Job ID = 2590073 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/SRR1198447.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:01 20117538 reads; of these: 20117538 (100.00%) were unpaired; of these: 1022132 (5.08%) aligned 0 times 15666271 (77.87%) aligned exactly 1 time 3429135 (17.05%) aligned >1 times 94.92% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 2624344 / 19095406 = 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 19:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.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 19:33:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.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 19:33:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.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 19:33:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:30: 1000000 INFO @ Mon, 12 Aug 2019 19:33:31: 1000000 INFO @ Mon, 12 Aug 2019 19:33:33: 1000000 INFO @ Mon, 12 Aug 2019 19:33:36: 2000000 INFO @ Mon, 12 Aug 2019 19:33:38: 2000000 INFO @ Mon, 12 Aug 2019 19:33:41: 2000000 INFO @ Mon, 12 Aug 2019 19:33:43: 3000000 INFO @ Mon, 12 Aug 2019 19:33:45: 3000000 INFO @ Mon, 12 Aug 2019 19:33:49: 3000000 INFO @ Mon, 12 Aug 2019 19:33:50: 4000000 INFO @ Mon, 12 Aug 2019 19:33:52: 4000000 INFO @ Mon, 12 Aug 2019 19:33:57: 5000000 INFO @ Mon, 12 Aug 2019 19:33:57: 4000000 INFO @ Mon, 12 Aug 2019 19:34:00: 5000000 INFO @ Mon, 12 Aug 2019 19:34:04: 6000000 INFO @ Mon, 12 Aug 2019 19:34:05: 5000000 INFO @ Mon, 12 Aug 2019 19:34:07: 6000000 INFO @ Mon, 12 Aug 2019 19:34:10: 7000000 INFO @ Mon, 12 Aug 2019 19:34:13: 6000000 INFO @ Mon, 12 Aug 2019 19:34:14: 7000000 INFO @ Mon, 12 Aug 2019 19:34:17: 8000000 INFO @ Mon, 12 Aug 2019 19:34:21: 7000000 INFO @ Mon, 12 Aug 2019 19:34:22: 8000000 INFO @ Mon, 12 Aug 2019 19:34:24: 9000000 INFO @ Mon, 12 Aug 2019 19:34:29: 9000000 INFO @ Mon, 12 Aug 2019 19:34:29: 8000000 INFO @ Mon, 12 Aug 2019 19:34:31: 10000000 INFO @ Mon, 12 Aug 2019 19:34:36: 10000000 INFO @ Mon, 12 Aug 2019 19:34:37: 9000000 INFO @ Mon, 12 Aug 2019 19:34:38: 11000000 INFO @ Mon, 12 Aug 2019 19:34:43: 11000000 INFO @ Mon, 12 Aug 2019 19:34:44: 12000000 INFO @ Mon, 12 Aug 2019 19:34:45: 10000000 INFO @ Mon, 12 Aug 2019 19:34:51: 12000000 INFO @ Mon, 12 Aug 2019 19:34:51: 13000000 INFO @ Mon, 12 Aug 2019 19:34:53: 11000000 INFO @ Mon, 12 Aug 2019 19:34:58: 14000000 INFO @ Mon, 12 Aug 2019 19:34:58: 13000000 INFO @ Mon, 12 Aug 2019 19:35:01: 12000000 INFO @ Mon, 12 Aug 2019 19:35:05: 15000000 INFO @ Mon, 12 Aug 2019 19:35:05: 14000000 INFO @ Mon, 12 Aug 2019 19:35:09: 13000000 INFO @ Mon, 12 Aug 2019 19:35:12: 16000000 INFO @ Mon, 12 Aug 2019 19:35:13: 15000000 INFO @ Mon, 12 Aug 2019 19:35:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:16: #1 total tags in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:16: #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 19:35:16: #1 tags after filtering in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:17: 14000000 INFO @ Mon, 12 Aug 2019 19:35:18: #2 number of paired peaks: 240 WARNING @ Mon, 12 Aug 2019 19:35:18: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:18: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:18: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:18: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:18: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:18: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:35:18: #2 alternative fragment length(s) may be 1,41,560,576,582 bps INFO @ Mon, 12 Aug 2019 19:35:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05_model.r WARNING @ Mon, 12 Aug 2019 19:35:18: #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 19:35:18: #2 You may need to consider one of the other alternative d(s): 1,41,560,576,582 WARNING @ Mon, 12 Aug 2019 19:35:18: #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 19:35:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:20: 16000000 INFO @ Mon, 12 Aug 2019 19:35:24: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:24: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:24: #1 total tags in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:24: #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 19:35:24: #1 tags after filtering in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:24: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:25: 15000000 INFO @ Mon, 12 Aug 2019 19:35:26: #2 number of paired peaks: 240 WARNING @ Mon, 12 Aug 2019 19:35:26: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:26: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:26: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:26: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:26: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:26: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:35:26: #2 alternative fragment length(s) may be 1,41,560,576,582 bps INFO @ Mon, 12 Aug 2019 19:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10_model.r WARNING @ Mon, 12 Aug 2019 19:35:26: #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 19:35:26: #2 You may need to consider one of the other alternative d(s): 1,41,560,576,582 WARNING @ Mon, 12 Aug 2019 19:35:26: #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 19:35:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:32: 16000000 INFO @ Mon, 12 Aug 2019 19:35:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:35:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:35:36: #1 total tags in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:35:36: #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 19:35:36: #1 tags after filtering in treatment: 16471062 INFO @ Mon, 12 Aug 2019 19:35:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:35:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:35:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:35:38: #2 number of paired peaks: 240 WARNING @ Mon, 12 Aug 2019 19:35:38: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Mon, 12 Aug 2019 19:35:38: start model_add_line... INFO @ Mon, 12 Aug 2019 19:35:38: start X-correlation... INFO @ Mon, 12 Aug 2019 19:35:38: end of X-cor INFO @ Mon, 12 Aug 2019 19:35:38: #2 finished! INFO @ Mon, 12 Aug 2019 19:35:38: #2 predicted fragment length is 1 bps INFO @ Mon, 12 Aug 2019 19:35:38: #2 alternative fragment length(s) may be 1,41,560,576,582 bps INFO @ Mon, 12 Aug 2019 19:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20_model.r WARNING @ Mon, 12 Aug 2019 19:35:38: #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 19:35:38: #2 You may need to consider one of the other alternative d(s): 1,41,560,576,582 WARNING @ Mon, 12 Aug 2019 19:35:38: #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 19:35:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:35:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:35:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.05_summits.bed INFO @ Mon, 12 Aug 2019 19:36:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:36:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.10_summits.bed INFO @ Mon, 12 Aug 2019 19:36:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494915/SRX494915.20_summits.bed INFO @ Mon, 12 Aug 2019 19:36:33: 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。