Job ID = 1292884 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,932,478 reads read : 45,864,956 reads written : 45,864,956 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: 00:42:25 22932478 reads; of these: 22932478 (100.00%) were paired; of these: 3309641 (14.43%) aligned concordantly 0 times 16700018 (72.82%) aligned concordantly exactly 1 time 2922819 (12.75%) aligned concordantly >1 times ---- 3309641 pairs aligned concordantly 0 times; of these: 2252177 (68.05%) aligned discordantly 1 time ---- 1057464 pairs aligned 0 times concordantly or discordantly; of these: 2114928 mates make up the pairs; of these: 903604 (42.73%) aligned 0 times 621445 (29.38%) aligned exactly 1 time 589879 (27.89%) aligned >1 times 98.03% overall alignment rate Time searching: 00:42:25 Overall time: 00:42:25 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] 612891 / 21854713 = 0.0280 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 22:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.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 22:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.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 22:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.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 22:13:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:31: 1000000 INFO @ Sun, 02 Jun 2019 22:13:33: 1000000 INFO @ Sun, 02 Jun 2019 22:13:34: 1000000 INFO @ Sun, 02 Jun 2019 22:13:45: 2000000 INFO @ Sun, 02 Jun 2019 22:13:49: 2000000 INFO @ Sun, 02 Jun 2019 22:13:50: 2000000 INFO @ Sun, 02 Jun 2019 22:13:58: 3000000 INFO @ Sun, 02 Jun 2019 22:14:04: 3000000 INFO @ Sun, 02 Jun 2019 22:14:06: 3000000 INFO @ Sun, 02 Jun 2019 22:14:11: 4000000 INFO @ Sun, 02 Jun 2019 22:14:20: 4000000 INFO @ Sun, 02 Jun 2019 22:14:21: 4000000 INFO @ Sun, 02 Jun 2019 22:14:24: 5000000 INFO @ Sun, 02 Jun 2019 22:14:35: 5000000 INFO @ Sun, 02 Jun 2019 22:14:37: 5000000 INFO @ Sun, 02 Jun 2019 22:14:37: 6000000 INFO @ Sun, 02 Jun 2019 22:14:49: 7000000 INFO @ Sun, 02 Jun 2019 22:14:50: 6000000 INFO @ Sun, 02 Jun 2019 22:14:53: 6000000 INFO @ Sun, 02 Jun 2019 22:15:02: 8000000 INFO @ Sun, 02 Jun 2019 22:15:06: 7000000 INFO @ Sun, 02 Jun 2019 22:15:08: 7000000 INFO @ Sun, 02 Jun 2019 22:15:15: 9000000 INFO @ Sun, 02 Jun 2019 22:15:21: 8000000 INFO @ Sun, 02 Jun 2019 22:15:24: 8000000 INFO @ Sun, 02 Jun 2019 22:15:29: 10000000 INFO @ Sun, 02 Jun 2019 22:15:37: 9000000 INFO @ Sun, 02 Jun 2019 22:15:40: 9000000 INFO @ Sun, 02 Jun 2019 22:15:41: 11000000 INFO @ Sun, 02 Jun 2019 22:15:52: 10000000 INFO @ Sun, 02 Jun 2019 22:15:54: 12000000 INFO @ Sun, 02 Jun 2019 22:15:56: 10000000 INFO @ Sun, 02 Jun 2019 22:16:07: 11000000 INFO @ Sun, 02 Jun 2019 22:16:08: 13000000 INFO @ Sun, 02 Jun 2019 22:16:13: 11000000 INFO @ Sun, 02 Jun 2019 22:16:20: 12000000 INFO @ Sun, 02 Jun 2019 22:16:21: 14000000 INFO @ Sun, 02 Jun 2019 22:16:29: 12000000 INFO @ Sun, 02 Jun 2019 22:16:34: 13000000 INFO @ Sun, 02 Jun 2019 22:16:35: 15000000 INFO @ Sun, 02 Jun 2019 22:16:45: 13000000 INFO @ Sun, 02 Jun 2019 22:16:48: 16000000 INFO @ Sun, 02 Jun 2019 22:16:48: 14000000 INFO @ Sun, 02 Jun 2019 22:17:00: 14000000 INFO @ Sun, 02 Jun 2019 22:17:00: 17000000 INFO @ Sun, 02 Jun 2019 22:17:04: 15000000 INFO @ Sun, 02 Jun 2019 22:17:14: 18000000 INFO @ Sun, 02 Jun 2019 22:17:16: 15000000 INFO @ Sun, 02 Jun 2019 22:17:20: 16000000 INFO @ Sun, 02 Jun 2019 22:17:27: 19000000 INFO @ Sun, 02 Jun 2019 22:17:31: 16000000 INFO @ Sun, 02 Jun 2019 22:17:35: 17000000 INFO @ Sun, 02 Jun 2019 22:17:39: 20000000 INFO @ Sun, 02 Jun 2019 22:17:47: 17000000 INFO @ Sun, 02 Jun 2019 22:17:51: 18000000 INFO @ Sun, 02 Jun 2019 22:17:53: 21000000 INFO @ Sun, 02 Jun 2019 22:18:03: 18000000 INFO @ Sun, 02 Jun 2019 22:18:07: 22000000 INFO @ Sun, 02 Jun 2019 22:18:07: 19000000 INFO @ Sun, 02 Jun 2019 22:18:18: 19000000 INFO @ Sun, 02 Jun 2019 22:18:21: 23000000 INFO @ Sun, 02 Jun 2019 22:18:23: 20000000 INFO @ Sun, 02 Jun 2019 22:18:31: 20000000 INFO @ Sun, 02 Jun 2019 22:18:34: 24000000 INFO @ Sun, 02 Jun 2019 22:18:37: 21000000 INFO @ Sun, 02 Jun 2019 22:18:44: 21000000 INFO @ Sun, 02 Jun 2019 22:18:47: 25000000 INFO @ Sun, 02 Jun 2019 22:18:52: 22000000 INFO @ Sun, 02 Jun 2019 22:18:58: 22000000 INFO @ Sun, 02 Jun 2019 22:19:01: 26000000 INFO @ Sun, 02 Jun 2019 22:19:08: 23000000 INFO @ Sun, 02 Jun 2019 22:19:10: 23000000 INFO @ Sun, 02 Jun 2019 22:19:14: 27000000 INFO @ Sun, 02 Jun 2019 22:19:22: 24000000 INFO @ Sun, 02 Jun 2019 22:19:22: 24000000 INFO @ Sun, 02 Jun 2019 22:19:27: 28000000 INFO @ Sun, 02 Jun 2019 22:19:35: 25000000 INFO @ Sun, 02 Jun 2019 22:19:38: 25000000 INFO @ Sun, 02 Jun 2019 22:19:41: 29000000 INFO @ Sun, 02 Jun 2019 22:19:49: 26000000 INFO @ Sun, 02 Jun 2019 22:19:52: 26000000 INFO @ Sun, 02 Jun 2019 22:19:54: 30000000 INFO @ Sun, 02 Jun 2019 22:20:02: 27000000 INFO @ Sun, 02 Jun 2019 22:20:06: 31000000 INFO @ Sun, 02 Jun 2019 22:20:07: 27000000 INFO @ Sun, 02 Jun 2019 22:20:15: 28000000 INFO @ Sun, 02 Jun 2019 22:20:19: 32000000 INFO @ Sun, 02 Jun 2019 22:20:22: 28000000 INFO @ Sun, 02 Jun 2019 22:20:29: 29000000 INFO @ Sun, 02 Jun 2019 22:20:33: 33000000 INFO @ Sun, 02 Jun 2019 22:20:37: 29000000 INFO @ Sun, 02 Jun 2019 22:20:42: 30000000 INFO @ Sun, 02 Jun 2019 22:20:46: 34000000 INFO @ Sun, 02 Jun 2019 22:20:51: 30000000 INFO @ Sun, 02 Jun 2019 22:20:54: 31000000 INFO @ Sun, 02 Jun 2019 22:21:00: 35000000 INFO @ Sun, 02 Jun 2019 22:21:05: 31000000 INFO @ Sun, 02 Jun 2019 22:21:07: 32000000 INFO @ Sun, 02 Jun 2019 22:21:14: 36000000 INFO @ Sun, 02 Jun 2019 22:21:21: 33000000 INFO @ Sun, 02 Jun 2019 22:21:21: 32000000 INFO @ Sun, 02 Jun 2019 22:21:27: 37000000 INFO @ Sun, 02 Jun 2019 22:21:33: 34000000 INFO @ Sun, 02 Jun 2019 22:21:36: 33000000 INFO @ Sun, 02 Jun 2019 22:21:41: 38000000 INFO @ Sun, 02 Jun 2019 22:21:46: 35000000 INFO @ Sun, 02 Jun 2019 22:21:51: 34000000 INFO @ Sun, 02 Jun 2019 22:21:54: 39000000 INFO @ Sun, 02 Jun 2019 22:22:00: 36000000 INFO @ Sun, 02 Jun 2019 22:22:06: 35000000 INFO @ Sun, 02 Jun 2019 22:22:08: 40000000 INFO @ Sun, 02 Jun 2019 22:22:13: 37000000 INFO @ Sun, 02 Jun 2019 22:22:20: 36000000 INFO @ Sun, 02 Jun 2019 22:22:21: 41000000 INFO @ Sun, 02 Jun 2019 22:22:26: 38000000 INFO @ Sun, 02 Jun 2019 22:22:35: 37000000 INFO @ Sun, 02 Jun 2019 22:22:35: 42000000 INFO @ Sun, 02 Jun 2019 22:22:39: 39000000 INFO @ Sun, 02 Jun 2019 22:22:49: 43000000 INFO @ Sun, 02 Jun 2019 22:22:49: 38000000 INFO @ Sun, 02 Jun 2019 22:22:53: 40000000 INFO @ Sun, 02 Jun 2019 22:22:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:22:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:22:58: #1 total tags in treatment: 19037954 INFO @ Sun, 02 Jun 2019 22:22:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:22:58: #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 22:22:59: #1 tags after filtering in treatment: 17143045 INFO @ Sun, 02 Jun 2019 22:22:59: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 22:22:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:22:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:23:01: #2 number of paired peaks: 317 WARNING @ Sun, 02 Jun 2019 22:23:01: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sun, 02 Jun 2019 22:23:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:23:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:23:02: end of X-cor INFO @ Sun, 02 Jun 2019 22:23:02: #2 finished! INFO @ Sun, 02 Jun 2019 22:23:02: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 22:23:02: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Sun, 02 Jun 2019 22:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05_model.r INFO @ Sun, 02 Jun 2019 22:23:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:23:03: 39000000 INFO @ Sun, 02 Jun 2019 22:23:09: 41000000 INFO @ Sun, 02 Jun 2019 22:23:16: 40000000 INFO @ Sun, 02 Jun 2019 22:23:23: 42000000 INFO @ Sun, 02 Jun 2019 22:23:30: 41000000 INFO @ Sun, 02 Jun 2019 22:23:40: 43000000 INFO @ Sun, 02 Jun 2019 22:23:43: 42000000 INFO @ Sun, 02 Jun 2019 22:23:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:23:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:23:50: #1 total tags in treatment: 19037954 INFO @ Sun, 02 Jun 2019 22:23:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:23:50: #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 22:23:51: #1 tags after filtering in treatment: 17143045 INFO @ Sun, 02 Jun 2019 22:23:51: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 22:23:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:23:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:23:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:23:53: #2 number of paired peaks: 317 WARNING @ Sun, 02 Jun 2019 22:23:53: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sun, 02 Jun 2019 22:23:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:23:53: start X-correlation... INFO @ Sun, 02 Jun 2019 22:23:53: end of X-cor INFO @ Sun, 02 Jun 2019 22:23:53: #2 finished! INFO @ Sun, 02 Jun 2019 22:23:53: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 22:23:53: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Sun, 02 Jun 2019 22:23:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10_model.r INFO @ Sun, 02 Jun 2019 22:23:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:23:56: 43000000 INFO @ Sun, 02 Jun 2019 22:24:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:24:06: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:24:06: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:24:06: #1 total tags in treatment: 19037954 INFO @ Sun, 02 Jun 2019 22:24:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:24:06: #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 22:24:07: #1 tags after filtering in treatment: 17143045 INFO @ Sun, 02 Jun 2019 22:24:07: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 22:24:07: #1 finished! INFO @ Sun, 02 Jun 2019 22:24:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:24:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:24:09: #2 number of paired peaks: 317 WARNING @ Sun, 02 Jun 2019 22:24:09: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Sun, 02 Jun 2019 22:24:09: start model_add_line... INFO @ Sun, 02 Jun 2019 22:24:09: start X-correlation... INFO @ Sun, 02 Jun 2019 22:24:09: end of X-cor INFO @ Sun, 02 Jun 2019 22:24:09: #2 finished! INFO @ Sun, 02 Jun 2019 22:24:09: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 22:24:09: #2 alternative fragment length(s) may be 3,122,143 bps INFO @ Sun, 02 Jun 2019 22:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20_model.r INFO @ Sun, 02 Jun 2019 22:24:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:24:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.05_summits.bed INFO @ Sun, 02 Jun 2019 22:24:28: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (474 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:24:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:25:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.10_summits.bed INFO @ Sun, 02 Jun 2019 22:25:22: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (362 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:25:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:25:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996815/SRX4996815.20_summits.bed INFO @ Sun, 02 Jun 2019 22:25:38: Done! pass1 - making usageList (6 chroms): 2 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。