019 23:15:09: end of X-cor INFO @ Fri, 05 Jul 2019 23:15:09: #2 finished! INFO @ Fri, 05 Jul 2019 23:15:09: #2 predicted fragment length is 193 bps INFO @ Fri, 05 Jul 2019 23:15:09: #2 alternative fragment length(s) may be 0,148,193,226 bps INFO @ Fri, 05 Jul 2019 23:15:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10_model.r INFO @ Fri, 05 Jul 2019 23:15:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:15:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:15:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.20_summits.bed INFO @ Fri, 05 Jul 2019 23:15:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 23:15:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:15:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.05_summits.bed INFO @ Fri, 05 Jul 2019 23:15:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381261/SRX381261.10_summits.bed INFO @ Fri, 05 Jul 2019 23:15:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling