Job ID = 2590012 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,117,538 reads read : 20,117,538 reads written : 20,117,538 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1198388.sra.cache’: 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: 00:04:53 20117538 reads; of these: 20117538 (100.00%) were unpaired; of these: 1022164 (5.08%) aligned 0 times 15666161 (77.87%) aligned exactly 1 time 3429213 (17.05%) aligned >1 times 94.92% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 2624578 / 19095374 = 0.1374 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 19:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.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 19:14:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.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 19:14:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.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 19:14:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:14:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:14:22: 1000000 INFO @ Mon, 12 Aug 2019 19:14:23: 1000000 INFO @ Mon, 12 Aug 2019 19:14:24: 1000000 INFO @ Mon, 12 Aug 2019 19:14:30: 2000000 INFO @ Mon, 12 Aug 2019 19:14:31: 2000000 INFO @ Mon, 12 Aug 2019 19:14:31: 2000000 INFO @ Mon, 12 Aug 2019 19:14:38: 3000000 INFO @ Mon, 12 Aug 2019 19:14:39: 3000000 INFO @ Mon, 12 Aug 2019 19:14:39: 3000000 INFO @ Mon, 12 Aug 2019 19:14:45: 4000000 INFO @ Mon, 12 Aug 2019 19:14:46: 4000000 INFO @ Mon, 12 Aug 2019 19:14:47: 4000000 INFO @ Mon, 12 Aug 2019 19:14:52: 5000000 INFO @ Mon, 12 Aug 2019 19:14:53: 5000000 INFO @ Mon, 12 Aug 2019 19:14:55: 5000000 INFO @ Mon, 12 Aug 2019 19:14:59: 6000000 INFO @ Mon, 12 Aug 2019 19:15:00: 6000000 INFO @ Mon, 12 Aug 2019 19:15:03: 6000000 INFO @ Mon, 12 Aug 2019 19:15:06: 7000000 INFO @ Mon, 12 Aug 2019 19:15:07: 7000000 INFO @ Mon, 12 Aug 2019 19:15:11: 7000000 INFO @ Mon, 12 Aug 2019 19:15:13: 8000000 INFO @ Mon, 12 Aug 2019 19:15:14: 8000000 INFO @ Mon, 12 Aug 2019 19:15:19: 8000000 INFO @ Mon, 12 Aug 2019 19:15:20: 9000000 INFO @ Mon, 12 Aug 2019 19:15:21: 9000000 INFO @ Mon, 12 Aug 2019 19:15:26: 9000000 INFO @ Mon, 12 Aug 2019 19:15:27: 10000000 INFO @ Mon, 12 Aug 2019 19:15:28: 10000000 INFO @ Mon, 12 Aug 2019 19:15:34: 11000000 INFO @ Mon, 12 Aug 2019 19:15:34: 10000000 INFO @ Mon, 12 Aug 2019 19:15:35: 11000000 INFO @ Mon, 12 Aug 2019 19:15:41: 12000000 INFO @ Mon, 12 Aug 2019 19:15:42: 12000000 INFO @ Mon, 12 Aug 2019 19:15:42: 11000000 INFO @ Mon, 12 Aug 2019 19:15:48: 13000000 INFO @ Mon, 12 Aug 2019 19:15:49: 13000000 INFO @ Mon, 12 Aug 2019 19:15:50: 12000000 INFO @ Mon, 12 Aug 2019 19:15:55: 14000000 INFO @ Mon, 12 Aug 2019 19:15:55: 14000000 INFO @ Mon, 12 Aug 2019 19:15:58: 13000000 INFO @ Mon, 12 Aug 2019 19:16:02: 15000000 INFO @ Mon, 12 Aug 2019 19:16:02: 15000000 INFO @ Mon, 12 Aug 2019 19:16:05: 14000000 INFO @ Mon, 12 Aug 2019 19:16:09: 16000000 INFO @ Mon, 12 Aug 2019 19:16:09: 16000000 INFO @ Mon, 12 Aug 2019 19:16:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:16:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:16:12: #1 total tags in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:16:12: #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 19:16:12: #1 tags after filtering in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:16:12: #1 finished! INFO @ Mon, 12 Aug 2019 19:16:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:16:13: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:16:13: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:16:13: #1 total tags in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:13: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:16:13: #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 19:16:13: #1 tags after filtering in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:16:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:16:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:16:13: 15000000 INFO @ Mon, 12 Aug 2019 19:16:14: #2 number of paired peaks: 230 WARNING @ Mon, 12 Aug 2019 19:16:14: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Mon, 12 Aug 2019 19:16:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:16:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:16:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:16:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:16:14: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:16:14: #2 alternative fragment length(s) may be 1,45,511,594 bps INFO @ Mon, 12 Aug 2019 19:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10_model.r WARNING @ Mon, 12 Aug 2019 19:16:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:16:14: #2 You may need to consider one of the other alternative d(s): 1,45,511,594 WARNING @ Mon, 12 Aug 2019 19:16:14: #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 19:16:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:16:14: #2 number of paired peaks: 230 WARNING @ Mon, 12 Aug 2019 19:16:14: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Mon, 12 Aug 2019 19:16:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:16:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:16:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:16:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:16:14: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:16:14: #2 alternative fragment length(s) may be 1,45,511,594 bps INFO @ Mon, 12 Aug 2019 19:16:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20_model.r WARNING @ Mon, 12 Aug 2019 19:16:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:16:14: #2 You may need to consider one of the other alternative d(s): 1,45,511,594 WARNING @ Mon, 12 Aug 2019 19:16:14: #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 19:16:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:16:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:16:21: 16000000 INFO @ Mon, 12 Aug 2019 19:16:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:16:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:16:24: #1 total tags in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:16:24: #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 19:16:25: #1 tags after filtering in treatment: 16470796 INFO @ Mon, 12 Aug 2019 19:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:16:25: #1 finished! INFO @ Mon, 12 Aug 2019 19:16:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:16:26: #2 number of paired peaks: 230 WARNING @ Mon, 12 Aug 2019 19:16:26: Fewer paired peaks (230) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 230 pairs to build model! INFO @ Mon, 12 Aug 2019 19:16:26: start model_add_line... INFO @ Mon, 12 Aug 2019 19:16:26: start X-correlation... INFO @ Mon, 12 Aug 2019 19:16:26: end of X-cor INFO @ Mon, 12 Aug 2019 19:16:26: #2 finished! INFO @ Mon, 12 Aug 2019 19:16:26: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 19:16:26: #2 alternative fragment length(s) may be 1,45,511,594 bps INFO @ Mon, 12 Aug 2019 19:16:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05_model.r WARNING @ Mon, 12 Aug 2019 19:16:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:16:26: #2 You may need to consider one of the other alternative d(s): 1,45,511,594 WARNING @ Mon, 12 Aug 2019 19:16:26: #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 19:16:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:16:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:16:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:17:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.10_summits.bed INFO @ Mon, 12 Aug 2019 19:17:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:17:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.20_summits.bed INFO @ Mon, 12 Aug 2019 19:17:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494856/SRX494856.05_summits.bed INFO @ Mon, 12 Aug 2019 19:17:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。