Job ID = 1292369 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,826,866 reads read : 51,653,732 reads written : 51,653,732 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:38:49 25826866 reads; of these: 25826866 (100.00%) were paired; of these: 3304147 (12.79%) aligned concordantly 0 times 19995445 (77.42%) aligned concordantly exactly 1 time 2527274 (9.79%) aligned concordantly >1 times ---- 3304147 pairs aligned concordantly 0 times; of these: 855198 (25.88%) aligned discordantly 1 time ---- 2448949 pairs aligned 0 times concordantly or discordantly; of these: 4897898 mates make up the pairs; of these: 3993342 (81.53%) aligned 0 times 562836 (11.49%) aligned exactly 1 time 341720 (6.98%) aligned >1 times 92.27% overall alignment rate Time searching: 00:38:49 Overall time: 00:38:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 15665371 / 23284633 = 0.6728 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 @ Sun, 02 Jun 2019 19:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 19:22:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 19:22:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 19:22:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:22:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:22:31: 1000000 INFO @ Sun, 02 Jun 2019 19:22:31: 1000000 INFO @ Sun, 02 Jun 2019 19:22:33: 1000000 INFO @ Sun, 02 Jun 2019 19:22:42: 2000000 INFO @ Sun, 02 Jun 2019 19:22:42: 2000000 INFO @ Sun, 02 Jun 2019 19:22:46: 2000000 INFO @ Sun, 02 Jun 2019 19:22:53: 3000000 INFO @ Sun, 02 Jun 2019 19:22:53: 3000000 INFO @ Sun, 02 Jun 2019 19:22:58: 3000000 INFO @ Sun, 02 Jun 2019 19:23:03: 4000000 INFO @ Sun, 02 Jun 2019 19:23:04: 4000000 INFO @ Sun, 02 Jun 2019 19:23:10: 4000000 INFO @ Sun, 02 Jun 2019 19:23:13: 5000000 INFO @ Sun, 02 Jun 2019 19:23:14: 5000000 INFO @ Sun, 02 Jun 2019 19:23:22: 5000000 INFO @ Sun, 02 Jun 2019 19:23:24: 6000000 INFO @ Sun, 02 Jun 2019 19:23:25: 6000000 INFO @ Sun, 02 Jun 2019 19:23:34: 7000000 INFO @ Sun, 02 Jun 2019 19:23:34: 6000000 INFO @ Sun, 02 Jun 2019 19:23:35: 7000000 INFO @ Sun, 02 Jun 2019 19:23:43: 8000000 INFO @ Sun, 02 Jun 2019 19:23:45: 8000000 INFO @ Sun, 02 Jun 2019 19:23:46: 7000000 INFO @ Sun, 02 Jun 2019 19:23:53: 9000000 INFO @ Sun, 02 Jun 2019 19:23:54: 9000000 INFO @ Sun, 02 Jun 2019 19:23:58: 8000000 INFO @ Sun, 02 Jun 2019 19:24:03: 10000000 INFO @ Sun, 02 Jun 2019 19:24:04: 10000000 INFO @ Sun, 02 Jun 2019 19:24:10: 9000000 INFO @ Sun, 02 Jun 2019 19:24:13: 11000000 INFO @ Sun, 02 Jun 2019 19:24:14: 11000000 INFO @ Sun, 02 Jun 2019 19:24:21: 10000000 INFO @ Sun, 02 Jun 2019 19:24:24: 12000000 INFO @ Sun, 02 Jun 2019 19:24:24: 12000000 INFO @ Sun, 02 Jun 2019 19:24:33: 11000000 INFO @ Sun, 02 Jun 2019 19:24:34: 13000000 INFO @ Sun, 02 Jun 2019 19:24:34: 13000000 INFO @ Sun, 02 Jun 2019 19:24:44: 14000000 INFO @ Sun, 02 Jun 2019 19:24:44: 14000000 INFO @ Sun, 02 Jun 2019 19:24:45: 12000000 INFO @ Sun, 02 Jun 2019 19:24:54: 15000000 INFO @ Sun, 02 Jun 2019 19:24:54: 15000000 INFO @ Sun, 02 Jun 2019 19:24:56: 13000000 INFO @ Sun, 02 Jun 2019 19:25:04: 16000000 INFO @ Sun, 02 Jun 2019 19:25:04: 16000000 INFO @ Sun, 02 Jun 2019 19:25:07: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:25:07: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:25:07: #1 total tags in treatment: 7309840 INFO @ Sun, 02 Jun 2019 19:25:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:25:08: #1 tags after filtering in treatment: 5981554 INFO @ Sun, 02 Jun 2019 19:25:08: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:25:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:25:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:25:08: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:25:08: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:25:08: #1 total tags in treatment: 7309840 INFO @ Sun, 02 Jun 2019 19:25:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:25:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:25:08: #1 tags after filtering in treatment: 5981554 INFO @ Sun, 02 Jun 2019 19:25:08: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:25:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:25:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:25:08: 14000000 INFO @ Sun, 02 Jun 2019 19:25:08: #2 number of paired peaks: 631 WARNING @ Sun, 02 Jun 2019 19:25:08: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sun, 02 Jun 2019 19:25:08: start model_add_line... INFO @ Sun, 02 Jun 2019 19:25:08: start X-correlation... INFO @ Sun, 02 Jun 2019 19:25:08: end of X-cor INFO @ Sun, 02 Jun 2019 19:25:08: #2 finished! INFO @ Sun, 02 Jun 2019 19:25:08: #2 predicted fragment length is 161 bps INFO @ Sun, 02 Jun 2019 19:25:08: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 02 Jun 2019 19:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10_model.r INFO @ Sun, 02 Jun 2019 19:25:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:25:08: #2 number of paired peaks: 631 WARNING @ Sun, 02 Jun 2019 19:25:08: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sun, 02 Jun 2019 19:25:08: start model_add_line... INFO @ Sun, 02 Jun 2019 19:25:08: start X-correlation... INFO @ Sun, 02 Jun 2019 19:25:08: end of X-cor INFO @ Sun, 02 Jun 2019 19:25:08: #2 finished! INFO @ Sun, 02 Jun 2019 19:25:08: #2 predicted fragment length is 161 bps INFO @ Sun, 02 Jun 2019 19:25:08: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 02 Jun 2019 19:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20_model.r INFO @ Sun, 02 Jun 2019 19:25:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:25:19: 15000000 INFO @ Sun, 02 Jun 2019 19:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:25:30: 16000000 INFO @ Sun, 02 Jun 2019 19:25:34: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:25:34: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:25:34: #1 total tags in treatment: 7309840 INFO @ Sun, 02 Jun 2019 19:25:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:25:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:25:34: #1 tags after filtering in treatment: 5981554 INFO @ Sun, 02 Jun 2019 19:25:34: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:25:34: #1 finished! INFO @ Sun, 02 Jun 2019 19:25:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:25:34: #2 number of paired peaks: 631 WARNING @ Sun, 02 Jun 2019 19:25:34: Fewer paired peaks (631) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 631 pairs to build model! INFO @ Sun, 02 Jun 2019 19:25:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:25:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:25:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:25:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:25:34: #2 predicted fragment length is 161 bps INFO @ Sun, 02 Jun 2019 19:25:34: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 02 Jun 2019 19:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05_model.r INFO @ Sun, 02 Jun 2019 19:25:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.10_summits.bed INFO @ Sun, 02 Jun 2019 19:25:36: Done! INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.20_summits.bed INFO @ Sun, 02 Jun 2019 19:25:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:25:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733156/SRX3733156.05_summits.bed INFO @ Sun, 02 Jun 2019 19:26:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。