Job ID = 1292001 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,679,435 reads read : 37,358,870 reads written : 37,358,870 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: 00:20:40 18679435 reads; of these: 18679435 (100.00%) were paired; of these: 2901594 (15.53%) aligned concordantly 0 times 13261559 (71.00%) aligned concordantly exactly 1 time 2516282 (13.47%) aligned concordantly >1 times ---- 2901594 pairs aligned concordantly 0 times; of these: 1756836 (60.55%) aligned discordantly 1 time ---- 1144758 pairs aligned 0 times concordantly or discordantly; of these: 2289516 mates make up the pairs; of these: 1211768 (52.93%) aligned 0 times 615996 (26.91%) aligned exactly 1 time 461752 (20.17%) aligned >1 times 96.76% overall alignment rate Time searching: 00:20:40 Overall time: 00:20:40 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 16 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] 3307051 / 17525175 = 0.1887 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 17:51:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.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 17:51:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:51:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.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 17:51:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:51:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:51:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.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 17:51:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:51:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:51:14: 1000000 INFO @ Sun, 02 Jun 2019 17:51:15: 1000000 INFO @ Sun, 02 Jun 2019 17:51:15: 1000000 INFO @ Sun, 02 Jun 2019 17:51:23: 2000000 INFO @ Sun, 02 Jun 2019 17:51:25: 2000000 INFO @ Sun, 02 Jun 2019 17:51:26: 2000000 INFO @ Sun, 02 Jun 2019 17:51:32: 3000000 INFO @ Sun, 02 Jun 2019 17:51:35: 3000000 INFO @ Sun, 02 Jun 2019 17:51:36: 3000000 INFO @ Sun, 02 Jun 2019 17:51:40: 4000000 INFO @ Sun, 02 Jun 2019 17:51:45: 4000000 INFO @ Sun, 02 Jun 2019 17:51:47: 4000000 INFO @ Sun, 02 Jun 2019 17:51:49: 5000000 INFO @ Sun, 02 Jun 2019 17:51:55: 5000000 INFO @ Sun, 02 Jun 2019 17:51:57: 5000000 INFO @ Sun, 02 Jun 2019 17:51:58: 6000000 INFO @ Sun, 02 Jun 2019 17:52:07: 6000000 INFO @ Sun, 02 Jun 2019 17:52:07: 7000000 INFO @ Sun, 02 Jun 2019 17:52:08: 6000000 INFO @ Sun, 02 Jun 2019 17:52:16: 8000000 INFO @ Sun, 02 Jun 2019 17:52:18: 7000000 INFO @ Sun, 02 Jun 2019 17:52:19: 7000000 INFO @ Sun, 02 Jun 2019 17:52:25: 9000000 INFO @ Sun, 02 Jun 2019 17:52:28: 8000000 INFO @ Sun, 02 Jun 2019 17:52:29: 8000000 INFO @ Sun, 02 Jun 2019 17:52:33: 10000000 INFO @ Sun, 02 Jun 2019 17:52:38: 9000000 INFO @ Sun, 02 Jun 2019 17:52:39: 9000000 INFO @ Sun, 02 Jun 2019 17:52:42: 11000000 INFO @ Sun, 02 Jun 2019 17:52:48: 10000000 INFO @ Sun, 02 Jun 2019 17:52:49: 10000000 INFO @ Sun, 02 Jun 2019 17:52:51: 12000000 INFO @ Sun, 02 Jun 2019 17:52:58: 11000000 INFO @ Sun, 02 Jun 2019 17:52:59: 11000000 INFO @ Sun, 02 Jun 2019 17:53:00: 13000000 INFO @ Sun, 02 Jun 2019 17:53:08: 12000000 INFO @ Sun, 02 Jun 2019 17:53:09: 14000000 INFO @ Sun, 02 Jun 2019 17:53:09: 12000000 INFO @ Sun, 02 Jun 2019 17:53:17: 15000000 INFO @ Sun, 02 Jun 2019 17:53:18: 13000000 INFO @ Sun, 02 Jun 2019 17:53:19: 13000000 INFO @ Sun, 02 Jun 2019 17:53:26: 16000000 INFO @ Sun, 02 Jun 2019 17:53:28: 14000000 INFO @ Sun, 02 Jun 2019 17:53:29: 14000000 INFO @ Sun, 02 Jun 2019 17:53:35: 17000000 INFO @ Sun, 02 Jun 2019 17:53:38: 15000000 INFO @ Sun, 02 Jun 2019 17:53:39: 15000000 INFO @ Sun, 02 Jun 2019 17:53:44: 18000000 INFO @ Sun, 02 Jun 2019 17:53:48: 16000000 INFO @ Sun, 02 Jun 2019 17:53:50: 16000000 INFO @ Sun, 02 Jun 2019 17:53:53: 19000000 INFO @ Sun, 02 Jun 2019 17:53:58: 17000000 INFO @ Sun, 02 Jun 2019 17:54:00: 17000000 INFO @ Sun, 02 Jun 2019 17:54:02: 20000000 INFO @ Sun, 02 Jun 2019 17:54:09: 18000000 INFO @ Sun, 02 Jun 2019 17:54:11: 18000000 INFO @ Sun, 02 Jun 2019 17:54:11: 21000000 INFO @ Sun, 02 Jun 2019 17:54:19: 19000000 INFO @ Sun, 02 Jun 2019 17:54:19: 22000000 INFO @ Sun, 02 Jun 2019 17:54:21: 19000000 INFO @ Sun, 02 Jun 2019 17:54:27: 23000000 INFO @ Sun, 02 Jun 2019 17:54:29: 20000000 INFO @ Sun, 02 Jun 2019 17:54:32: 20000000 INFO @ Sun, 02 Jun 2019 17:54:36: 24000000 INFO @ Sun, 02 Jun 2019 17:54:40: 21000000 INFO @ Sun, 02 Jun 2019 17:54:43: 21000000 INFO @ Sun, 02 Jun 2019 17:54:46: 25000000 INFO @ Sun, 02 Jun 2019 17:54:49: 22000000 INFO @ Sun, 02 Jun 2019 17:54:52: 22000000 INFO @ Sun, 02 Jun 2019 17:54:55: 26000000 INFO @ Sun, 02 Jun 2019 17:54:59: 23000000 INFO @ Sun, 02 Jun 2019 17:55:02: 23000000 INFO @ Sun, 02 Jun 2019 17:55:04: 27000000 INFO @ Sun, 02 Jun 2019 17:55:09: 24000000 INFO @ Sun, 02 Jun 2019 17:55:12: 24000000 INFO @ Sun, 02 Jun 2019 17:55:13: 28000000 INFO @ Sun, 02 Jun 2019 17:55:19: 25000000 INFO @ Sun, 02 Jun 2019 17:55:22: 29000000 INFO @ Sun, 02 Jun 2019 17:55:23: 25000000 INFO @ Sun, 02 Jun 2019 17:55:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:55:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:55:26: #1 total tags in treatment: 12614113 INFO @ Sun, 02 Jun 2019 17:55:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:55:26: #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 17:55:27: #1 tags after filtering in treatment: 11514001 INFO @ Sun, 02 Jun 2019 17:55:27: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 17:55:27: #1 finished! INFO @ Sun, 02 Jun 2019 17:55:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:55:28: #2 number of paired peaks: 481 WARNING @ Sun, 02 Jun 2019 17:55:28: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 02 Jun 2019 17:55:28: start model_add_line... INFO @ Sun, 02 Jun 2019 17:55:28: start X-correlation... INFO @ Sun, 02 Jun 2019 17:55:28: end of X-cor INFO @ Sun, 02 Jun 2019 17:55:28: #2 finished! INFO @ Sun, 02 Jun 2019 17:55:28: #2 predicted fragment length is 129 bps INFO @ Sun, 02 Jun 2019 17:55:28: #2 alternative fragment length(s) may be 4,129 bps INFO @ Sun, 02 Jun 2019 17:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05_model.r INFO @ Sun, 02 Jun 2019 17:55:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:55:31: 26000000 INFO @ Sun, 02 Jun 2019 17:55:34: 26000000 INFO @ Sun, 02 Jun 2019 17:55:42: 27000000 INFO @ Sun, 02 Jun 2019 17:55:44: 27000000 INFO @ Sun, 02 Jun 2019 17:55:52: 28000000 INFO @ Sun, 02 Jun 2019 17:55:55: 28000000 INFO @ Sun, 02 Jun 2019 17:56:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:56:02: 29000000 INFO @ Sun, 02 Jun 2019 17:56:05: 29000000 INFO @ Sun, 02 Jun 2019 17:56:07: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:56:07: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:56:07: #1 total tags in treatment: 12614113 INFO @ Sun, 02 Jun 2019 17:56:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:56:07: #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 17:56:08: #1 tags after filtering in treatment: 11514001 INFO @ Sun, 02 Jun 2019 17:56:08: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 17:56:08: #1 finished! INFO @ Sun, 02 Jun 2019 17:56:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:56:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:56:09: #2 number of paired peaks: 481 WARNING @ Sun, 02 Jun 2019 17:56:09: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 02 Jun 2019 17:56:09: start model_add_line... INFO @ Sun, 02 Jun 2019 17:56:09: start X-correlation... INFO @ Sun, 02 Jun 2019 17:56:09: end of X-cor INFO @ Sun, 02 Jun 2019 17:56:09: #2 finished! INFO @ Sun, 02 Jun 2019 17:56:09: #2 predicted fragment length is 129 bps INFO @ Sun, 02 Jun 2019 17:56:09: #2 alternative fragment length(s) may be 4,129 bps INFO @ Sun, 02 Jun 2019 17:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10_model.r INFO @ Sun, 02 Jun 2019 17:56:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:56:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:56:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:56:11: #1 total tags in treatment: 12614113 INFO @ Sun, 02 Jun 2019 17:56:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:56:11: #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 17:56:11: #1 tags after filtering in treatment: 11514001 INFO @ Sun, 02 Jun 2019 17:56:11: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 17:56:11: #1 finished! INFO @ Sun, 02 Jun 2019 17:56:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:56:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:56:12: #2 number of paired peaks: 481 WARNING @ Sun, 02 Jun 2019 17:56:12: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Sun, 02 Jun 2019 17:56:12: start model_add_line... INFO @ Sun, 02 Jun 2019 17:56:12: start X-correlation... INFO @ Sun, 02 Jun 2019 17:56:12: end of X-cor INFO @ Sun, 02 Jun 2019 17:56:12: #2 finished! INFO @ Sun, 02 Jun 2019 17:56:12: #2 predicted fragment length is 129 bps INFO @ Sun, 02 Jun 2019 17:56:12: #2 alternative fragment length(s) may be 4,129 bps INFO @ Sun, 02 Jun 2019 17:56:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20_model.r INFO @ Sun, 02 Jun 2019 17:56:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:56:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.05_summits.bed INFO @ Sun, 02 Jun 2019 17:56:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:56:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:56:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.10_summits.bed INFO @ Sun, 02 Jun 2019 17:56:55: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (347 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978697/SRX2978697.20_summits.bed INFO @ Sun, 02 Jun 2019 17:56:59: Done! pass1 - making usageList (7 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。