Job ID = 1292009 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,248,963 reads read : 42,497,926 reads written : 42,497,926 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: 00:23:00 21248963 reads; of these: 21248963 (100.00%) were paired; of these: 1226798 (5.77%) aligned concordantly 0 times 17217671 (81.03%) aligned concordantly exactly 1 time 2804494 (13.20%) aligned concordantly >1 times ---- 1226798 pairs aligned concordantly 0 times; of these: 702574 (57.27%) aligned discordantly 1 time ---- 524224 pairs aligned 0 times concordantly or discordantly; of these: 1048448 mates make up the pairs; of these: 603461 (57.56%) aligned 0 times 261285 (24.92%) aligned exactly 1 time 183702 (17.52%) aligned >1 times 98.58% overall alignment rate Time searching: 00:23:00 Overall time: 00:23:00 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] 358986 / 20714058 = 0.0173 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 17:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.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 17:58:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.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 17:58:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.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 17:58:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:11: 1000000 INFO @ Sun, 02 Jun 2019 17:58:13: 1000000 INFO @ Sun, 02 Jun 2019 17:58:13: 1000000 INFO @ Sun, 02 Jun 2019 17:58:18: 2000000 INFO @ Sun, 02 Jun 2019 17:58:22: 2000000 INFO @ Sun, 02 Jun 2019 17:58:22: 2000000 INFO @ Sun, 02 Jun 2019 17:58:24: 3000000 INFO @ Sun, 02 Jun 2019 17:58:31: 3000000 INFO @ Sun, 02 Jun 2019 17:58:31: 3000000 INFO @ Sun, 02 Jun 2019 17:58:31: 4000000 INFO @ Sun, 02 Jun 2019 17:58:38: 5000000 INFO @ Sun, 02 Jun 2019 17:58:39: 4000000 INFO @ Sun, 02 Jun 2019 17:58:39: 4000000 INFO @ Sun, 02 Jun 2019 17:58:45: 6000000 INFO @ Sun, 02 Jun 2019 17:58:48: 5000000 INFO @ Sun, 02 Jun 2019 17:58:49: 5000000 INFO @ Sun, 02 Jun 2019 17:58:52: 7000000 INFO @ Sun, 02 Jun 2019 17:58:56: 6000000 INFO @ Sun, 02 Jun 2019 17:58:57: 6000000 INFO @ Sun, 02 Jun 2019 17:58:59: 8000000 INFO @ Sun, 02 Jun 2019 17:59:05: 7000000 INFO @ Sun, 02 Jun 2019 17:59:05: 9000000 INFO @ Sun, 02 Jun 2019 17:59:06: 7000000 INFO @ Sun, 02 Jun 2019 17:59:12: 10000000 INFO @ Sun, 02 Jun 2019 17:59:13: 8000000 INFO @ Sun, 02 Jun 2019 17:59:14: 8000000 INFO @ Sun, 02 Jun 2019 17:59:19: 11000000 INFO @ Sun, 02 Jun 2019 17:59:21: 9000000 INFO @ Sun, 02 Jun 2019 17:59:23: 9000000 INFO @ Sun, 02 Jun 2019 17:59:26: 12000000 INFO @ Sun, 02 Jun 2019 17:59:29: 10000000 INFO @ Sun, 02 Jun 2019 17:59:31: 10000000 INFO @ Sun, 02 Jun 2019 17:59:33: 13000000 INFO @ Sun, 02 Jun 2019 17:59:38: 11000000 INFO @ Sun, 02 Jun 2019 17:59:39: 14000000 INFO @ Sun, 02 Jun 2019 17:59:39: 11000000 INFO @ Sun, 02 Jun 2019 17:59:46: 15000000 INFO @ Sun, 02 Jun 2019 17:59:46: 12000000 INFO @ Sun, 02 Jun 2019 17:59:47: 12000000 INFO @ Sun, 02 Jun 2019 17:59:52: 16000000 INFO @ Sun, 02 Jun 2019 17:59:55: 13000000 INFO @ Sun, 02 Jun 2019 17:59:56: 13000000 INFO @ Sun, 02 Jun 2019 17:59:58: 17000000 INFO @ Sun, 02 Jun 2019 18:00:03: 14000000 INFO @ Sun, 02 Jun 2019 18:00:04: 14000000 INFO @ Sun, 02 Jun 2019 18:00:05: 18000000 INFO @ Sun, 02 Jun 2019 18:00:11: 19000000 INFO @ Sun, 02 Jun 2019 18:00:12: 15000000 INFO @ Sun, 02 Jun 2019 18:00:12: 15000000 INFO @ Sun, 02 Jun 2019 18:00:17: 20000000 INFO @ Sun, 02 Jun 2019 18:00:20: 16000000 INFO @ Sun, 02 Jun 2019 18:00:21: 16000000 INFO @ Sun, 02 Jun 2019 18:00:23: 21000000 INFO @ Sun, 02 Jun 2019 18:00:29: 22000000 INFO @ Sun, 02 Jun 2019 18:00:29: 17000000 INFO @ Sun, 02 Jun 2019 18:00:30: 17000000 INFO @ Sun, 02 Jun 2019 18:00:36: 23000000 INFO @ Sun, 02 Jun 2019 18:00:38: 18000000 INFO @ Sun, 02 Jun 2019 18:00:39: 18000000 INFO @ Sun, 02 Jun 2019 18:00:42: 24000000 INFO @ Sun, 02 Jun 2019 18:00:46: 19000000 INFO @ Sun, 02 Jun 2019 18:00:48: 19000000 INFO @ Sun, 02 Jun 2019 18:00:48: 25000000 INFO @ Sun, 02 Jun 2019 18:00:54: 26000000 INFO @ Sun, 02 Jun 2019 18:00:54: 20000000 INFO @ Sun, 02 Jun 2019 18:00:56: 20000000 INFO @ Sun, 02 Jun 2019 18:01:00: 27000000 INFO @ Sun, 02 Jun 2019 18:01:03: 21000000 INFO @ Sun, 02 Jun 2019 18:01:05: 21000000 INFO @ Sun, 02 Jun 2019 18:01:06: 28000000 INFO @ Sun, 02 Jun 2019 18:01:11: 22000000 INFO @ Sun, 02 Jun 2019 18:01:13: 29000000 INFO @ Sun, 02 Jun 2019 18:01:14: 22000000 INFO @ Sun, 02 Jun 2019 18:01:19: 30000000 INFO @ Sun, 02 Jun 2019 18:01:19: 23000000 INFO @ Sun, 02 Jun 2019 18:01:22: 23000000 INFO @ Sun, 02 Jun 2019 18:01:25: 31000000 INFO @ Sun, 02 Jun 2019 18:01:27: 24000000 INFO @ Sun, 02 Jun 2019 18:01:31: 24000000 INFO @ Sun, 02 Jun 2019 18:01:31: 32000000 INFO @ Sun, 02 Jun 2019 18:01:35: 25000000 INFO @ Sun, 02 Jun 2019 18:01:37: 33000000 INFO @ Sun, 02 Jun 2019 18:01:39: 25000000 INFO @ Sun, 02 Jun 2019 18:01:43: 26000000 INFO @ Sun, 02 Jun 2019 18:01:43: 34000000 INFO @ Sun, 02 Jun 2019 18:01:48: 26000000 INFO @ Sun, 02 Jun 2019 18:01:50: 35000000 INFO @ Sun, 02 Jun 2019 18:01:51: 27000000 INFO @ Sun, 02 Jun 2019 18:01:56: 36000000 INFO @ Sun, 02 Jun 2019 18:01:56: 27000000 INFO @ Sun, 02 Jun 2019 18:01:58: 28000000 INFO @ Sun, 02 Jun 2019 18:02:02: 37000000 INFO @ Sun, 02 Jun 2019 18:02:05: 28000000 INFO @ Sun, 02 Jun 2019 18:02:05: 29000000 INFO @ Sun, 02 Jun 2019 18:02:08: 38000000 INFO @ Sun, 02 Jun 2019 18:02:12: 30000000 INFO @ Sun, 02 Jun 2019 18:02:13: 29000000 INFO @ Sun, 02 Jun 2019 18:02:14: 39000000 INFO @ Sun, 02 Jun 2019 18:02:19: 31000000 INFO @ Sun, 02 Jun 2019 18:02:21: 40000000 INFO @ Sun, 02 Jun 2019 18:02:22: 30000000 INFO @ Sun, 02 Jun 2019 18:02:25: 32000000 INFO @ Sun, 02 Jun 2019 18:02:27: 41000000 INFO @ Sun, 02 Jun 2019 18:02:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:02:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:02:28: #1 total tags in treatment: 19667483 INFO @ Sun, 02 Jun 2019 18:02:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:02:28: #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 18:02:29: #1 tags after filtering in treatment: 17629492 INFO @ Sun, 02 Jun 2019 18:02:29: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:02:29: #1 finished! INFO @ Sun, 02 Jun 2019 18:02:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:02:30: 31000000 INFO @ Sun, 02 Jun 2019 18:02:30: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 18:02:30: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 18:02:30: start model_add_line... INFO @ Sun, 02 Jun 2019 18:02:31: start X-correlation... INFO @ Sun, 02 Jun 2019 18:02:31: end of X-cor INFO @ Sun, 02 Jun 2019 18:02:31: #2 finished! INFO @ Sun, 02 Jun 2019 18:02:31: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:02:31: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 02 Jun 2019 18:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10_model.r INFO @ Sun, 02 Jun 2019 18:02:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:32: 33000000 INFO @ Sun, 02 Jun 2019 18:02:38: 32000000 INFO @ Sun, 02 Jun 2019 18:02:39: 34000000 INFO @ Sun, 02 Jun 2019 18:02:46: 35000000 INFO @ Sun, 02 Jun 2019 18:02:47: 33000000 INFO @ Sun, 02 Jun 2019 18:02:53: 36000000 INFO @ Sun, 02 Jun 2019 18:02:55: 34000000 INFO @ Sun, 02 Jun 2019 18:02:59: 37000000 INFO @ Sun, 02 Jun 2019 18:03:03: 35000000 INFO @ Sun, 02 Jun 2019 18:03:07: 38000000 INFO @ Sun, 02 Jun 2019 18:03:12: 36000000 INFO @ Sun, 02 Jun 2019 18:03:14: 39000000 INFO @ Sun, 02 Jun 2019 18:03:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:03:20: 37000000 INFO @ Sun, 02 Jun 2019 18:03:21: 40000000 INFO @ Sun, 02 Jun 2019 18:03:28: 41000000 INFO @ Sun, 02 Jun 2019 18:03:29: 38000000 INFO @ Sun, 02 Jun 2019 18:03:29: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:03:29: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:03:29: #1 total tags in treatment: 19667483 INFO @ Sun, 02 Jun 2019 18:03:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:29: #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 18:03:30: #1 tags after filtering in treatment: 17629492 INFO @ Sun, 02 Jun 2019 18:03:30: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:03:30: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:32: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 18:03:32: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:32: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:32: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:32: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:32: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:32: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:03:32: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 02 Jun 2019 18:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05_model.r INFO @ Sun, 02 Jun 2019 18:03:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:37: 39000000 INFO @ Sun, 02 Jun 2019 18:03:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:03:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:03:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.10_summits.bed INFO @ Sun, 02 Jun 2019 18:03:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:03:46: 40000000 INFO @ Sun, 02 Jun 2019 18:03:55: 41000000 INFO @ Sun, 02 Jun 2019 18:03:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:03:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:03:56: #1 total tags in treatment: 19667483 INFO @ Sun, 02 Jun 2019 18:03:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:56: #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 18:03:57: #1 tags after filtering in treatment: 17629492 INFO @ Sun, 02 Jun 2019 18:03:57: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:03:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:59: #2 number of paired peaks: 285 WARNING @ Sun, 02 Jun 2019 18:03:59: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:59: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:59: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:59: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:59: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:59: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 18:03:59: #2 alternative fragment length(s) may be 4,105 bps INFO @ Sun, 02 Jun 2019 18:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20_model.r INFO @ Sun, 02 Jun 2019 18:03:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:04:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.05_summits.bed INFO @ Sun, 02 Jun 2019 18:04:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978705/SRX2978705.20_summits.bed INFO @ Sun, 02 Jun 2019 18:05:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 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。