Job ID = 2590208 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,310,035 reads read : 19,310,035 reads written : 19,310,035 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:59 19310035 reads; of these: 19310035 (100.00%) were unpaired; of these: 1047751 (5.43%) aligned 0 times 14912114 (77.22%) aligned exactly 1 time 3350170 (17.35%) aligned >1 times 94.57% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 1735884 / 18262284 = 0.0951 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 @ Mon, 12 Aug 2019 20:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.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 @ Mon, 12 Aug 2019 20:13:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.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 @ Mon, 12 Aug 2019 20:13:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.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 @ Mon, 12 Aug 2019 20:13:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:13:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:14:04: 1000000 INFO @ Mon, 12 Aug 2019 20:14:04: 1000000 INFO @ Mon, 12 Aug 2019 20:14:08: 1000000 INFO @ Mon, 12 Aug 2019 20:14:11: 2000000 INFO @ Mon, 12 Aug 2019 20:14:13: 2000000 INFO @ Mon, 12 Aug 2019 20:14:16: 2000000 INFO @ Mon, 12 Aug 2019 20:14:18: 3000000 INFO @ Mon, 12 Aug 2019 20:14:20: 3000000 INFO @ Mon, 12 Aug 2019 20:14:24: 3000000 INFO @ Mon, 12 Aug 2019 20:14:25: 4000000 INFO @ Mon, 12 Aug 2019 20:14:27: 4000000 INFO @ Mon, 12 Aug 2019 20:14:32: 5000000 INFO @ Mon, 12 Aug 2019 20:14:33: 4000000 INFO @ Mon, 12 Aug 2019 20:14:34: 5000000 INFO @ Mon, 12 Aug 2019 20:14:39: 6000000 INFO @ Mon, 12 Aug 2019 20:14:41: 5000000 INFO @ Mon, 12 Aug 2019 20:14:41: 6000000 INFO @ Mon, 12 Aug 2019 20:14:46: 7000000 INFO @ Mon, 12 Aug 2019 20:14:48: 7000000 INFO @ Mon, 12 Aug 2019 20:14:49: 6000000 INFO @ Mon, 12 Aug 2019 20:14:53: 8000000 INFO @ Mon, 12 Aug 2019 20:14:55: 8000000 INFO @ Mon, 12 Aug 2019 20:14:57: 7000000 INFO @ Mon, 12 Aug 2019 20:15:00: 9000000 INFO @ Mon, 12 Aug 2019 20:15:02: 9000000 INFO @ Mon, 12 Aug 2019 20:15:05: 8000000 INFO @ Mon, 12 Aug 2019 20:15:07: 10000000 INFO @ Mon, 12 Aug 2019 20:15:09: 10000000 INFO @ Mon, 12 Aug 2019 20:15:13: 9000000 INFO @ Mon, 12 Aug 2019 20:15:14: 11000000 INFO @ Mon, 12 Aug 2019 20:15:16: 11000000 INFO @ Mon, 12 Aug 2019 20:15:21: 12000000 INFO @ Mon, 12 Aug 2019 20:15:22: 10000000 INFO @ Mon, 12 Aug 2019 20:15:23: 12000000 INFO @ Mon, 12 Aug 2019 20:15:28: 13000000 INFO @ Mon, 12 Aug 2019 20:15:30: 11000000 INFO @ Mon, 12 Aug 2019 20:15:30: 13000000 INFO @ Mon, 12 Aug 2019 20:15:35: 14000000 INFO @ Mon, 12 Aug 2019 20:15:37: 14000000 INFO @ Mon, 12 Aug 2019 20:15:38: 12000000 INFO @ Mon, 12 Aug 2019 20:15:42: 15000000 INFO @ Mon, 12 Aug 2019 20:15:44: 15000000 INFO @ Mon, 12 Aug 2019 20:15:46: 13000000 INFO @ Mon, 12 Aug 2019 20:15:49: 16000000 INFO @ Mon, 12 Aug 2019 20:15:51: 16000000 INFO @ Mon, 12 Aug 2019 20:15:53: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:15:53: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:15:53: #1 total tags in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:15:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:15:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:15:53: #1 tags after filtering in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:15:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:15:53: #1 finished! INFO @ Mon, 12 Aug 2019 20:15:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:15:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:15:54: 14000000 INFO @ Mon, 12 Aug 2019 20:15:54: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:15:54: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:15:54: #1 total tags in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:15:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:15:54: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:15:54: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:15:54: start model_add_line... INFO @ Mon, 12 Aug 2019 20:15:55: #1 tags after filtering in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:15:55: #1 finished! INFO @ Mon, 12 Aug 2019 20:15:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:15:55: start X-correlation... INFO @ Mon, 12 Aug 2019 20:15:55: end of X-cor INFO @ Mon, 12 Aug 2019 20:15:55: #2 finished! INFO @ Mon, 12 Aug 2019 20:15:55: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:15:55: #2 alternative fragment length(s) may be 1,25,568,585 bps INFO @ Mon, 12 Aug 2019 20:15:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10_model.r WARNING @ Mon, 12 Aug 2019 20:15:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:15:55: #2 You may need to consider one of the other alternative d(s): 1,25,568,585 WARNING @ Mon, 12 Aug 2019 20:15:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:15:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:15:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:15:56: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:15:56: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:15:56: start model_add_line... INFO @ Mon, 12 Aug 2019 20:15:56: start X-correlation... INFO @ Mon, 12 Aug 2019 20:15:56: end of X-cor INFO @ Mon, 12 Aug 2019 20:15:56: #2 finished! INFO @ Mon, 12 Aug 2019 20:15:56: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:15:56: #2 alternative fragment length(s) may be 1,25,568,585 bps INFO @ Mon, 12 Aug 2019 20:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05_model.r WARNING @ Mon, 12 Aug 2019 20:15:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:15:56: #2 You may need to consider one of the other alternative d(s): 1,25,568,585 WARNING @ Mon, 12 Aug 2019 20:15:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:15:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:02: 15000000 INFO @ Mon, 12 Aug 2019 20:16:10: 16000000 INFO @ Mon, 12 Aug 2019 20:16:14: #1 tag size is determined as 28 bps INFO @ Mon, 12 Aug 2019 20:16:14: #1 tag size = 28 INFO @ Mon, 12 Aug 2019 20:16:14: #1 total tags in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:16:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:16:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:16:14: #1 tags after filtering in treatment: 16526400 INFO @ Mon, 12 Aug 2019 20:16:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:16:14: #1 finished! INFO @ Mon, 12 Aug 2019 20:16:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:16:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:16:16: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 20:16:16: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 20:16:16: start model_add_line... INFO @ Mon, 12 Aug 2019 20:16:16: start X-correlation... INFO @ Mon, 12 Aug 2019 20:16:16: end of X-cor INFO @ Mon, 12 Aug 2019 20:16:16: #2 finished! INFO @ Mon, 12 Aug 2019 20:16:16: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 20:16:16: #2 alternative fragment length(s) may be 1,25,568,585 bps INFO @ Mon, 12 Aug 2019 20:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20_model.r WARNING @ Mon, 12 Aug 2019 20:16:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:16:16: #2 You may need to consider one of the other alternative d(s): 1,25,568,585 WARNING @ Mon, 12 Aug 2019 20:16:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:16:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:16:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:16:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.05_summits.bed INFO @ Mon, 12 Aug 2019 20:16:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.10_summits.bed INFO @ Mon, 12 Aug 2019 20:16:51: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:16:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529215/SRX529215.20_summits.bed INFO @ Mon, 12 Aug 2019 20:17:10: Done! pass1 - making usageList (0 chroms): 2 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。