Job ID = 1291851 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,010,900 reads read : 23,010,900 reads written : 23,010,900 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: 00:04:47 23010900 reads; of these: 23010900 (100.00%) were unpaired; of these: 1928914 (8.38%) aligned 0 times 17586720 (76.43%) aligned exactly 1 time 3495266 (15.19%) aligned >1 times 91.62% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 8 files... [bam_rmdupse_core] 4390317 / 21081986 = 0.2082 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 17:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.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 17:07:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:07:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.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 17:07:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:07:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.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 17:07:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:07:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:07:39: 1000000 INFO @ Sun, 02 Jun 2019 17:07:39: 1000000 INFO @ Sun, 02 Jun 2019 17:07:41: 1000000 INFO @ Sun, 02 Jun 2019 17:07:45: 2000000 INFO @ Sun, 02 Jun 2019 17:07:47: 2000000 INFO @ Sun, 02 Jun 2019 17:07:49: 2000000 INFO @ Sun, 02 Jun 2019 17:07:52: 3000000 INFO @ Sun, 02 Jun 2019 17:07:54: 3000000 INFO @ Sun, 02 Jun 2019 17:07:57: 3000000 INFO @ Sun, 02 Jun 2019 17:07:59: 4000000 INFO @ Sun, 02 Jun 2019 17:08:01: 4000000 INFO @ Sun, 02 Jun 2019 17:08:05: 5000000 INFO @ Sun, 02 Jun 2019 17:08:06: 4000000 INFO @ Sun, 02 Jun 2019 17:08:08: 5000000 INFO @ Sun, 02 Jun 2019 17:08:11: 6000000 INFO @ Sun, 02 Jun 2019 17:08:14: 5000000 INFO @ Sun, 02 Jun 2019 17:08:15: 6000000 INFO @ Sun, 02 Jun 2019 17:08:18: 7000000 INFO @ Sun, 02 Jun 2019 17:08:22: 7000000 INFO @ Sun, 02 Jun 2019 17:08:22: 6000000 INFO @ Sun, 02 Jun 2019 17:08:24: 8000000 INFO @ Sun, 02 Jun 2019 17:08:29: 8000000 INFO @ Sun, 02 Jun 2019 17:08:30: 7000000 INFO @ Sun, 02 Jun 2019 17:08:31: 9000000 INFO @ Sun, 02 Jun 2019 17:08:36: 9000000 INFO @ Sun, 02 Jun 2019 17:08:37: 10000000 INFO @ Sun, 02 Jun 2019 17:08:38: 8000000 INFO @ Sun, 02 Jun 2019 17:08:42: 10000000 INFO @ Sun, 02 Jun 2019 17:08:44: 11000000 INFO @ Sun, 02 Jun 2019 17:08:46: 9000000 INFO @ Sun, 02 Jun 2019 17:08:49: 11000000 INFO @ Sun, 02 Jun 2019 17:08:50: 12000000 INFO @ Sun, 02 Jun 2019 17:08:54: 10000000 INFO @ Sun, 02 Jun 2019 17:08:56: 12000000 INFO @ Sun, 02 Jun 2019 17:08:57: 13000000 INFO @ Sun, 02 Jun 2019 17:09:02: 11000000 INFO @ Sun, 02 Jun 2019 17:09:03: 13000000 INFO @ Sun, 02 Jun 2019 17:09:03: 14000000 INFO @ Sun, 02 Jun 2019 17:09:10: 15000000 INFO @ Sun, 02 Jun 2019 17:09:10: 14000000 INFO @ Sun, 02 Jun 2019 17:09:10: 12000000 INFO @ Sun, 02 Jun 2019 17:09:16: 16000000 INFO @ Sun, 02 Jun 2019 17:09:17: 15000000 INFO @ Sun, 02 Jun 2019 17:09:19: 13000000 INFO @ Sun, 02 Jun 2019 17:09:21: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:09:21: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:09:21: #1 total tags in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:09:21: #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 17:09:21: #1 tags after filtering in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:09:21: #1 finished! INFO @ Sun, 02 Jun 2019 17:09:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:09:23: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 17:09:23: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 17:09:23: start model_add_line... INFO @ Sun, 02 Jun 2019 17:09:23: start X-correlation... INFO @ Sun, 02 Jun 2019 17:09:23: end of X-cor INFO @ Sun, 02 Jun 2019 17:09:23: #2 finished! INFO @ Sun, 02 Jun 2019 17:09:23: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 17:09:23: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 02 Jun 2019 17:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05_model.r WARNING @ Sun, 02 Jun 2019 17:09:23: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:09:23: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 02 Jun 2019 17:09:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:09:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:09:24: 16000000 INFO @ Sun, 02 Jun 2019 17:09:27: 14000000 INFO @ Sun, 02 Jun 2019 17:09:29: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:09:29: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:09:29: #1 total tags in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:09:29: #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 17:09:30: #1 tags after filtering in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:09:30: #1 finished! INFO @ Sun, 02 Jun 2019 17:09:30: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:09:31: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 17:09:31: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 17:09:31: start model_add_line... INFO @ Sun, 02 Jun 2019 17:09:31: start X-correlation... INFO @ Sun, 02 Jun 2019 17:09:31: end of X-cor INFO @ Sun, 02 Jun 2019 17:09:31: #2 finished! INFO @ Sun, 02 Jun 2019 17:09:31: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 17:09:31: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 02 Jun 2019 17:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20_model.r WARNING @ Sun, 02 Jun 2019 17:09:31: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:09:31: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 02 Jun 2019 17:09:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:09:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:09:34: 15000000 INFO @ Sun, 02 Jun 2019 17:09:42: 16000000 INFO @ Sun, 02 Jun 2019 17:09:48: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 17:09:48: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 17:09:48: #1 total tags in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:09:48: #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 17:09:48: #1 tags after filtering in treatment: 16691669 INFO @ Sun, 02 Jun 2019 17:09:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:09:48: #1 finished! INFO @ Sun, 02 Jun 2019 17:09:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:09:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:09:50: #2 number of paired peaks: 290 WARNING @ Sun, 02 Jun 2019 17:09:50: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sun, 02 Jun 2019 17:09:50: start model_add_line... INFO @ Sun, 02 Jun 2019 17:09:50: start X-correlation... INFO @ Sun, 02 Jun 2019 17:09:50: end of X-cor INFO @ Sun, 02 Jun 2019 17:09:50: #2 finished! INFO @ Sun, 02 Jun 2019 17:09:50: #2 predicted fragment length is 42 bps INFO @ Sun, 02 Jun 2019 17:09:50: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 02 Jun 2019 17:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10_model.r WARNING @ Sun, 02 Jun 2019 17:09:50: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:09:50: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 02 Jun 2019 17:09:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:09:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:10:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:10:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.05_summits.bed INFO @ Sun, 02 Jun 2019 17:10:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1154 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.20_summits.bed INFO @ Sun, 02 Jun 2019 17:10:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (155 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:10:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257686/SRX257686.10_summits.bed INFO @ Sun, 02 Jun 2019 17:10:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 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。