Job ID = 1292892 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,208,238 reads read : 42,416,476 reads written : 42,416,476 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:15 21208238 reads; of these: 21208238 (100.00%) were paired; of these: 2005849 (9.46%) aligned concordantly 0 times 16405943 (77.36%) aligned concordantly exactly 1 time 2796446 (13.19%) aligned concordantly >1 times ---- 2005849 pairs aligned concordantly 0 times; of these: 1425333 (71.06%) aligned discordantly 1 time ---- 580516 pairs aligned 0 times concordantly or discordantly; of these: 1161032 mates make up the pairs; of these: 474840 (40.90%) aligned 0 times 331740 (28.57%) aligned exactly 1 time 354452 (30.53%) aligned >1 times 98.88% overall alignment rate Time searching: 00:23:16 Overall time: 00:23:16 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] 246710 / 20612539 = 0.0120 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 21:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.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 21:46:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:46:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.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 21:46:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:46:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.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 21:46:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:46:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:46:53: 1000000 INFO @ Sun, 02 Jun 2019 21:46:54: 1000000 INFO @ Sun, 02 Jun 2019 21:46:56: 1000000 INFO @ Sun, 02 Jun 2019 21:46:59: 2000000 INFO @ Sun, 02 Jun 2019 21:47:02: 2000000 INFO @ Sun, 02 Jun 2019 21:47:06: 2000000 INFO @ Sun, 02 Jun 2019 21:47:06: 3000000 INFO @ Sun, 02 Jun 2019 21:47:10: 3000000 INFO @ Sun, 02 Jun 2019 21:47:13: 4000000 INFO @ Sun, 02 Jun 2019 21:47:16: 3000000 INFO @ Sun, 02 Jun 2019 21:47:18: 4000000 INFO @ Sun, 02 Jun 2019 21:47:20: 5000000 INFO @ Sun, 02 Jun 2019 21:47:26: 5000000 INFO @ Sun, 02 Jun 2019 21:47:26: 4000000 INFO @ Sun, 02 Jun 2019 21:47:27: 6000000 INFO @ Sun, 02 Jun 2019 21:47:34: 7000000 INFO @ Sun, 02 Jun 2019 21:47:34: 6000000 INFO @ Sun, 02 Jun 2019 21:47:36: 5000000 INFO @ Sun, 02 Jun 2019 21:47:41: 8000000 INFO @ Sun, 02 Jun 2019 21:47:42: 7000000 INFO @ Sun, 02 Jun 2019 21:47:46: 6000000 INFO @ Sun, 02 Jun 2019 21:47:47: 9000000 INFO @ Sun, 02 Jun 2019 21:47:50: 8000000 INFO @ Sun, 02 Jun 2019 21:47:54: 10000000 INFO @ Sun, 02 Jun 2019 21:47:56: 7000000 INFO @ Sun, 02 Jun 2019 21:47:58: 9000000 INFO @ Sun, 02 Jun 2019 21:48:01: 11000000 INFO @ Sun, 02 Jun 2019 21:48:06: 10000000 INFO @ Sun, 02 Jun 2019 21:48:06: 8000000 INFO @ Sun, 02 Jun 2019 21:48:08: 12000000 INFO @ Sun, 02 Jun 2019 21:48:14: 11000000 INFO @ Sun, 02 Jun 2019 21:48:15: 13000000 INFO @ Sun, 02 Jun 2019 21:48:16: 9000000 INFO @ Sun, 02 Jun 2019 21:48:22: 14000000 INFO @ Sun, 02 Jun 2019 21:48:22: 12000000 INFO @ Sun, 02 Jun 2019 21:48:26: 10000000 INFO @ Sun, 02 Jun 2019 21:48:28: 15000000 INFO @ Sun, 02 Jun 2019 21:48:30: 13000000 INFO @ Sun, 02 Jun 2019 21:48:35: 16000000 INFO @ Sun, 02 Jun 2019 21:48:36: 11000000 INFO @ Sun, 02 Jun 2019 21:48:38: 14000000 INFO @ Sun, 02 Jun 2019 21:48:42: 17000000 INFO @ Sun, 02 Jun 2019 21:48:46: 12000000 INFO @ Sun, 02 Jun 2019 21:48:46: 15000000 INFO @ Sun, 02 Jun 2019 21:48:49: 18000000 INFO @ Sun, 02 Jun 2019 21:48:54: 16000000 INFO @ Sun, 02 Jun 2019 21:48:56: 13000000 INFO @ Sun, 02 Jun 2019 21:48:56: 19000000 INFO @ Sun, 02 Jun 2019 21:49:02: 17000000 INFO @ Sun, 02 Jun 2019 21:49:03: 20000000 INFO @ Sun, 02 Jun 2019 21:49:06: 14000000 INFO @ Sun, 02 Jun 2019 21:49:10: 21000000 INFO @ Sun, 02 Jun 2019 21:49:10: 18000000 INFO @ Sun, 02 Jun 2019 21:49:16: 15000000 INFO @ Sun, 02 Jun 2019 21:49:16: 22000000 INFO @ Sun, 02 Jun 2019 21:49:18: 19000000 INFO @ Sun, 02 Jun 2019 21:49:23: 23000000 INFO @ Sun, 02 Jun 2019 21:49:26: 16000000 INFO @ Sun, 02 Jun 2019 21:49:26: 20000000 INFO @ Sun, 02 Jun 2019 21:49:30: 24000000 INFO @ Sun, 02 Jun 2019 21:49:34: 21000000 INFO @ Sun, 02 Jun 2019 21:49:35: 17000000 INFO @ Sun, 02 Jun 2019 21:49:37: 25000000 INFO @ Sun, 02 Jun 2019 21:49:42: 22000000 INFO @ Sun, 02 Jun 2019 21:49:44: 26000000 INFO @ Sun, 02 Jun 2019 21:49:45: 18000000 INFO @ Sun, 02 Jun 2019 21:49:49: 23000000 INFO @ Sun, 02 Jun 2019 21:49:50: 27000000 INFO @ Sun, 02 Jun 2019 21:49:55: 19000000 INFO @ Sun, 02 Jun 2019 21:49:57: 28000000 INFO @ Sun, 02 Jun 2019 21:49:57: 24000000 INFO @ Sun, 02 Jun 2019 21:50:04: 29000000 INFO @ Sun, 02 Jun 2019 21:50:05: 25000000 INFO @ Sun, 02 Jun 2019 21:50:05: 20000000 INFO @ Sun, 02 Jun 2019 21:50:11: 30000000 INFO @ Sun, 02 Jun 2019 21:50:13: 26000000 INFO @ Sun, 02 Jun 2019 21:50:15: 21000000 INFO @ Sun, 02 Jun 2019 21:50:18: 31000000 INFO @ Sun, 02 Jun 2019 21:50:21: 27000000 INFO @ Sun, 02 Jun 2019 21:50:24: 32000000 INFO @ Sun, 02 Jun 2019 21:50:25: 22000000 INFO @ Sun, 02 Jun 2019 21:50:29: 28000000 INFO @ Sun, 02 Jun 2019 21:50:31: 33000000 INFO @ Sun, 02 Jun 2019 21:50:35: 23000000 INFO @ Sun, 02 Jun 2019 21:50:37: 29000000 INFO @ Sun, 02 Jun 2019 21:50:38: 34000000 INFO @ Sun, 02 Jun 2019 21:50:44: 24000000 INFO @ Sun, 02 Jun 2019 21:50:45: 30000000 INFO @ Sun, 02 Jun 2019 21:50:45: 35000000 INFO @ Sun, 02 Jun 2019 21:50:52: 36000000 INFO @ Sun, 02 Jun 2019 21:50:52: 31000000 INFO @ Sun, 02 Jun 2019 21:50:54: 25000000 INFO @ Sun, 02 Jun 2019 21:50:58: 37000000 INFO @ Sun, 02 Jun 2019 21:51:00: 32000000 INFO @ Sun, 02 Jun 2019 21:51:04: 26000000 INFO @ Sun, 02 Jun 2019 21:51:05: 38000000 INFO @ Sun, 02 Jun 2019 21:51:08: 33000000 INFO @ Sun, 02 Jun 2019 21:51:12: 39000000 INFO @ Sun, 02 Jun 2019 21:51:14: 27000000 INFO @ Sun, 02 Jun 2019 21:51:16: 34000000 INFO @ Sun, 02 Jun 2019 21:51:19: 40000000 INFO @ Sun, 02 Jun 2019 21:51:24: 28000000 INFO @ Sun, 02 Jun 2019 21:51:24: 35000000 INFO @ Sun, 02 Jun 2019 21:51:26: 41000000 INFO @ Sun, 02 Jun 2019 21:51:29: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:51:29: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:51:29: #1 total tags in treatment: 18962659 INFO @ Sun, 02 Jun 2019 21:51:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:51:29: #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 21:51:29: #1 tags after filtering in treatment: 17185742 INFO @ Sun, 02 Jun 2019 21:51:29: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:51:29: #1 finished! INFO @ Sun, 02 Jun 2019 21:51:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:51:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:51:31: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:51:31: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:51:31: start model_add_line... INFO @ Sun, 02 Jun 2019 21:51:31: start X-correlation... INFO @ Sun, 02 Jun 2019 21:51:31: end of X-cor INFO @ Sun, 02 Jun 2019 21:51:31: #2 finished! INFO @ Sun, 02 Jun 2019 21:51:31: #2 predicted fragment length is 142 bps INFO @ Sun, 02 Jun 2019 21:51:31: #2 alternative fragment length(s) may be 3,142,171 bps INFO @ Sun, 02 Jun 2019 21:51:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20_model.r INFO @ Sun, 02 Jun 2019 21:51:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:51:32: 36000000 INFO @ Sun, 02 Jun 2019 21:51:33: 29000000 INFO @ Sun, 02 Jun 2019 21:51:40: 37000000 INFO @ Sun, 02 Jun 2019 21:51:43: 30000000 INFO @ Sun, 02 Jun 2019 21:51:48: 38000000 INFO @ Sun, 02 Jun 2019 21:51:53: 31000000 INFO @ Sun, 02 Jun 2019 21:51:55: 39000000 INFO @ Sun, 02 Jun 2019 21:52:02: 32000000 INFO @ Sun, 02 Jun 2019 21:52:03: 40000000 INFO @ Sun, 02 Jun 2019 21:52:11: 41000000 INFO @ Sun, 02 Jun 2019 21:52:12: 33000000 INFO @ Sun, 02 Jun 2019 21:52:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:52:15: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:52:15: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:52:15: #1 total tags in treatment: 18962659 INFO @ Sun, 02 Jun 2019 21:52:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:52:15: #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 21:52:15: #1 tags after filtering in treatment: 17185742 INFO @ Sun, 02 Jun 2019 21:52:15: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:52:15: #1 finished! INFO @ Sun, 02 Jun 2019 21:52:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:52:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:52:17: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:52:17: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:52:17: start model_add_line... INFO @ Sun, 02 Jun 2019 21:52:17: start X-correlation... INFO @ Sun, 02 Jun 2019 21:52:17: end of X-cor INFO @ Sun, 02 Jun 2019 21:52:17: #2 finished! INFO @ Sun, 02 Jun 2019 21:52:17: #2 predicted fragment length is 142 bps INFO @ Sun, 02 Jun 2019 21:52:17: #2 alternative fragment length(s) may be 3,142,171 bps INFO @ Sun, 02 Jun 2019 21:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05_model.r INFO @ Sun, 02 Jun 2019 21:52:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:52:21: 34000000 INFO @ Sun, 02 Jun 2019 21:52:31: 35000000 INFO @ Sun, 02 Jun 2019 21:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.20_summits.bed INFO @ Sun, 02 Jun 2019 21:52:33: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (219 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:52:40: 36000000 INFO @ Sun, 02 Jun 2019 21:52:49: 37000000 INFO @ Sun, 02 Jun 2019 21:52:58: 38000000 INFO @ Sun, 02 Jun 2019 21:53:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:53:07: 39000000 INFO @ Sun, 02 Jun 2019 21:53:17: 40000000 INFO @ Sun, 02 Jun 2019 21:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.05_summits.bed INFO @ Sun, 02 Jun 2019 21:53:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:53:26: 41000000 INFO @ Sun, 02 Jun 2019 21:53:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:53:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:53:30: #1 total tags in treatment: 18962659 INFO @ Sun, 02 Jun 2019 21:53:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:30: #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 21:53:30: #1 tags after filtering in treatment: 17185742 INFO @ Sun, 02 Jun 2019 21:53:30: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:53:30: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:32: #2 number of paired peaks: 312 WARNING @ Sun, 02 Jun 2019 21:53:32: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:32: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:32: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:32: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:32: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:32: #2 predicted fragment length is 142 bps INFO @ Sun, 02 Jun 2019 21:53:32: #2 alternative fragment length(s) may be 3,142,171 bps INFO @ Sun, 02 Jun 2019 21:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10_model.r INFO @ Sun, 02 Jun 2019 21:53:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996821/SRX4996821.10_summits.bed INFO @ Sun, 02 Jun 2019 21:54:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 182 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。