Job ID = 2010534 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,168,805 reads read : 14,337,610 reads written : 14,337,610 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: 00:06:43 7168805 reads; of these: 7168805 (100.00%) were paired; of these: 859358 (11.99%) aligned concordantly 0 times 4995243 (69.68%) aligned concordantly exactly 1 time 1314204 (18.33%) aligned concordantly >1 times ---- 859358 pairs aligned concordantly 0 times; of these: 31128 (3.62%) aligned discordantly 1 time ---- 828230 pairs aligned 0 times concordantly or discordantly; of these: 1656460 mates make up the pairs; of these: 1502657 (90.71%) aligned 0 times 93387 (5.64%) aligned exactly 1 time 60416 (3.65%) aligned >1 times 89.52% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 410971 / 6334811 = 0.0649 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 23:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.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 23:11:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:11:12: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.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 23:11:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:11:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.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 23:11:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:11:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:19: 1000000 INFO @ Fri, 05 Jul 2019 23:11:20: 1000000 INFO @ Fri, 05 Jul 2019 23:11:22: 1000000 INFO @ Fri, 05 Jul 2019 23:11:26: 2000000 INFO @ Fri, 05 Jul 2019 23:11:27: 2000000 INFO @ Fri, 05 Jul 2019 23:11:29: 2000000 INFO @ Fri, 05 Jul 2019 23:11:33: 3000000 INFO @ Fri, 05 Jul 2019 23:11:34: 3000000 INFO @ Fri, 05 Jul 2019 23:11:36: 3000000 INFO @ Fri, 05 Jul 2019 23:11:39: 4000000 INFO @ Fri, 05 Jul 2019 23:11:41: 4000000 INFO @ Fri, 05 Jul 2019 23:11:43: 4000000 INFO @ Fri, 05 Jul 2019 23:11:46: 5000000 INFO @ Fri, 05 Jul 2019 23:11:48: 5000000 INFO @ Fri, 05 Jul 2019 23:11:51: 5000000 INFO @ Fri, 05 Jul 2019 23:11:53: 6000000 INFO @ Fri, 05 Jul 2019 23:11:54: 6000000 INFO @ Fri, 05 Jul 2019 23:11:58: 6000000 INFO @ Fri, 05 Jul 2019 23:11:59: 7000000 INFO @ Fri, 05 Jul 2019 23:12:01: 7000000 INFO @ Fri, 05 Jul 2019 23:12:05: 7000000 INFO @ Fri, 05 Jul 2019 23:12:06: 8000000 INFO @ Fri, 05 Jul 2019 23:12:08: 8000000 INFO @ Fri, 05 Jul 2019 23:12:13: 8000000 INFO @ Fri, 05 Jul 2019 23:12:13: 9000000 INFO @ Fri, 05 Jul 2019 23:12:15: 9000000 INFO @ Fri, 05 Jul 2019 23:12:20: 10000000 INFO @ Fri, 05 Jul 2019 23:12:20: 9000000 INFO @ Fri, 05 Jul 2019 23:12:22: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:12:26: 11000000 INFO @ Fri, 05 Jul 2019 23:12:27: 10000000 INFO @ Fri, 05 Jul 2019 23:12:29: 11000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:12:33: 12000000 INFO @ Fri, 05 Jul 2019 23:12:33: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:12:33: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:12:33: #1 total tags in treatment: 5898809 INFO @ Fri, 05 Jul 2019 23:12:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:12:33: #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 23:12:33: #1 tags after filtering in treatment: 2189748 INFO @ Fri, 05 Jul 2019 23:12:33: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 23:12:33: #1 finished! INFO @ Fri, 05 Jul 2019 23:12:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:12:33: #2 number of paired peaks: 1386 INFO @ Fri, 05 Jul 2019 23:12:33: start model_add_line... INFO @ Fri, 05 Jul 2019 23:12:33: start X-correlation... INFO @ Fri, 05 Jul 2019 23:12:34: end of X-cor INFO @ Fri, 05 Jul 2019 23:12:34: #2 finished! INFO @ Fri, 05 Jul 2019 23:12:34: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 23:12:34: #2 alternative fragment length(s) may be 0,134,152,191,245,303 bps INFO @ Fri, 05 Jul 2019 23:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05_model.r INFO @ Fri, 05 Jul 2019 23:12:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:12:34: 11000000 INFO @ Fri, 05 Jul 2019 23:12:35: 12000000 INFO @ Fri, 05 Jul 2019 23:12:36: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:12:36: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:12:36: #1 total tags in treatment: 5898809 INFO @ Fri, 05 Jul 2019 23:12:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:12:36: #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 23:12:36: #1 tags after filtering in treatment: 2189748 INFO @ Fri, 05 Jul 2019 23:12:36: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 23:12:36: #1 finished! INFO @ Fri, 05 Jul 2019 23:12:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:12:36: #2 number of paired peaks: 1386 INFO @ Fri, 05 Jul 2019 23:12:36: start model_add_line... INFO @ Fri, 05 Jul 2019 23:12:36: start X-correlation... INFO @ Fri, 05 Jul 2019 23:12:36: end of X-cor INFO @ Fri, 05 Jul 2019 23:12:36: #2 finished! INFO @ Fri, 05 Jul 2019 23:12:36: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 23:12:36: #2 alternative fragment length(s) may be 0,134,152,191,245,303 bps INFO @ Fri, 05 Jul 2019 23:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10_model.r INFO @ Fri, 05 Jul 2019 23:12:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:12:42: 12000000 INFO @ Fri, 05 Jul 2019 23:12:42: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:12:42: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:12:42: #1 total tags in treatment: 5898809 INFO @ Fri, 05 Jul 2019 23:12:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:12:42: #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 23:12:42: #1 tags after filtering in treatment: 2189748 INFO @ Fri, 05 Jul 2019 23:12:42: #1 Redundant rate of treatment: 0.63 INFO @ Fri, 05 Jul 2019 23:12:42: #1 finished! INFO @ Fri, 05 Jul 2019 23:12:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:12:42: #2 number of paired peaks: 1386 INFO @ Fri, 05 Jul 2019 23:12:42: start model_add_line... INFO @ Fri, 05 Jul 2019 23:12:42: start X-correlation... INFO @ Fri, 05 Jul 2019 23:12:42: end of X-cor INFO @ Fri, 05 Jul 2019 23:12:42: #2 finished! INFO @ Fri, 05 Jul 2019 23:12:42: #2 predicted fragment length is 191 bps INFO @ Fri, 05 Jul 2019 23:12:42: #2 alternative fragment length(s) may be 0,134,152,191,245,303 bps INFO @ Fri, 05 Jul 2019 23:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20_model.r INFO @ Fri, 05 Jul 2019 23:12:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:12:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:12:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.05_summits.bed INFO @ Fri, 05 Jul 2019 23:12:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (699 records, 4 fields): 7 millis INFO @ Fri, 05 Jul 2019 23:12:51: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:12:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:12:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.20_summits.bed INFO @ Fri, 05 Jul 2019 23:13:28: Done! INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:13:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381237/SRX381237.10_summits.bed INFO @ Fri, 05 Jul 2019 23:13:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling