Job ID = 2009912 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,654,023 reads read : 13,308,046 reads written : 13,308,046 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: 00:05:41 6654023 reads; of these: 6654023 (100.00%) were paired; of these: 852868 (12.82%) aligned concordantly 0 times 4191947 (63.00%) aligned concordantly exactly 1 time 1609208 (24.18%) aligned concordantly >1 times ---- 852868 pairs aligned concordantly 0 times; of these: 22917 (2.69%) aligned discordantly 1 time ---- 829951 pairs aligned 0 times concordantly or discordantly; of these: 1659902 mates make up the pairs; of these: 1335327 (80.45%) aligned 0 times 216856 (13.06%) aligned exactly 1 time 107719 (6.49%) aligned >1 times 89.97% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 1015297 / 5819108 = 0.1745 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 20:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.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 20:53:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.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 20:53:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.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 20:53:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:53:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:53:17: 1000000 INFO @ Fri, 05 Jul 2019 20:53:17: 1000000 INFO @ Fri, 05 Jul 2019 20:53:19: 1000000 INFO @ Fri, 05 Jul 2019 20:53:27: 2000000 INFO @ Fri, 05 Jul 2019 20:53:28: 2000000 INFO @ Fri, 05 Jul 2019 20:53:29: 2000000 INFO @ Fri, 05 Jul 2019 20:53:37: 3000000 INFO @ Fri, 05 Jul 2019 20:53:39: 3000000 INFO @ Fri, 05 Jul 2019 20:53:40: 3000000 INFO @ Fri, 05 Jul 2019 20:53:48: 4000000 INFO @ Fri, 05 Jul 2019 20:53:50: 4000000 INFO @ Fri, 05 Jul 2019 20:53:51: 4000000 INFO @ Fri, 05 Jul 2019 20:53:58: 5000000 INFO @ Fri, 05 Jul 2019 20:54:01: 5000000 INFO @ Fri, 05 Jul 2019 20:54:03: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 20:54:09: 6000000 INFO @ Fri, 05 Jul 2019 20:54:10: 6000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:54:14: 6000000 INFO @ Fri, 05 Jul 2019 20:54:20: 7000000 INFO @ Fri, 05 Jul 2019 20:54:20: 7000000 INFO @ Fri, 05 Jul 2019 20:54:25: 7000000 INFO @ Fri, 05 Jul 2019 20:54:29: 8000000 INFO @ Fri, 05 Jul 2019 20:54:31: 8000000 INFO @ Fri, 05 Jul 2019 20:54:35: 8000000 INFO @ Fri, 05 Jul 2019 20:54:40: 9000000 INFO @ Fri, 05 Jul 2019 20:54:42: 9000000 INFO @ Fri, 05 Jul 2019 20:54:45: 9000000 INFO @ Fri, 05 Jul 2019 20:54:50: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:54:50: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:54:50: #1 total tags in treatment: 4786879 INFO @ Fri, 05 Jul 2019 20:54:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:54:50: #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 20:54:50: #1 tags after filtering in treatment: 1683402 INFO @ Fri, 05 Jul 2019 20:54:50: #1 Redundant rate of treatment: 0.65 INFO @ Fri, 05 Jul 2019 20:54:50: #1 finished! INFO @ Fri, 05 Jul 2019 20:54:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:54:51: #2 number of paired peaks: 1145 INFO @ Fri, 05 Jul 2019 20:54:51: start model_add_line... INFO @ Fri, 05 Jul 2019 20:54:51: start X-correlation... INFO @ Fri, 05 Jul 2019 20:54:51: end of X-cor INFO @ Fri, 05 Jul 2019 20:54:51: #2 finished! INFO @ Fri, 05 Jul 2019 20:54:51: #2 predicted fragment length is 328 bps INFO @ Fri, 05 Jul 2019 20:54:51: #2 alternative fragment length(s) may be 4,305,328 bps INFO @ Fri, 05 Jul 2019 20:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10_model.r INFO @ Fri, 05 Jul 2019 20:54:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:54:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:54:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:54:52: #1 total tags in treatment: 4786879 INFO @ Fri, 05 Jul 2019 20:54:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:54:52: #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 20:54:52: #1 tags after filtering in treatment: 1683402 INFO @ Fri, 05 Jul 2019 20:54:52: #1 Redundant rate of treatment: 0.65 INFO @ Fri, 05 Jul 2019 20:54:52: #1 finished! INFO @ Fri, 05 Jul 2019 20:54:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:54:53: #2 number of paired peaks: 1145 INFO @ Fri, 05 Jul 2019 20:54:53: start model_add_line... INFO @ Fri, 05 Jul 2019 20:54:53: start X-correlation... INFO @ Fri, 05 Jul 2019 20:54:53: end of X-cor INFO @ Fri, 05 Jul 2019 20:54:53: #2 finished! INFO @ Fri, 05 Jul 2019 20:54:53: #2 predicted fragment length is 328 bps INFO @ Fri, 05 Jul 2019 20:54:53: #2 alternative fragment length(s) may be 4,305,328 bps INFO @ Fri, 05 Jul 2019 20:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05_model.r INFO @ Fri, 05 Jul 2019 20:54:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:54:55: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:54:55: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:54:55: #1 total tags in treatment: 4786879 INFO @ Fri, 05 Jul 2019 20:54:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:54:55: #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 20:54:55: #1 tags after filtering in treatment: 1683402 INFO @ Fri, 05 Jul 2019 20:54:55: #1 Redundant rate of treatment: 0.65 INFO @ Fri, 05 Jul 2019 20:54:55: #1 finished! INFO @ Fri, 05 Jul 2019 20:54:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:54:55: #2 number of paired peaks: 1145 INFO @ Fri, 05 Jul 2019 20:54:55: start model_add_line... INFO @ Fri, 05 Jul 2019 20:54:55: start X-correlation... INFO @ Fri, 05 Jul 2019 20:54:55: end of X-cor INFO @ Fri, 05 Jul 2019 20:54:55: #2 finished! INFO @ Fri, 05 Jul 2019 20:54:55: #2 predicted fragment length is 328 bps INFO @ Fri, 05 Jul 2019 20:54:55: #2 alternative fragment length(s) may be 4,305,328 bps INFO @ Fri, 05 Jul 2019 20:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20_model.r INFO @ Fri, 05 Jul 2019 20:54:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:55:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.10_summits.bed INFO @ Fri, 05 Jul 2019 20:55:07: Done! pass1 - making usageList (17 chroms): 1 millis INFO @ Fri, 05 Jul 2019 20:55:07: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (515 records, 4 fields): 482 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.05_summits.bed INFO @ Fri, 05 Jul 2019 20:55:09: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (557 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 20:55:09: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339848/SRX2339848.20_summits.bed INFO @ Fri, 05 Jul 2019 20:55:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 3 millis CompletedMACS2peakCalling