Job ID = 2010567 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,174,715 reads read : 14,349,430 reads written : 14,349,430 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: 00:06:34 7174715 reads; of these: 7174715 (100.00%) were paired; of these: 687644 (9.58%) aligned concordantly 0 times 5209702 (72.61%) aligned concordantly exactly 1 time 1277369 (17.80%) aligned concordantly >1 times ---- 687644 pairs aligned concordantly 0 times; of these: 35847 (5.21%) aligned discordantly 1 time ---- 651797 pairs aligned 0 times concordantly or discordantly; of these: 1303594 mates make up the pairs; of these: 1143924 (87.75%) aligned 0 times 99877 (7.66%) aligned exactly 1 time 59793 (4.59%) aligned >1 times 92.03% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 441195 / 6517216 = 0.0677 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 23:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.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 23:25:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.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 23:25:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:22: 1000000 INFO @ Fri, 05 Jul 2019 23:25:25: 1000000 INFO @ Fri, 05 Jul 2019 23:25:33: 2000000 INFO @ Fri, 05 Jul 2019 23:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.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 23:25:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:25:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:25:36: 2000000 INFO @ Fri, 05 Jul 2019 23:25:45: 3000000 INFO @ Fri, 05 Jul 2019 23:25:47: 1000000 INFO @ Fri, 05 Jul 2019 23:25:47: 3000000 INFO @ Fri, 05 Jul 2019 23:25:56: 4000000 INFO @ Fri, 05 Jul 2019 23:25:58: 4000000 INFO @ Fri, 05 Jul 2019 23:25:58: 2000000 INFO @ Fri, 05 Jul 2019 23:26:07: 5000000 INFO @ Fri, 05 Jul 2019 23:26:09: 5000000 INFO @ Fri, 05 Jul 2019 23:26:10: 3000000 INFO @ Fri, 05 Jul 2019 23:26:18: 6000000 INFO @ Fri, 05 Jul 2019 23:26:20: 6000000 INFO @ Fri, 05 Jul 2019 23:26:21: 4000000 INFO @ Fri, 05 Jul 2019 23:26:29: 7000000 INFO @ Fri, 05 Jul 2019 23:26:31: 7000000 INFO @ Fri, 05 Jul 2019 23:26:32: 5000000 INFO @ Fri, 05 Jul 2019 23:26:40: 8000000 INFO @ Fri, 05 Jul 2019 23:26:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:26:44: 6000000 INFO @ Fri, 05 Jul 2019 23:26:51: 9000000 INFO @ Fri, 05 Jul 2019 23:26:53: 9000000 INFO @ Fri, 05 Jul 2019 23:26:55: 7000000 INFO @ Fri, 05 Jul 2019 23:27:02: 10000000 INFO @ Fri, 05 Jul 2019 23:27:04: 10000000 INFO @ Fri, 05 Jul 2019 23:27:06: 8000000 INFO @ Fri, 05 Jul 2019 23:27:13: 11000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:27:15: 11000000 INFO @ Fri, 05 Jul 2019 23:27:18: 9000000 INFO @ Fri, 05 Jul 2019 23:27:24: 12000000 INFO @ Fri, 05 Jul 2019 23:27:26: 12000000 INFO @ Fri, 05 Jul 2019 23:27:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:27:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:27:27: #1 total tags in treatment: 6046346 INFO @ Fri, 05 Jul 2019 23:27:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:27:27: #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 23:27:27: #1 tags after filtering in treatment: 2171275 INFO @ Fri, 05 Jul 2019 23:27:27: #1 Redundant rate of treatment: 0.64 INFO @ Fri, 05 Jul 2019 23:27:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:27:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:27:28: #2 number of paired peaks: 1353 INFO @ Fri, 05 Jul 2019 23:27:28: start model_add_line... INFO @ Fri, 05 Jul 2019 23:27:28: start X-correlation... INFO @ Fri, 05 Jul 2019 23:27:28: end of X-cor INFO @ Fri, 05 Jul 2019 23:27:28: #2 finished! INFO @ Fri, 05 Jul 2019 23:27:28: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 23:27:28: #2 alternative fragment length(s) may be 0,68,111,150,208,300,463 bps INFO @ Fri, 05 Jul 2019 23:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05_model.r INFO @ Fri, 05 Jul 2019 23:27:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:27:29: 10000000 INFO @ Fri, 05 Jul 2019 23:27:29: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:27:29: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:27:29: #1 total tags in treatment: 6046346 INFO @ Fri, 05 Jul 2019 23:27:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:27:29: #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 23:27:29: #1 tags after filtering in treatment: 2171275 INFO @ Fri, 05 Jul 2019 23:27:29: #1 Redundant rate of treatment: 0.64 INFO @ Fri, 05 Jul 2019 23:27:29: #1 finished! INFO @ Fri, 05 Jul 2019 23:27:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:27:30: #2 number of paired peaks: 1353 INFO @ Fri, 05 Jul 2019 23:27:30: start model_add_line... INFO @ Fri, 05 Jul 2019 23:27:30: start X-correlation... INFO @ Fri, 05 Jul 2019 23:27:30: end of X-cor INFO @ Fri, 05 Jul 2019 23:27:30: #2 finished! INFO @ Fri, 05 Jul 2019 23:27:30: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 23:27:30: #2 alternative fragment length(s) may be 0,68,111,150,208,300,463 bps INFO @ Fri, 05 Jul 2019 23:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10_model.r INFO @ Fri, 05 Jul 2019 23:27:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:27:40: 11000000 INFO @ Fri, 05 Jul 2019 23:27:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.05_summits.bed INFO @ Fri, 05 Jul 2019 23:27:46: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:27:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.10_summits.bed INFO @ Fri, 05 Jul 2019 23:27:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (495 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:27:51: 12000000 INFO @ Fri, 05 Jul 2019 23:27:54: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:27:54: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:27:54: #1 total tags in treatment: 6046346 INFO @ Fri, 05 Jul 2019 23:27:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:27:54: #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 23:27:54: #1 tags after filtering in treatment: 2171275 INFO @ Fri, 05 Jul 2019 23:27:54: #1 Redundant rate of treatment: 0.64 INFO @ Fri, 05 Jul 2019 23:27:54: #1 finished! INFO @ Fri, 05 Jul 2019 23:27:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:27:55: #2 number of paired peaks: 1353 INFO @ Fri, 05 Jul 2019 23:27:55: start model_add_line... INFO @ Fri, 05 Jul 2019 23:27:55: start X-correlation... INFO @ Fri, 05 Jul 2019 23:27:55: end of X-cor INFO @ Fri, 05 Jul 2019 23:27:55: #2 finished! INFO @ Fri, 05 Jul 2019 23:27:55: #2 predicted fragment length is 208 bps INFO @ Fri, 05 Jul 2019 23:27:55: #2 alternative fragment length(s) may be 0,68,111,150,208,300,463 bps INFO @ Fri, 05 Jul 2019 23:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20_model.r INFO @ Fri, 05 Jul 2019 23:27:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:28:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381268/SRX381268.20_summits.bed INFO @ Fri, 05 Jul 2019 23:28:27: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (242 records, 4 fields): 3 millis CompletedMACS2peakCalling