Job ID = 1292364 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 43,231,688 reads read : 86,463,376 reads written : 86,463,376 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: 00:59:42 43231688 reads; of these: 43231688 (100.00%) were paired; of these: 2207060 (5.11%) aligned concordantly 0 times 37960382 (87.81%) aligned concordantly exactly 1 time 3064246 (7.09%) aligned concordantly >1 times ---- 2207060 pairs aligned concordantly 0 times; of these: 499221 (22.62%) aligned discordantly 1 time ---- 1707839 pairs aligned 0 times concordantly or discordantly; of these: 3415678 mates make up the pairs; of these: 2618526 (76.66%) aligned 0 times 576054 (16.86%) aligned exactly 1 time 221098 (6.47%) aligned >1 times 96.97% overall alignment rate Time searching: 00:59:42 Overall time: 00:59:42 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 36 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] 18805975 / 41469866 = 0.4535 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 20:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.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 20:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.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 20:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.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 20:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:13:28: 1000000 INFO @ Sun, 02 Jun 2019 20:13:28: 1000000 INFO @ Sun, 02 Jun 2019 20:13:29: 1000000 INFO @ Sun, 02 Jun 2019 20:13:38: 2000000 INFO @ Sun, 02 Jun 2019 20:13:38: 2000000 INFO @ Sun, 02 Jun 2019 20:13:39: 2000000 INFO @ Sun, 02 Jun 2019 20:13:47: 3000000 INFO @ Sun, 02 Jun 2019 20:13:48: 3000000 INFO @ Sun, 02 Jun 2019 20:13:49: 3000000 INFO @ Sun, 02 Jun 2019 20:13:56: 4000000 INFO @ Sun, 02 Jun 2019 20:13:58: 4000000 INFO @ Sun, 02 Jun 2019 20:13:59: 4000000 INFO @ Sun, 02 Jun 2019 20:14:06: 5000000 INFO @ Sun, 02 Jun 2019 20:14:07: 5000000 INFO @ Sun, 02 Jun 2019 20:14:09: 5000000 INFO @ Sun, 02 Jun 2019 20:14:15: 6000000 INFO @ Sun, 02 Jun 2019 20:14:18: 6000000 INFO @ Sun, 02 Jun 2019 20:14:20: 6000000 INFO @ Sun, 02 Jun 2019 20:14:24: 7000000 INFO @ Sun, 02 Jun 2019 20:14:28: 7000000 INFO @ Sun, 02 Jun 2019 20:14:30: 7000000 INFO @ Sun, 02 Jun 2019 20:14:33: 8000000 INFO @ Sun, 02 Jun 2019 20:14:39: 8000000 INFO @ Sun, 02 Jun 2019 20:14:41: 8000000 INFO @ Sun, 02 Jun 2019 20:14:43: 9000000 INFO @ Sun, 02 Jun 2019 20:14:49: 9000000 INFO @ Sun, 02 Jun 2019 20:14:51: 9000000 INFO @ Sun, 02 Jun 2019 20:14:51: 10000000 INFO @ Sun, 02 Jun 2019 20:14:59: 10000000 INFO @ Sun, 02 Jun 2019 20:15:00: 11000000 INFO @ Sun, 02 Jun 2019 20:15:02: 10000000 INFO @ Sun, 02 Jun 2019 20:15:10: 12000000 INFO @ Sun, 02 Jun 2019 20:15:10: 11000000 INFO @ Sun, 02 Jun 2019 20:15:12: 11000000 INFO @ Sun, 02 Jun 2019 20:15:19: 13000000 INFO @ Sun, 02 Jun 2019 20:15:20: 12000000 INFO @ Sun, 02 Jun 2019 20:15:22: 12000000 INFO @ Sun, 02 Jun 2019 20:15:28: 14000000 INFO @ Sun, 02 Jun 2019 20:15:30: 13000000 INFO @ Sun, 02 Jun 2019 20:15:32: 13000000 INFO @ Sun, 02 Jun 2019 20:15:37: 15000000 INFO @ Sun, 02 Jun 2019 20:15:41: 14000000 INFO @ Sun, 02 Jun 2019 20:15:43: 14000000 INFO @ Sun, 02 Jun 2019 20:15:46: 16000000 INFO @ Sun, 02 Jun 2019 20:15:52: 15000000 INFO @ Sun, 02 Jun 2019 20:15:54: 15000000 INFO @ Sun, 02 Jun 2019 20:15:55: 17000000 INFO @ Sun, 02 Jun 2019 20:16:03: 16000000 INFO @ Sun, 02 Jun 2019 20:16:05: 18000000 INFO @ Sun, 02 Jun 2019 20:16:05: 16000000 INFO @ Sun, 02 Jun 2019 20:16:13: 17000000 INFO @ Sun, 02 Jun 2019 20:16:13: 19000000 INFO @ Sun, 02 Jun 2019 20:16:15: 17000000 INFO @ Sun, 02 Jun 2019 20:16:22: 20000000 INFO @ Sun, 02 Jun 2019 20:16:23: 18000000 INFO @ Sun, 02 Jun 2019 20:16:25: 18000000 INFO @ Sun, 02 Jun 2019 20:16:31: 21000000 INFO @ Sun, 02 Jun 2019 20:16:33: 19000000 INFO @ Sun, 02 Jun 2019 20:16:35: 19000000 INFO @ Sun, 02 Jun 2019 20:16:40: 22000000 INFO @ Sun, 02 Jun 2019 20:16:43: 20000000 INFO @ Sun, 02 Jun 2019 20:16:45: 20000000 INFO @ Sun, 02 Jun 2019 20:16:49: 23000000 INFO @ Sun, 02 Jun 2019 20:16:54: 21000000 INFO @ Sun, 02 Jun 2019 20:16:56: 21000000 INFO @ Sun, 02 Jun 2019 20:16:58: 24000000 INFO @ Sun, 02 Jun 2019 20:17:04: 22000000 INFO @ Sun, 02 Jun 2019 20:17:06: 22000000 INFO @ Sun, 02 Jun 2019 20:17:07: 25000000 INFO @ Sun, 02 Jun 2019 20:17:14: 23000000 INFO @ Sun, 02 Jun 2019 20:17:16: 23000000 INFO @ Sun, 02 Jun 2019 20:17:16: 26000000 INFO @ Sun, 02 Jun 2019 20:17:24: 24000000 INFO @ Sun, 02 Jun 2019 20:17:25: 27000000 INFO @ Sun, 02 Jun 2019 20:17:26: 24000000 INFO @ Sun, 02 Jun 2019 20:17:34: 28000000 INFO @ Sun, 02 Jun 2019 20:17:34: 25000000 INFO @ Sun, 02 Jun 2019 20:17:37: 25000000 INFO @ Sun, 02 Jun 2019 20:17:43: 29000000 INFO @ Sun, 02 Jun 2019 20:17:45: 26000000 INFO @ Sun, 02 Jun 2019 20:17:47: 26000000 INFO @ Sun, 02 Jun 2019 20:17:52: 30000000 INFO @ Sun, 02 Jun 2019 20:17:55: 27000000 INFO @ Sun, 02 Jun 2019 20:17:57: 27000000 INFO @ Sun, 02 Jun 2019 20:18:01: 31000000 INFO @ Sun, 02 Jun 2019 20:18:05: 28000000 INFO @ Sun, 02 Jun 2019 20:18:07: 28000000 INFO @ Sun, 02 Jun 2019 20:18:10: 32000000 INFO @ Sun, 02 Jun 2019 20:18:15: 29000000 INFO @ Sun, 02 Jun 2019 20:18:17: 29000000 INFO @ Sun, 02 Jun 2019 20:18:19: 33000000 INFO @ Sun, 02 Jun 2019 20:18:25: 30000000 INFO @ Sun, 02 Jun 2019 20:18:28: 30000000 INFO @ Sun, 02 Jun 2019 20:18:28: 34000000 INFO @ Sun, 02 Jun 2019 20:18:35: 31000000 INFO @ Sun, 02 Jun 2019 20:18:37: 35000000 INFO @ Sun, 02 Jun 2019 20:18:38: 31000000 INFO @ Sun, 02 Jun 2019 20:18:46: 32000000 INFO @ Sun, 02 Jun 2019 20:18:46: 36000000 INFO @ Sun, 02 Jun 2019 20:18:48: 32000000 INFO @ Sun, 02 Jun 2019 20:18:55: 37000000 INFO @ Sun, 02 Jun 2019 20:18:56: 33000000 INFO @ Sun, 02 Jun 2019 20:18:58: 33000000 INFO @ Sun, 02 Jun 2019 20:19:05: 38000000 INFO @ Sun, 02 Jun 2019 20:19:05: 34000000 INFO @ Sun, 02 Jun 2019 20:19:08: 34000000 INFO @ Sun, 02 Jun 2019 20:19:14: 39000000 INFO @ Sun, 02 Jun 2019 20:19:16: 35000000 INFO @ Sun, 02 Jun 2019 20:19:19: 35000000 INFO @ Sun, 02 Jun 2019 20:19:23: 40000000 INFO @ Sun, 02 Jun 2019 20:19:26: 36000000 INFO @ Sun, 02 Jun 2019 20:19:29: 36000000 INFO @ Sun, 02 Jun 2019 20:19:31: 41000000 INFO @ Sun, 02 Jun 2019 20:19:36: 37000000 INFO @ Sun, 02 Jun 2019 20:19:39: 37000000 INFO @ Sun, 02 Jun 2019 20:19:40: 42000000 INFO @ Sun, 02 Jun 2019 20:19:48: 38000000 INFO @ Sun, 02 Jun 2019 20:19:49: 43000000 INFO @ Sun, 02 Jun 2019 20:19:51: 38000000 INFO @ Sun, 02 Jun 2019 20:19:58: 44000000 INFO @ Sun, 02 Jun 2019 20:19:58: 39000000 INFO @ Sun, 02 Jun 2019 20:20:01: 39000000 INFO @ Sun, 02 Jun 2019 20:20:07: 45000000 INFO @ Sun, 02 Jun 2019 20:20:08: 40000000 INFO @ Sun, 02 Jun 2019 20:20:11: 40000000 INFO @ Sun, 02 Jun 2019 20:20:15: 46000000 INFO @ Sun, 02 Jun 2019 20:20:18: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:20:18: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:20:18: #1 total tags in treatment: 22298052 INFO @ Sun, 02 Jun 2019 20:20:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:20:18: #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 20:20:18: 41000000 INFO @ Sun, 02 Jun 2019 20:20:18: #1 tags after filtering in treatment: 18531294 INFO @ Sun, 02 Jun 2019 20:20:18: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:20:18: #1 finished! INFO @ Sun, 02 Jun 2019 20:20:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:20:20: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 20:20:20: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 20:20:20: start model_add_line... INFO @ Sun, 02 Jun 2019 20:20:20: start X-correlation... INFO @ Sun, 02 Jun 2019 20:20:20: end of X-cor INFO @ Sun, 02 Jun 2019 20:20:20: #2 finished! INFO @ Sun, 02 Jun 2019 20:20:20: #2 predicted fragment length is 166 bps INFO @ Sun, 02 Jun 2019 20:20:20: #2 alternative fragment length(s) may be 4,145,166 bps INFO @ Sun, 02 Jun 2019 20:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10_model.r INFO @ Sun, 02 Jun 2019 20:20:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:20:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:20:21: 41000000 INFO @ Sun, 02 Jun 2019 20:20:28: 42000000 INFO @ Sun, 02 Jun 2019 20:20:31: 42000000 INFO @ Sun, 02 Jun 2019 20:20:37: 43000000 INFO @ Sun, 02 Jun 2019 20:20:40: 43000000 INFO @ Sun, 02 Jun 2019 20:20:47: 44000000 INFO @ Sun, 02 Jun 2019 20:20:51: 44000000 INFO @ Sun, 02 Jun 2019 20:20:57: 45000000 INFO @ Sun, 02 Jun 2019 20:21:00: 45000000 INFO @ Sun, 02 Jun 2019 20:21:07: 46000000 INFO @ Sun, 02 Jun 2019 20:21:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:21:10: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:21:10: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:21:10: #1 total tags in treatment: 22298052 INFO @ Sun, 02 Jun 2019 20:21:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:21:10: #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 20:21:10: 46000000 INFO @ Sun, 02 Jun 2019 20:21:10: #1 tags after filtering in treatment: 18531294 INFO @ Sun, 02 Jun 2019 20:21:10: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:21:10: #1 finished! INFO @ Sun, 02 Jun 2019 20:21:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:21:12: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 20:21:12: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 20:21:12: start model_add_line... INFO @ Sun, 02 Jun 2019 20:21:12: start X-correlation... INFO @ Sun, 02 Jun 2019 20:21:12: end of X-cor INFO @ Sun, 02 Jun 2019 20:21:12: #2 finished! INFO @ Sun, 02 Jun 2019 20:21:12: #2 predicted fragment length is 166 bps INFO @ Sun, 02 Jun 2019 20:21:12: #2 alternative fragment length(s) may be 4,145,166 bps INFO @ Sun, 02 Jun 2019 20:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05_model.r INFO @ Sun, 02 Jun 2019 20:21:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:21:12: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:21:12: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:21:12: #1 total tags in treatment: 22298052 INFO @ Sun, 02 Jun 2019 20:21:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:21:12: #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 20:21:13: #1 tags after filtering in treatment: 18531294 INFO @ Sun, 02 Jun 2019 20:21:13: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:21:13: #1 finished! INFO @ Sun, 02 Jun 2019 20:21:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:21:14: #2 number of paired peaks: 212 WARNING @ Sun, 02 Jun 2019 20:21:14: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Sun, 02 Jun 2019 20:21:14: start model_add_line... INFO @ Sun, 02 Jun 2019 20:21:15: start X-correlation... INFO @ Sun, 02 Jun 2019 20:21:15: end of X-cor INFO @ Sun, 02 Jun 2019 20:21:15: #2 finished! INFO @ Sun, 02 Jun 2019 20:21:15: #2 predicted fragment length is 166 bps INFO @ Sun, 02 Jun 2019 20:21:15: #2 alternative fragment length(s) may be 4,145,166 bps INFO @ Sun, 02 Jun 2019 20:21:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20_model.r INFO @ Sun, 02 Jun 2019 20:21:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:21:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.10_summits.bed INFO @ Sun, 02 Jun 2019 20:21:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2188 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:22:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:22:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:22:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:22:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:22:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.05_summits.bed INFO @ Sun, 02 Jun 2019 20:22:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4192 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:22:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:22:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:22:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733151/SRX3733151.20_summits.bed INFO @ Sun, 02 Jun 2019 20:22:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (875 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。