Job ID = 1292875 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,937,560 reads read : 37,875,120 reads written : 37,875,120 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: 00:20:42 18937560 reads; of these: 18937560 (100.00%) were paired; of these: 2052367 (10.84%) aligned concordantly 0 times 14266433 (75.33%) aligned concordantly exactly 1 time 2618760 (13.83%) aligned concordantly >1 times ---- 2052367 pairs aligned concordantly 0 times; of these: 646583 (31.50%) aligned discordantly 1 time ---- 1405784 pairs aligned 0 times concordantly or discordantly; of these: 2811568 mates make up the pairs; of these: 2324668 (82.68%) aligned 0 times 286021 (10.17%) aligned exactly 1 time 200879 (7.14%) aligned >1 times 93.86% overall alignment rate Time searching: 00:20:42 Overall time: 00:20:42 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 16 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] 2030123 / 17522505 = 0.1159 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 21:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.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 21:36:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.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 21:36:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.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 21:36:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:32: 1000000 INFO @ Sun, 02 Jun 2019 21:36:33: 1000000 INFO @ Sun, 02 Jun 2019 21:36:34: 1000000 INFO @ Sun, 02 Jun 2019 21:36:39: 2000000 INFO @ Sun, 02 Jun 2019 21:36:42: 2000000 INFO @ Sun, 02 Jun 2019 21:36:42: 2000000 INFO @ Sun, 02 Jun 2019 21:36:45: 3000000 INFO @ Sun, 02 Jun 2019 21:36:49: 3000000 INFO @ Sun, 02 Jun 2019 21:36:51: 3000000 INFO @ Sun, 02 Jun 2019 21:36:52: 4000000 INFO @ Sun, 02 Jun 2019 21:36:57: 4000000 INFO @ Sun, 02 Jun 2019 21:36:59: 5000000 INFO @ Sun, 02 Jun 2019 21:36:59: 4000000 INFO @ Sun, 02 Jun 2019 21:37:05: 5000000 INFO @ Sun, 02 Jun 2019 21:37:06: 6000000 INFO @ Sun, 02 Jun 2019 21:37:07: 5000000 INFO @ Sun, 02 Jun 2019 21:37:12: 7000000 INFO @ Sun, 02 Jun 2019 21:37:13: 6000000 INFO @ Sun, 02 Jun 2019 21:37:15: 6000000 INFO @ Sun, 02 Jun 2019 21:37:19: 8000000 INFO @ Sun, 02 Jun 2019 21:37:21: 7000000 INFO @ Sun, 02 Jun 2019 21:37:23: 7000000 INFO @ Sun, 02 Jun 2019 21:37:26: 9000000 INFO @ Sun, 02 Jun 2019 21:37:29: 8000000 INFO @ Sun, 02 Jun 2019 21:37:31: 8000000 INFO @ Sun, 02 Jun 2019 21:37:32: 10000000 INFO @ Sun, 02 Jun 2019 21:37:37: 9000000 INFO @ Sun, 02 Jun 2019 21:37:38: 11000000 INFO @ Sun, 02 Jun 2019 21:37:38: 9000000 INFO @ Sun, 02 Jun 2019 21:37:44: 10000000 INFO @ Sun, 02 Jun 2019 21:37:45: 12000000 INFO @ Sun, 02 Jun 2019 21:37:46: 10000000 INFO @ Sun, 02 Jun 2019 21:37:51: 13000000 INFO @ Sun, 02 Jun 2019 21:37:52: 11000000 INFO @ Sun, 02 Jun 2019 21:37:54: 11000000 INFO @ Sun, 02 Jun 2019 21:37:58: 14000000 INFO @ Sun, 02 Jun 2019 21:38:00: 12000000 INFO @ Sun, 02 Jun 2019 21:38:01: 12000000 INFO @ Sun, 02 Jun 2019 21:38:04: 15000000 INFO @ Sun, 02 Jun 2019 21:38:08: 13000000 INFO @ Sun, 02 Jun 2019 21:38:09: 13000000 INFO @ Sun, 02 Jun 2019 21:38:11: 16000000 INFO @ Sun, 02 Jun 2019 21:38:16: 14000000 INFO @ Sun, 02 Jun 2019 21:38:17: 14000000 INFO @ Sun, 02 Jun 2019 21:38:17: 17000000 INFO @ Sun, 02 Jun 2019 21:38:23: 15000000 INFO @ Sun, 02 Jun 2019 21:38:24: 18000000 INFO @ Sun, 02 Jun 2019 21:38:24: 15000000 INFO @ Sun, 02 Jun 2019 21:38:30: 19000000 INFO @ Sun, 02 Jun 2019 21:38:31: 16000000 INFO @ Sun, 02 Jun 2019 21:38:32: 16000000 INFO @ Sun, 02 Jun 2019 21:38:37: 20000000 INFO @ Sun, 02 Jun 2019 21:38:39: 17000000 INFO @ Sun, 02 Jun 2019 21:38:39: 17000000 INFO @ Sun, 02 Jun 2019 21:38:43: 21000000 INFO @ Sun, 02 Jun 2019 21:38:47: 18000000 INFO @ Sun, 02 Jun 2019 21:38:47: 18000000 INFO @ Sun, 02 Jun 2019 21:38:50: 22000000 INFO @ Sun, 02 Jun 2019 21:38:54: 19000000 INFO @ Sun, 02 Jun 2019 21:38:55: 19000000 INFO @ Sun, 02 Jun 2019 21:38:56: 23000000 INFO @ Sun, 02 Jun 2019 21:39:01: 20000000 INFO @ Sun, 02 Jun 2019 21:39:03: 24000000 INFO @ Sun, 02 Jun 2019 21:39:03: 20000000 INFO @ Sun, 02 Jun 2019 21:39:08: 21000000 INFO @ Sun, 02 Jun 2019 21:39:09: 25000000 INFO @ Sun, 02 Jun 2019 21:39:11: 21000000 INFO @ Sun, 02 Jun 2019 21:39:15: 22000000 INFO @ Sun, 02 Jun 2019 21:39:16: 26000000 INFO @ Sun, 02 Jun 2019 21:39:19: 22000000 INFO @ Sun, 02 Jun 2019 21:39:22: 27000000 INFO @ Sun, 02 Jun 2019 21:39:22: 23000000 INFO @ Sun, 02 Jun 2019 21:39:26: 23000000 INFO @ Sun, 02 Jun 2019 21:39:29: 28000000 INFO @ Sun, 02 Jun 2019 21:39:30: 24000000 INFO @ Sun, 02 Jun 2019 21:39:34: 24000000 INFO @ Sun, 02 Jun 2019 21:39:35: 29000000 INFO @ Sun, 02 Jun 2019 21:39:37: 25000000 INFO @ Sun, 02 Jun 2019 21:39:41: 30000000 INFO @ Sun, 02 Jun 2019 21:39:42: 25000000 INFO @ Sun, 02 Jun 2019 21:39:44: 26000000 INFO @ Sun, 02 Jun 2019 21:39:48: 31000000 INFO @ Sun, 02 Jun 2019 21:39:49: 26000000 INFO @ Sun, 02 Jun 2019 21:39:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:39:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:39:51: #1 total tags in treatment: 14880582 INFO @ Sun, 02 Jun 2019 21:39:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:51: #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 21:39:51: 27000000 INFO @ Sun, 02 Jun 2019 21:39:52: #1 tags after filtering in treatment: 13620123 INFO @ Sun, 02 Jun 2019 21:39:52: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:39:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:53: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 21:39:53: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:53: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:53: #2 predicted fragment length is 143 bps INFO @ Sun, 02 Jun 2019 21:39:53: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 02 Jun 2019 21:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05_model.r INFO @ Sun, 02 Jun 2019 21:39:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:57: 27000000 INFO @ Sun, 02 Jun 2019 21:39:58: 28000000 INFO @ Sun, 02 Jun 2019 21:40:04: 28000000 INFO @ Sun, 02 Jun 2019 21:40:05: 29000000 INFO @ Sun, 02 Jun 2019 21:40:12: 29000000 INFO @ Sun, 02 Jun 2019 21:40:13: 30000000 INFO @ Sun, 02 Jun 2019 21:40:19: 30000000 INFO @ Sun, 02 Jun 2019 21:40:20: 31000000 INFO @ Sun, 02 Jun 2019 21:40:23: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:40:23: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:40:23: #1 total tags in treatment: 14880582 INFO @ Sun, 02 Jun 2019 21:40:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:40:23: #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 21:40:24: #1 tags after filtering in treatment: 13620123 INFO @ Sun, 02 Jun 2019 21:40:24: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:40:24: #1 finished! INFO @ Sun, 02 Jun 2019 21:40:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:40:25: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 21:40:25: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 21:40:25: start model_add_line... INFO @ Sun, 02 Jun 2019 21:40:25: start X-correlation... INFO @ Sun, 02 Jun 2019 21:40:25: end of X-cor INFO @ Sun, 02 Jun 2019 21:40:25: #2 finished! INFO @ Sun, 02 Jun 2019 21:40:25: #2 predicted fragment length is 143 bps INFO @ Sun, 02 Jun 2019 21:40:25: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 02 Jun 2019 21:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20_model.r INFO @ Sun, 02 Jun 2019 21:40:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:40:27: 31000000 INFO @ Sun, 02 Jun 2019 21:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:30: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:40:30: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:40:30: #1 total tags in treatment: 14880582 INFO @ Sun, 02 Jun 2019 21:40:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:40:30: #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 21:40:31: #1 tags after filtering in treatment: 13620123 INFO @ Sun, 02 Jun 2019 21:40:31: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:40:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:40:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:40:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:40:32: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 21:40:32: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 21:40:32: start model_add_line... INFO @ Sun, 02 Jun 2019 21:40:32: start X-correlation... INFO @ Sun, 02 Jun 2019 21:40:32: end of X-cor INFO @ Sun, 02 Jun 2019 21:40:32: #2 finished! INFO @ Sun, 02 Jun 2019 21:40:32: #2 predicted fragment length is 143 bps INFO @ Sun, 02 Jun 2019 21:40:32: #2 alternative fragment length(s) may be 4,143 bps INFO @ Sun, 02 Jun 2019 21:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10_model.r INFO @ Sun, 02 Jun 2019 21:40:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:40:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.05_summits.bed INFO @ Sun, 02 Jun 2019 21:40:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (457 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:41:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:41:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.20_summits.bed INFO @ Sun, 02 Jun 2019 21:41:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996806/SRX4996806.10_summits.bed INFO @ Sun, 02 Jun 2019 21:41:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (350 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。