Job ID = 1292438 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,396,890 reads read : 24,793,780 reads written : 24,793,780 spots read : 11,378,854 reads read : 22,757,708 reads written : 22,757,708 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: 00:25:04 23775744 reads; of these: 23775744 (100.00%) were paired; of these: 2912508 (12.25%) aligned concordantly 0 times 17575296 (73.92%) aligned concordantly exactly 1 time 3287940 (13.83%) aligned concordantly >1 times ---- 2912508 pairs aligned concordantly 0 times; of these: 641498 (22.03%) aligned discordantly 1 time ---- 2271010 pairs aligned 0 times concordantly or discordantly; of these: 4542020 mates make up the pairs; of these: 3587012 (78.97%) aligned 0 times 632303 (13.92%) aligned exactly 1 time 322705 (7.10%) aligned >1 times 92.46% overall alignment rate Time searching: 00:25:04 Overall time: 00:25:04 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] 881553 / 21286764 = 0.0414 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 19:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.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 19:24:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.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 19:24:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.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 19:24:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:24:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:24:29: 1000000 INFO @ Sun, 02 Jun 2019 19:24:29: 1000000 INFO @ Sun, 02 Jun 2019 19:24:30: 1000000 INFO @ Sun, 02 Jun 2019 19:24:36: 2000000 INFO @ Sun, 02 Jun 2019 19:24:36: 2000000 INFO @ Sun, 02 Jun 2019 19:24:38: 2000000 INFO @ Sun, 02 Jun 2019 19:24:43: 3000000 INFO @ Sun, 02 Jun 2019 19:24:44: 3000000 INFO @ Sun, 02 Jun 2019 19:24:45: 3000000 INFO @ Sun, 02 Jun 2019 19:24:50: 4000000 INFO @ Sun, 02 Jun 2019 19:24:51: 4000000 INFO @ Sun, 02 Jun 2019 19:24:53: 4000000 INFO @ Sun, 02 Jun 2019 19:24:57: 5000000 INFO @ Sun, 02 Jun 2019 19:24:58: 5000000 INFO @ Sun, 02 Jun 2019 19:25:01: 5000000 INFO @ Sun, 02 Jun 2019 19:25:04: 6000000 INFO @ Sun, 02 Jun 2019 19:25:05: 6000000 INFO @ Sun, 02 Jun 2019 19:25:08: 6000000 INFO @ Sun, 02 Jun 2019 19:25:11: 7000000 INFO @ Sun, 02 Jun 2019 19:25:12: 7000000 INFO @ Sun, 02 Jun 2019 19:25:16: 7000000 INFO @ Sun, 02 Jun 2019 19:25:18: 8000000 INFO @ Sun, 02 Jun 2019 19:25:19: 8000000 INFO @ Sun, 02 Jun 2019 19:25:24: 8000000 INFO @ Sun, 02 Jun 2019 19:25:25: 9000000 INFO @ Sun, 02 Jun 2019 19:25:26: 9000000 INFO @ Sun, 02 Jun 2019 19:25:31: 9000000 INFO @ Sun, 02 Jun 2019 19:25:32: 10000000 INFO @ Sun, 02 Jun 2019 19:25:33: 10000000 INFO @ Sun, 02 Jun 2019 19:25:39: 10000000 INFO @ Sun, 02 Jun 2019 19:25:39: 11000000 INFO @ Sun, 02 Jun 2019 19:25:40: 11000000 INFO @ Sun, 02 Jun 2019 19:25:46: 12000000 INFO @ Sun, 02 Jun 2019 19:25:47: 11000000 INFO @ Sun, 02 Jun 2019 19:25:48: 12000000 INFO @ Sun, 02 Jun 2019 19:25:53: 13000000 INFO @ Sun, 02 Jun 2019 19:25:54: 12000000 INFO @ Sun, 02 Jun 2019 19:25:54: 13000000 INFO @ Sun, 02 Jun 2019 19:26:00: 14000000 INFO @ Sun, 02 Jun 2019 19:26:01: 14000000 INFO @ Sun, 02 Jun 2019 19:26:02: 13000000 INFO @ Sun, 02 Jun 2019 19:26:07: 15000000 INFO @ Sun, 02 Jun 2019 19:26:08: 15000000 INFO @ Sun, 02 Jun 2019 19:26:10: 14000000 INFO @ Sun, 02 Jun 2019 19:26:13: 16000000 INFO @ Sun, 02 Jun 2019 19:26:15: 16000000 INFO @ Sun, 02 Jun 2019 19:26:17: 15000000 INFO @ Sun, 02 Jun 2019 19:26:20: 17000000 INFO @ Sun, 02 Jun 2019 19:26:22: 17000000 INFO @ Sun, 02 Jun 2019 19:26:25: 16000000 INFO @ Sun, 02 Jun 2019 19:26:27: 18000000 INFO @ Sun, 02 Jun 2019 19:26:29: 18000000 INFO @ Sun, 02 Jun 2019 19:26:33: 17000000 INFO @ Sun, 02 Jun 2019 19:26:34: 19000000 INFO @ Sun, 02 Jun 2019 19:26:35: 19000000 INFO @ Sun, 02 Jun 2019 19:26:40: 18000000 INFO @ Sun, 02 Jun 2019 19:26:41: 20000000 INFO @ Sun, 02 Jun 2019 19:26:42: 20000000 INFO @ Sun, 02 Jun 2019 19:26:47: 21000000 INFO @ Sun, 02 Jun 2019 19:26:48: 19000000 INFO @ Sun, 02 Jun 2019 19:26:49: 21000000 INFO @ Sun, 02 Jun 2019 19:26:54: 22000000 INFO @ Sun, 02 Jun 2019 19:26:56: 22000000 INFO @ Sun, 02 Jun 2019 19:26:56: 20000000 INFO @ Sun, 02 Jun 2019 19:27:01: 23000000 INFO @ Sun, 02 Jun 2019 19:27:03: 23000000 INFO @ Sun, 02 Jun 2019 19:27:05: 21000000 INFO @ Sun, 02 Jun 2019 19:27:09: 24000000 INFO @ Sun, 02 Jun 2019 19:27:10: 24000000 INFO @ Sun, 02 Jun 2019 19:27:13: 22000000 INFO @ Sun, 02 Jun 2019 19:27:15: 25000000 INFO @ Sun, 02 Jun 2019 19:27:17: 25000000 INFO @ Sun, 02 Jun 2019 19:27:20: 23000000 INFO @ Sun, 02 Jun 2019 19:27:22: 26000000 INFO @ Sun, 02 Jun 2019 19:27:24: 26000000 INFO @ Sun, 02 Jun 2019 19:27:28: 24000000 INFO @ Sun, 02 Jun 2019 19:27:29: 27000000 INFO @ Sun, 02 Jun 2019 19:27:31: 27000000 INFO @ Sun, 02 Jun 2019 19:27:35: 25000000 INFO @ Sun, 02 Jun 2019 19:27:36: 28000000 INFO @ Sun, 02 Jun 2019 19:27:37: 28000000 INFO @ Sun, 02 Jun 2019 19:27:42: 29000000 INFO @ Sun, 02 Jun 2019 19:27:43: 26000000 INFO @ Sun, 02 Jun 2019 19:27:44: 29000000 INFO @ Sun, 02 Jun 2019 19:27:49: 30000000 INFO @ Sun, 02 Jun 2019 19:27:50: 27000000 INFO @ Sun, 02 Jun 2019 19:27:51: 30000000 INFO @ Sun, 02 Jun 2019 19:27:56: 31000000 INFO @ Sun, 02 Jun 2019 19:27:58: 31000000 INFO @ Sun, 02 Jun 2019 19:27:58: 28000000 INFO @ Sun, 02 Jun 2019 19:28:03: 32000000 INFO @ Sun, 02 Jun 2019 19:28:04: 32000000 INFO @ Sun, 02 Jun 2019 19:28:06: 29000000 INFO @ Sun, 02 Jun 2019 19:28:09: 33000000 INFO @ Sun, 02 Jun 2019 19:28:11: 33000000 INFO @ Sun, 02 Jun 2019 19:28:13: 30000000 INFO @ Sun, 02 Jun 2019 19:28:16: 34000000 INFO @ Sun, 02 Jun 2019 19:28:18: 34000000 INFO @ Sun, 02 Jun 2019 19:28:21: 31000000 INFO @ Sun, 02 Jun 2019 19:28:23: 35000000 INFO @ Sun, 02 Jun 2019 19:28:25: 35000000 INFO @ Sun, 02 Jun 2019 19:28:29: 32000000 INFO @ Sun, 02 Jun 2019 19:28:30: 36000000 INFO @ Sun, 02 Jun 2019 19:28:32: 36000000 INFO @ Sun, 02 Jun 2019 19:28:36: 33000000 INFO @ Sun, 02 Jun 2019 19:28:36: 37000000 INFO @ Sun, 02 Jun 2019 19:28:38: 37000000 INFO @ Sun, 02 Jun 2019 19:28:43: 38000000 INFO @ Sun, 02 Jun 2019 19:28:44: 34000000 INFO @ Sun, 02 Jun 2019 19:28:45: 38000000 INFO @ Sun, 02 Jun 2019 19:28:50: 39000000 INFO @ Sun, 02 Jun 2019 19:28:51: 35000000 INFO @ Sun, 02 Jun 2019 19:28:52: 39000000 INFO @ Sun, 02 Jun 2019 19:28:57: 40000000 INFO @ Sun, 02 Jun 2019 19:28:59: 40000000 INFO @ Sun, 02 Jun 2019 19:28:59: 36000000 INFO @ Sun, 02 Jun 2019 19:29:04: 41000000 INFO @ Sun, 02 Jun 2019 19:29:05: 41000000 INFO @ Sun, 02 Jun 2019 19:29:07: 37000000 INFO @ Sun, 02 Jun 2019 19:29:11: 42000000 INFO @ Sun, 02 Jun 2019 19:29:12: 42000000 INFO @ Sun, 02 Jun 2019 19:29:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:29:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:29:13: #1 total tags in treatment: 19984577 INFO @ Sun, 02 Jun 2019 19:29:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:29:13: #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 19:29:13: #1 tags after filtering in treatment: 16308298 INFO @ Sun, 02 Jun 2019 19:29:13: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:29:13: #1 finished! INFO @ Sun, 02 Jun 2019 19:29:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:29:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:29:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:29:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:29:14: #1 total tags in treatment: 19984577 INFO @ Sun, 02 Jun 2019 19:29:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:29:14: #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 19:29:14: 38000000 INFO @ Sun, 02 Jun 2019 19:29:14: #1 tags after filtering in treatment: 16308298 INFO @ Sun, 02 Jun 2019 19:29:14: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:29:14: #1 finished! INFO @ Sun, 02 Jun 2019 19:29:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:29:14: #2 number of paired peaks: 170 WARNING @ Sun, 02 Jun 2019 19:29:14: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:14: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:15: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:15: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:15: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:15: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:29:15: #2 alternative fragment length(s) may be 3,67,83,102,139,158 bps INFO @ Sun, 02 Jun 2019 19:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20_model.r INFO @ Sun, 02 Jun 2019 19:29:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:15: #2 number of paired peaks: 170 WARNING @ Sun, 02 Jun 2019 19:29:15: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:15: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:16: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:16: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:16: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:16: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:29:16: #2 alternative fragment length(s) may be 3,67,83,102,139,158 bps INFO @ Sun, 02 Jun 2019 19:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10_model.r INFO @ Sun, 02 Jun 2019 19:29:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:21: 39000000 INFO @ Sun, 02 Jun 2019 19:29:29: 40000000 INFO @ Sun, 02 Jun 2019 19:29:36: 41000000 INFO @ Sun, 02 Jun 2019 19:29:43: 42000000 INFO @ Sun, 02 Jun 2019 19:29:45: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:29:45: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:29:45: #1 total tags in treatment: 19984577 INFO @ Sun, 02 Jun 2019 19:29:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:29:45: #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 19:29:45: #1 tags after filtering in treatment: 16308298 INFO @ Sun, 02 Jun 2019 19:29:45: #1 Redundant rate of treatment: 0.18 INFO @ Sun, 02 Jun 2019 19:29:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:29:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:29:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:29:47: #2 number of paired peaks: 170 WARNING @ Sun, 02 Jun 2019 19:29:47: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:47: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 19:29:47: #2 alternative fragment length(s) may be 3,67,83,102,139,158 bps INFO @ Sun, 02 Jun 2019 19:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05_model.r INFO @ Sun, 02 Jun 2019 19:29:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:29:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.20_summits.bed INFO @ Sun, 02 Jun 2019 19:30:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.10_summits.bed INFO @ Sun, 02 Jun 2019 19:30:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (226 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:30:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419817/SRX4419817.05_summits.bed INFO @ Sun, 02 Jun 2019 19:30:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。