Job ID = 1291691 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,546,628 reads read : 28,546,628 reads written : 28,546,628 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: 00:05:58 28546628 reads; of these: 28546628 (100.00%) were unpaired; of these: 3926492 (13.75%) aligned 0 times 21690498 (75.98%) aligned exactly 1 time 2929638 (10.26%) aligned >1 times 86.25% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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 12 files... [bam_rmdupse_core] 5921061 / 24620136 = 0.2405 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 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.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 16:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.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 16:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.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 16:30:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:30:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:30:15: 1000000 INFO @ Sun, 02 Jun 2019 16:30:15: 1000000 INFO @ Sun, 02 Jun 2019 16:30:16: 1000000 INFO @ Sun, 02 Jun 2019 16:30:23: 2000000 INFO @ Sun, 02 Jun 2019 16:30:23: 2000000 INFO @ Sun, 02 Jun 2019 16:30:25: 2000000 INFO @ Sun, 02 Jun 2019 16:30:31: 3000000 INFO @ Sun, 02 Jun 2019 16:30:31: 3000000 INFO @ Sun, 02 Jun 2019 16:30:34: 3000000 INFO @ Sun, 02 Jun 2019 16:30:39: 4000000 INFO @ Sun, 02 Jun 2019 16:30:40: 4000000 INFO @ Sun, 02 Jun 2019 16:30:44: 4000000 INFO @ Sun, 02 Jun 2019 16:30:47: 5000000 INFO @ Sun, 02 Jun 2019 16:30:48: 5000000 INFO @ Sun, 02 Jun 2019 16:30:53: 5000000 INFO @ Sun, 02 Jun 2019 16:30:56: 6000000 INFO @ Sun, 02 Jun 2019 16:30:56: 6000000 INFO @ Sun, 02 Jun 2019 16:31:02: 6000000 INFO @ Sun, 02 Jun 2019 16:31:04: 7000000 INFO @ Sun, 02 Jun 2019 16:31:04: 7000000 INFO @ Sun, 02 Jun 2019 16:31:11: 7000000 INFO @ Sun, 02 Jun 2019 16:31:12: 8000000 INFO @ Sun, 02 Jun 2019 16:31:13: 8000000 INFO @ Sun, 02 Jun 2019 16:31:20: 9000000 INFO @ Sun, 02 Jun 2019 16:31:21: 8000000 INFO @ Sun, 02 Jun 2019 16:31:21: 9000000 INFO @ Sun, 02 Jun 2019 16:31:28: 10000000 INFO @ Sun, 02 Jun 2019 16:31:29: 10000000 INFO @ Sun, 02 Jun 2019 16:31:30: 9000000 INFO @ Sun, 02 Jun 2019 16:31:36: 11000000 INFO @ Sun, 02 Jun 2019 16:31:37: 11000000 INFO @ Sun, 02 Jun 2019 16:31:39: 10000000 INFO @ Sun, 02 Jun 2019 16:31:44: 12000000 INFO @ Sun, 02 Jun 2019 16:31:45: 12000000 INFO @ Sun, 02 Jun 2019 16:31:48: 11000000 INFO @ Sun, 02 Jun 2019 16:31:52: 13000000 INFO @ Sun, 02 Jun 2019 16:31:53: 13000000 INFO @ Sun, 02 Jun 2019 16:31:58: 12000000 INFO @ Sun, 02 Jun 2019 16:32:00: 14000000 INFO @ Sun, 02 Jun 2019 16:32:02: 14000000 INFO @ Sun, 02 Jun 2019 16:32:08: 13000000 INFO @ Sun, 02 Jun 2019 16:32:08: 15000000 INFO @ Sun, 02 Jun 2019 16:32:10: 15000000 INFO @ Sun, 02 Jun 2019 16:32:17: 16000000 INFO @ Sun, 02 Jun 2019 16:32:17: 14000000 INFO @ Sun, 02 Jun 2019 16:32:18: 16000000 INFO @ Sun, 02 Jun 2019 16:32:25: 17000000 INFO @ Sun, 02 Jun 2019 16:32:27: 17000000 INFO @ Sun, 02 Jun 2019 16:32:27: 15000000 INFO @ Sun, 02 Jun 2019 16:32:33: 18000000 INFO @ Sun, 02 Jun 2019 16:32:35: 18000000 INFO @ Sun, 02 Jun 2019 16:32:37: 16000000 INFO @ Sun, 02 Jun 2019 16:32:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:32:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:32:38: #1 total tags in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:32:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:32:38: #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 16:32:39: #1 tags after filtering in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:32:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:32:39: #1 finished! INFO @ Sun, 02 Jun 2019 16:32:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:32:40: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 16:32:40: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 16:32:40: start model_add_line... INFO @ Sun, 02 Jun 2019 16:32:41: start X-correlation... INFO @ Sun, 02 Jun 2019 16:32:41: end of X-cor INFO @ Sun, 02 Jun 2019 16:32:41: #2 finished! INFO @ Sun, 02 Jun 2019 16:32:41: #2 predicted fragment length is 118 bps INFO @ Sun, 02 Jun 2019 16:32:41: #2 alternative fragment length(s) may be 3,118 bps INFO @ Sun, 02 Jun 2019 16:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10_model.r INFO @ Sun, 02 Jun 2019 16:32:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:32:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:32:41: #1 total tags in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:32:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:32:41: #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 16:32:41: #1 tags after filtering in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:32:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:32:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:32:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:32:43: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 16:32:43: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 16:32:43: start model_add_line... INFO @ Sun, 02 Jun 2019 16:32:43: start X-correlation... INFO @ Sun, 02 Jun 2019 16:32:43: end of X-cor INFO @ Sun, 02 Jun 2019 16:32:43: #2 finished! INFO @ Sun, 02 Jun 2019 16:32:43: #2 predicted fragment length is 118 bps INFO @ Sun, 02 Jun 2019 16:32:43: #2 alternative fragment length(s) may be 3,118 bps INFO @ Sun, 02 Jun 2019 16:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20_model.r INFO @ Sun, 02 Jun 2019 16:32:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:47: 17000000 INFO @ Sun, 02 Jun 2019 16:32:57: 18000000 INFO @ Sun, 02 Jun 2019 16:33:03: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:33:03: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:33:03: #1 total tags in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:33:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:33:03: #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 16:33:04: #1 tags after filtering in treatment: 18699075 INFO @ Sun, 02 Jun 2019 16:33:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:33:04: #1 finished! INFO @ Sun, 02 Jun 2019 16:33:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:33:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:33:05: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 16:33:05: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 16:33:05: start model_add_line... INFO @ Sun, 02 Jun 2019 16:33:05: start X-correlation... INFO @ Sun, 02 Jun 2019 16:33:05: end of X-cor INFO @ Sun, 02 Jun 2019 16:33:05: #2 finished! INFO @ Sun, 02 Jun 2019 16:33:05: #2 predicted fragment length is 118 bps INFO @ Sun, 02 Jun 2019 16:33:05: #2 alternative fragment length(s) may be 3,118 bps INFO @ Sun, 02 Jun 2019 16:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05_model.r INFO @ Sun, 02 Jun 2019 16:33:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:33:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:33:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:33:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:33:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:33:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.10_summits.bed INFO @ Sun, 02 Jun 2019 16:33:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2155 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.20_summits.bed INFO @ Sun, 02 Jun 2019 16:33:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:33:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216762/SRX216762.05_summits.bed INFO @ Sun, 02 Jun 2019 16:34:15: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4053 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。