Job ID = 1293032 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,421,054 reads read : 20,421,054 reads written : 20,421,054 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:00 20421054 reads; of these: 20421054 (100.00%) were unpaired; of these: 196286 (0.96%) aligned 0 times 16681418 (81.69%) aligned exactly 1 time 3543350 (17.35%) aligned >1 times 99.04% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 2102351 / 20224768 = 0.1039 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 21:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.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 21:37:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.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 21:37:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.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 21:37:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:37:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:38:04: 1000000 INFO @ Sun, 02 Jun 2019 21:38:05: 1000000 INFO @ Sun, 02 Jun 2019 21:38:05: 1000000 INFO @ Sun, 02 Jun 2019 21:38:10: 2000000 INFO @ Sun, 02 Jun 2019 21:38:12: 2000000 INFO @ Sun, 02 Jun 2019 21:38:12: 2000000 INFO @ Sun, 02 Jun 2019 21:38:16: 3000000 INFO @ Sun, 02 Jun 2019 21:38:19: 3000000 INFO @ Sun, 02 Jun 2019 21:38:19: 3000000 INFO @ Sun, 02 Jun 2019 21:38:23: 4000000 INFO @ Sun, 02 Jun 2019 21:38:26: 4000000 INFO @ Sun, 02 Jun 2019 21:38:26: 4000000 INFO @ Sun, 02 Jun 2019 21:38:29: 5000000 INFO @ Sun, 02 Jun 2019 21:38:32: 5000000 INFO @ Sun, 02 Jun 2019 21:38:34: 5000000 INFO @ Sun, 02 Jun 2019 21:38:35: 6000000 INFO @ Sun, 02 Jun 2019 21:38:39: 6000000 INFO @ Sun, 02 Jun 2019 21:38:42: 7000000 INFO @ Sun, 02 Jun 2019 21:38:42: 6000000 INFO @ Sun, 02 Jun 2019 21:38:46: 7000000 INFO @ Sun, 02 Jun 2019 21:38:48: 8000000 INFO @ Sun, 02 Jun 2019 21:38:50: 7000000 INFO @ Sun, 02 Jun 2019 21:38:53: 8000000 INFO @ Sun, 02 Jun 2019 21:38:55: 9000000 INFO @ Sun, 02 Jun 2019 21:38:57: 8000000 INFO @ Sun, 02 Jun 2019 21:39:00: 9000000 INFO @ Sun, 02 Jun 2019 21:39:01: 10000000 INFO @ Sun, 02 Jun 2019 21:39:04: 9000000 INFO @ Sun, 02 Jun 2019 21:39:06: 10000000 INFO @ Sun, 02 Jun 2019 21:39:07: 11000000 INFO @ Sun, 02 Jun 2019 21:39:11: 10000000 INFO @ Sun, 02 Jun 2019 21:39:13: 11000000 INFO @ Sun, 02 Jun 2019 21:39:14: 12000000 INFO @ Sun, 02 Jun 2019 21:39:18: 11000000 INFO @ Sun, 02 Jun 2019 21:39:20: 12000000 INFO @ Sun, 02 Jun 2019 21:39:20: 13000000 INFO @ Sun, 02 Jun 2019 21:39:24: 12000000 INFO @ Sun, 02 Jun 2019 21:39:26: 14000000 INFO @ Sun, 02 Jun 2019 21:39:27: 13000000 INFO @ Sun, 02 Jun 2019 21:39:31: 13000000 INFO @ Sun, 02 Jun 2019 21:39:32: 15000000 INFO @ Sun, 02 Jun 2019 21:39:33: 14000000 INFO @ Sun, 02 Jun 2019 21:39:38: 14000000 INFO @ Sun, 02 Jun 2019 21:39:39: 16000000 INFO @ Sun, 02 Jun 2019 21:39:40: 15000000 INFO @ Sun, 02 Jun 2019 21:39:45: 15000000 INFO @ Sun, 02 Jun 2019 21:39:45: 17000000 INFO @ Sun, 02 Jun 2019 21:39:47: 16000000 INFO @ Sun, 02 Jun 2019 21:39:51: 18000000 INFO @ Sun, 02 Jun 2019 21:39:52: 16000000 INFO @ Sun, 02 Jun 2019 21:39:52: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:52: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:52: #1 total tags in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:39:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:52: #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 21:39:53: #1 tags after filtering in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:54: 17000000 INFO @ Sun, 02 Jun 2019 21:39:54: #2 number of paired peaks: 244 WARNING @ Sun, 02 Jun 2019 21:39:54: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:54: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 21:39:54: #2 alternative fragment length(s) may be 1,41,584 bps INFO @ Sun, 02 Jun 2019 21:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20_model.r WARNING @ Sun, 02 Jun 2019 21:39:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:39:54: #2 You may need to consider one of the other alternative d(s): 1,41,584 WARNING @ Sun, 02 Jun 2019 21:39:54: #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 21:39:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:40:00: 17000000 INFO @ Sun, 02 Jun 2019 21:40:00: 18000000 INFO @ Sun, 02 Jun 2019 21:40:01: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:40:01: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:40:01: #1 total tags in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:40:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:40:01: #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 21:40:02: #1 tags after filtering in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:40:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:40:02: #1 finished! INFO @ Sun, 02 Jun 2019 21:40:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:40:03: #2 number of paired peaks: 244 WARNING @ Sun, 02 Jun 2019 21:40:03: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 02 Jun 2019 21:40:03: start model_add_line... INFO @ Sun, 02 Jun 2019 21:40:03: start X-correlation... INFO @ Sun, 02 Jun 2019 21:40:03: end of X-cor INFO @ Sun, 02 Jun 2019 21:40:03: #2 finished! INFO @ Sun, 02 Jun 2019 21:40:03: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 21:40:03: #2 alternative fragment length(s) may be 1,41,584 bps INFO @ Sun, 02 Jun 2019 21:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10_model.r WARNING @ Sun, 02 Jun 2019 21:40:03: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:40:03: #2 You may need to consider one of the other alternative d(s): 1,41,584 WARNING @ Sun, 02 Jun 2019 21:40:03: #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 21:40:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:40:07: 18000000 INFO @ Sun, 02 Jun 2019 21:40:08: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:40:08: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:40:08: #1 total tags in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:40:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:40:08: #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 21:40:08: #1 tags after filtering in treatment: 18122417 INFO @ Sun, 02 Jun 2019 21:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:40:08: #1 finished! INFO @ Sun, 02 Jun 2019 21:40:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:40:09: #2 number of paired peaks: 244 WARNING @ Sun, 02 Jun 2019 21:40:09: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Sun, 02 Jun 2019 21:40:09: start model_add_line... INFO @ Sun, 02 Jun 2019 21:40:10: start X-correlation... INFO @ Sun, 02 Jun 2019 21:40:10: end of X-cor INFO @ Sun, 02 Jun 2019 21:40:10: #2 finished! INFO @ Sun, 02 Jun 2019 21:40:10: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 21:40:10: #2 alternative fragment length(s) may be 1,41,584 bps INFO @ Sun, 02 Jun 2019 21:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05_model.r WARNING @ Sun, 02 Jun 2019 21:40:10: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:40:10: #2 You may need to consider one of the other alternative d(s): 1,41,584 WARNING @ Sun, 02 Jun 2019 21:40:10: #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 21:40:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:40:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:40:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.20_summits.bed INFO @ Sun, 02 Jun 2019 21:40:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.10_summits.bed INFO @ Sun, 02 Jun 2019 21:41:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:41:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:41:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:41:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020798/SRX5020798.05_summits.bed INFO @ Sun, 02 Jun 2019 21:41:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (726 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。