Job ID = 1292368 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 23,736,589 reads read : 47,473,178 reads written : 47,473,178 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: 00:37:19 23736589 reads; of these: 23736589 (100.00%) were paired; of these: 3028130 (12.76%) aligned concordantly 0 times 18389754 (77.47%) aligned concordantly exactly 1 time 2318705 (9.77%) aligned concordantly >1 times ---- 3028130 pairs aligned concordantly 0 times; of these: 581870 (19.22%) aligned discordantly 1 time ---- 2446260 pairs aligned 0 times concordantly or discordantly; of these: 4892520 mates make up the pairs; of these: 4188570 (85.61%) aligned 0 times 449672 (9.19%) aligned exactly 1 time 254278 (5.20%) aligned >1 times 91.18% overall alignment rate Time searching: 00:37:19 Overall time: 00:37:19 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] 14479579 / 21260259 = 0.6811 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 19:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.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 19:17:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.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 19:17:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.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 19:17:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:17:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:17:47: 1000000 INFO @ Sun, 02 Jun 2019 19:17:48: 1000000 INFO @ Sun, 02 Jun 2019 19:17:50: 1000000 INFO @ Sun, 02 Jun 2019 19:17:57: 2000000 INFO @ Sun, 02 Jun 2019 19:18:00: 2000000 INFO @ Sun, 02 Jun 2019 19:18:05: 2000000 INFO @ Sun, 02 Jun 2019 19:18:07: 3000000 INFO @ Sun, 02 Jun 2019 19:18:12: 3000000 INFO @ Sun, 02 Jun 2019 19:18:18: 4000000 INFO @ Sun, 02 Jun 2019 19:18:20: 3000000 INFO @ Sun, 02 Jun 2019 19:18:24: 4000000 INFO @ Sun, 02 Jun 2019 19:18:28: 5000000 INFO @ Sun, 02 Jun 2019 19:18:34: 4000000 INFO @ Sun, 02 Jun 2019 19:18:36: 5000000 INFO @ Sun, 02 Jun 2019 19:18:38: 6000000 INFO @ Sun, 02 Jun 2019 19:18:47: 6000000 INFO @ Sun, 02 Jun 2019 19:18:48: 7000000 INFO @ Sun, 02 Jun 2019 19:18:48: 5000000 INFO @ Sun, 02 Jun 2019 19:18:57: 8000000 INFO @ Sun, 02 Jun 2019 19:18:58: 7000000 INFO @ Sun, 02 Jun 2019 19:19:01: 6000000 INFO @ Sun, 02 Jun 2019 19:19:06: 9000000 INFO @ Sun, 02 Jun 2019 19:19:08: 8000000 INFO @ Sun, 02 Jun 2019 19:19:14: 7000000 INFO @ Sun, 02 Jun 2019 19:19:16: 10000000 INFO @ Sun, 02 Jun 2019 19:19:20: 9000000 INFO @ Sun, 02 Jun 2019 19:19:26: 11000000 INFO @ Sun, 02 Jun 2019 19:19:28: 8000000 INFO @ Sun, 02 Jun 2019 19:19:31: 10000000 INFO @ Sun, 02 Jun 2019 19:19:37: 12000000 INFO @ Sun, 02 Jun 2019 19:19:41: 9000000 INFO @ Sun, 02 Jun 2019 19:19:42: 11000000 INFO @ Sun, 02 Jun 2019 19:19:47: 13000000 INFO @ Sun, 02 Jun 2019 19:19:53: 12000000 INFO @ Sun, 02 Jun 2019 19:19:55: 10000000 INFO @ Sun, 02 Jun 2019 19:19:57: 14000000 INFO @ Sun, 02 Jun 2019 19:20:00: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:20:00: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:20:00: #1 total tags in treatment: 6509979 INFO @ Sun, 02 Jun 2019 19:20:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:20:00: #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 19:20:00: #1 tags after filtering in treatment: 5329193 INFO @ Sun, 02 Jun 2019 19:20:00: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:20:00: #1 finished! INFO @ Sun, 02 Jun 2019 19:20:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:20:01: #2 number of paired peaks: 643 WARNING @ Sun, 02 Jun 2019 19:20:01: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 02 Jun 2019 19:20:01: start model_add_line... INFO @ Sun, 02 Jun 2019 19:20:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:20:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:20:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:20:01: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 19:20:01: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 19:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10_model.r INFO @ Sun, 02 Jun 2019 19:20:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:20:04: 13000000 INFO @ Sun, 02 Jun 2019 19:20:06: 11000000 INFO @ Sun, 02 Jun 2019 19:20:15: 14000000 INFO @ Sun, 02 Jun 2019 19:20:18: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:20:18: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:20:18: #1 total tags in treatment: 6509979 INFO @ Sun, 02 Jun 2019 19:20:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:20:18: #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 19:20:18: #1 tags after filtering in treatment: 5329193 INFO @ Sun, 02 Jun 2019 19:20:18: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:20:18: #1 finished! INFO @ Sun, 02 Jun 2019 19:20:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:20:19: #2 number of paired peaks: 643 WARNING @ Sun, 02 Jun 2019 19:20:19: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 02 Jun 2019 19:20:19: start model_add_line... INFO @ Sun, 02 Jun 2019 19:20:19: start X-correlation... INFO @ Sun, 02 Jun 2019 19:20:19: end of X-cor INFO @ Sun, 02 Jun 2019 19:20:19: #2 finished! INFO @ Sun, 02 Jun 2019 19:20:19: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 19:20:19: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 19:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05_model.r INFO @ Sun, 02 Jun 2019 19:20:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:20:19: 12000000 INFO @ Sun, 02 Jun 2019 19:20:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.10_summits.bed INFO @ Sun, 02 Jun 2019 19:20:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:20:32: 13000000 INFO @ Sun, 02 Jun 2019 19:20:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:20:44: 14000000 INFO @ Sun, 02 Jun 2019 19:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.05_summits.bed INFO @ Sun, 02 Jun 2019 19:20:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:20:48: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 19:20:48: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 19:20:48: #1 total tags in treatment: 6509979 INFO @ Sun, 02 Jun 2019 19:20:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:20:48: #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 19:20:48: #1 tags after filtering in treatment: 5329193 INFO @ Sun, 02 Jun 2019 19:20:48: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:20:48: #1 finished! INFO @ Sun, 02 Jun 2019 19:20:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:20:49: #2 number of paired peaks: 643 WARNING @ Sun, 02 Jun 2019 19:20:49: Fewer paired peaks (643) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 643 pairs to build model! INFO @ Sun, 02 Jun 2019 19:20:49: start model_add_line... INFO @ Sun, 02 Jun 2019 19:20:49: start X-correlation... INFO @ Sun, 02 Jun 2019 19:20:49: end of X-cor INFO @ Sun, 02 Jun 2019 19:20:49: #2 finished! INFO @ Sun, 02 Jun 2019 19:20:49: #2 predicted fragment length is 154 bps INFO @ Sun, 02 Jun 2019 19:20:49: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 02 Jun 2019 19:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20_model.r INFO @ Sun, 02 Jun 2019 19:20:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:21:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733155/SRX3733155.20_summits.bed INFO @ Sun, 02 Jun 2019 19:21:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。