Job ID = 2589991 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,388,946 reads read : 18,388,946 reads written : 18,388,946 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163647.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: 00:04:00 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337586 (23.59%) aligned 0 times 11667748 (63.45%) aligned exactly 1 time 2383612 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1117944 / 14051360 = 0.0796 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 19:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.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 19:05:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.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 19:05:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.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 19:05:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:05:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:05:29: 1000000 INFO @ Mon, 12 Aug 2019 19:05:30: 1000000 INFO @ Mon, 12 Aug 2019 19:05:32: 1000000 INFO @ Mon, 12 Aug 2019 19:05:36: 2000000 INFO @ Mon, 12 Aug 2019 19:05:38: 2000000 INFO @ Mon, 12 Aug 2019 19:05:41: 2000000 INFO @ Mon, 12 Aug 2019 19:05:43: 3000000 INFO @ Mon, 12 Aug 2019 19:05:46: 3000000 INFO @ Mon, 12 Aug 2019 19:05:50: 3000000 INFO @ Mon, 12 Aug 2019 19:05:50: 4000000 INFO @ Mon, 12 Aug 2019 19:05:54: 4000000 INFO @ Mon, 12 Aug 2019 19:05:57: 5000000 INFO @ Mon, 12 Aug 2019 19:05:58: 4000000 INFO @ Mon, 12 Aug 2019 19:06:02: 5000000 INFO @ Mon, 12 Aug 2019 19:06:04: 6000000 INFO @ Mon, 12 Aug 2019 19:06:07: 5000000 INFO @ Mon, 12 Aug 2019 19:06:10: 6000000 INFO @ Mon, 12 Aug 2019 19:06:11: 7000000 INFO @ Mon, 12 Aug 2019 19:06:16: 6000000 INFO @ Mon, 12 Aug 2019 19:06:18: 8000000 INFO @ Mon, 12 Aug 2019 19:06:18: 7000000 INFO @ Mon, 12 Aug 2019 19:06:24: 7000000 INFO @ Mon, 12 Aug 2019 19:06:25: 9000000 INFO @ Mon, 12 Aug 2019 19:06:26: 8000000 INFO @ Mon, 12 Aug 2019 19:06:32: 10000000 INFO @ Mon, 12 Aug 2019 19:06:33: 8000000 INFO @ Mon, 12 Aug 2019 19:06:34: 9000000 INFO @ Mon, 12 Aug 2019 19:06:39: 11000000 INFO @ Mon, 12 Aug 2019 19:06:42: 9000000 INFO @ Mon, 12 Aug 2019 19:06:42: 10000000 INFO @ Mon, 12 Aug 2019 19:06:46: 12000000 INFO @ Mon, 12 Aug 2019 19:06:50: 11000000 INFO @ Mon, 12 Aug 2019 19:06:51: 10000000 INFO @ Mon, 12 Aug 2019 19:06:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:06:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:06:53: #1 total tags in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:06:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:06:53: #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 19:06:53: #1 tags after filtering in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:06:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:06:53: #1 finished! INFO @ Mon, 12 Aug 2019 19:06:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:06:54: #2 number of paired peaks: 350 WARNING @ Mon, 12 Aug 2019 19:06:54: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 12 Aug 2019 19:06:54: start model_add_line... INFO @ Mon, 12 Aug 2019 19:06:54: start X-correlation... INFO @ Mon, 12 Aug 2019 19:06:54: end of X-cor INFO @ Mon, 12 Aug 2019 19:06:54: #2 finished! INFO @ Mon, 12 Aug 2019 19:06:54: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:06:54: #2 alternative fragment length(s) may be 2,41 bps INFO @ Mon, 12 Aug 2019 19:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10_model.r WARNING @ Mon, 12 Aug 2019 19:06:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:06:54: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Mon, 12 Aug 2019 19:06:54: #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 19:06:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:06:58: 12000000 INFO @ Mon, 12 Aug 2019 19:06:59: 11000000 INFO @ Mon, 12 Aug 2019 19:07:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:07:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:07:05: #1 total tags in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:07:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:05: #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 19:07:05: #1 tags after filtering in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:05: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:06: #2 number of paired peaks: 350 WARNING @ Mon, 12 Aug 2019 19:07:06: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 12 Aug 2019 19:07:06: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:06: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:06: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:06: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:06: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:07:06: #2 alternative fragment length(s) may be 2,41 bps INFO @ Mon, 12 Aug 2019 19:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05_model.r WARNING @ Mon, 12 Aug 2019 19:07:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:06: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Mon, 12 Aug 2019 19:07:06: #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 19:07:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:08: 12000000 INFO @ Mon, 12 Aug 2019 19:07:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:07:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:07:16: #1 total tags in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:07:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:07:16: #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 19:07:16: #1 tags after filtering in treatment: 12933416 INFO @ Mon, 12 Aug 2019 19:07:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:07:16: #1 finished! INFO @ Mon, 12 Aug 2019 19:07:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:07:17: #2 number of paired peaks: 350 WARNING @ Mon, 12 Aug 2019 19:07:17: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Mon, 12 Aug 2019 19:07:17: start model_add_line... INFO @ Mon, 12 Aug 2019 19:07:17: start X-correlation... INFO @ Mon, 12 Aug 2019 19:07:17: end of X-cor INFO @ Mon, 12 Aug 2019 19:07:17: #2 finished! INFO @ Mon, 12 Aug 2019 19:07:17: #2 predicted fragment length is 2 bps INFO @ Mon, 12 Aug 2019 19:07:17: #2 alternative fragment length(s) may be 2,41 bps INFO @ Mon, 12 Aug 2019 19:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20_model.r WARNING @ Mon, 12 Aug 2019 19:07:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:07:17: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Mon, 12 Aug 2019 19:07:17: #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 19:07:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:07:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.10_summits.bed INFO @ Mon, 12 Aug 2019 19:07:41: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:07:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.05_summits.bed INFO @ Mon, 12 Aug 2019 19:07:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466581/SRX466581.20_summits.bed INFO @ Mon, 12 Aug 2019 19:08:05: 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。