Job ID = 1292525 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,509,609 reads read : 21,509,609 reads written : 21,509,609 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: 00:05:03 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 256469 (1.19%) aligned 0 times 17820564 (82.85%) aligned exactly 1 time 3432576 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 3667791 / 21253140 = 0.1726 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 19:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.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 19:28:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.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 19:28:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.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 19:28:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:28:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:28:09: 1000000 INFO @ Sun, 02 Jun 2019 19:28:09: 1000000 INFO @ Sun, 02 Jun 2019 19:28:10: 1000000 INFO @ Sun, 02 Jun 2019 19:28:15: 2000000 INFO @ Sun, 02 Jun 2019 19:28:16: 2000000 INFO @ Sun, 02 Jun 2019 19:28:18: 2000000 INFO @ Sun, 02 Jun 2019 19:28:22: 3000000 INFO @ Sun, 02 Jun 2019 19:28:23: 3000000 INFO @ Sun, 02 Jun 2019 19:28:26: 3000000 INFO @ Sun, 02 Jun 2019 19:28:29: 4000000 INFO @ Sun, 02 Jun 2019 19:28:30: 4000000 INFO @ Sun, 02 Jun 2019 19:28:34: 4000000 INFO @ Sun, 02 Jun 2019 19:28:36: 5000000 INFO @ Sun, 02 Jun 2019 19:28:37: 5000000 INFO @ Sun, 02 Jun 2019 19:28:42: 5000000 INFO @ Sun, 02 Jun 2019 19:28:42: 6000000 INFO @ Sun, 02 Jun 2019 19:28:44: 6000000 INFO @ Sun, 02 Jun 2019 19:28:49: 7000000 INFO @ Sun, 02 Jun 2019 19:28:49: 6000000 INFO @ Sun, 02 Jun 2019 19:28:51: 7000000 INFO @ Sun, 02 Jun 2019 19:28:56: 8000000 INFO @ Sun, 02 Jun 2019 19:28:57: 7000000 INFO @ Sun, 02 Jun 2019 19:28:59: 8000000 INFO @ Sun, 02 Jun 2019 19:29:03: 9000000 INFO @ Sun, 02 Jun 2019 19:29:05: 8000000 INFO @ Sun, 02 Jun 2019 19:29:06: 9000000 INFO @ Sun, 02 Jun 2019 19:29:09: 10000000 INFO @ Sun, 02 Jun 2019 19:29:12: 9000000 INFO @ Sun, 02 Jun 2019 19:29:12: 10000000 INFO @ Sun, 02 Jun 2019 19:29:17: 11000000 INFO @ Sun, 02 Jun 2019 19:29:19: 11000000 INFO @ Sun, 02 Jun 2019 19:29:20: 10000000 INFO @ Sun, 02 Jun 2019 19:29:25: 12000000 INFO @ Sun, 02 Jun 2019 19:29:26: 12000000 INFO @ Sun, 02 Jun 2019 19:29:27: 11000000 INFO @ Sun, 02 Jun 2019 19:29:32: 13000000 INFO @ Sun, 02 Jun 2019 19:29:33: 13000000 INFO @ Sun, 02 Jun 2019 19:29:34: 12000000 INFO @ Sun, 02 Jun 2019 19:29:39: 14000000 INFO @ Sun, 02 Jun 2019 19:29:40: 14000000 INFO @ Sun, 02 Jun 2019 19:29:42: 13000000 INFO @ Sun, 02 Jun 2019 19:29:47: 15000000 INFO @ Sun, 02 Jun 2019 19:29:48: 15000000 INFO @ Sun, 02 Jun 2019 19:29:49: 14000000 INFO @ Sun, 02 Jun 2019 19:29:54: 16000000 INFO @ Sun, 02 Jun 2019 19:29:55: 16000000 INFO @ Sun, 02 Jun 2019 19:29:56: 15000000 INFO @ Sun, 02 Jun 2019 19:30:01: 17000000 INFO @ Sun, 02 Jun 2019 19:30:03: 17000000 INFO @ Sun, 02 Jun 2019 19:30:04: 16000000 INFO @ Sun, 02 Jun 2019 19:30:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:30:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:30:05: #1 total tags in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:30:05: #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 19:30:05: #1 tags after filtering in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:30:05: #1 finished! INFO @ Sun, 02 Jun 2019 19:30:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:30:07: #2 number of paired peaks: 204 WARNING @ Sun, 02 Jun 2019 19:30:07: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 02 Jun 2019 19:30:07: start model_add_line... INFO @ Sun, 02 Jun 2019 19:30:07: start X-correlation... INFO @ Sun, 02 Jun 2019 19:30:07: end of X-cor INFO @ Sun, 02 Jun 2019 19:30:07: #2 finished! INFO @ Sun, 02 Jun 2019 19:30:07: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:30:07: #2 alternative fragment length(s) may be 1,37,506,526,566,568 bps INFO @ Sun, 02 Jun 2019 19:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05_model.r WARNING @ Sun, 02 Jun 2019 19:30:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:30:07: #2 You may need to consider one of the other alternative d(s): 1,37,506,526,566,568 WARNING @ Sun, 02 Jun 2019 19:30:07: #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 19:30:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:30:07: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:30:07: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:30:07: #1 total tags in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:30:07: #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 19:30:08: #1 tags after filtering in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:30:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:30:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:30:09: #2 number of paired peaks: 204 WARNING @ Sun, 02 Jun 2019 19:30:09: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 02 Jun 2019 19:30:09: start model_add_line... INFO @ Sun, 02 Jun 2019 19:30:09: start X-correlation... INFO @ Sun, 02 Jun 2019 19:30:09: end of X-cor INFO @ Sun, 02 Jun 2019 19:30:09: #2 finished! INFO @ Sun, 02 Jun 2019 19:30:09: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:30:09: #2 alternative fragment length(s) may be 1,37,506,526,566,568 bps INFO @ Sun, 02 Jun 2019 19:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20_model.r WARNING @ Sun, 02 Jun 2019 19:30:09: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:30:09: #2 You may need to consider one of the other alternative d(s): 1,37,506,526,566,568 WARNING @ Sun, 02 Jun 2019 19:30:09: #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 19:30:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:30:11: 17000000 INFO @ Sun, 02 Jun 2019 19:30:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:30:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:30:15: #1 total tags in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:30:15: #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 19:30:16: #1 tags after filtering in treatment: 17585349 INFO @ Sun, 02 Jun 2019 19:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:30:16: #1 finished! INFO @ Sun, 02 Jun 2019 19:30:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:30:17: #2 number of paired peaks: 204 WARNING @ Sun, 02 Jun 2019 19:30:17: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Sun, 02 Jun 2019 19:30:17: start model_add_line... INFO @ Sun, 02 Jun 2019 19:30:17: start X-correlation... INFO @ Sun, 02 Jun 2019 19:30:17: end of X-cor INFO @ Sun, 02 Jun 2019 19:30:17: #2 finished! INFO @ Sun, 02 Jun 2019 19:30:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 19:30:17: #2 alternative fragment length(s) may be 1,37,506,526,566,568 bps INFO @ Sun, 02 Jun 2019 19:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10_model.r WARNING @ Sun, 02 Jun 2019 19:30:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:30:17: #2 You may need to consider one of the other alternative d(s): 1,37,506,526,566,568 WARNING @ Sun, 02 Jun 2019 19:30:17: #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 19:30:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:30:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:30:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:30:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.05_summits.bed INFO @ Sun, 02 Jun 2019 19:31:04: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.20_summits.bed INFO @ Sun, 02 Jun 2019 19:31:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466539/SRX466539.10_summits.bed INFO @ Sun, 02 Jun 2019 19:31:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。