Job ID = 4303050 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,874,451 reads read : 19,874,451 reads written : 19,874,451 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1265811.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: 00:04:39 19874451 reads; of these: 19874451 (100.00%) were unpaired; of these: 312807 (1.57%) aligned 0 times 16204313 (81.53%) aligned exactly 1 time 3357331 (16.89%) aligned >1 times 98.43% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 2055282 / 19561644 = 0.1051 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:46:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.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 @ Thu, 12 Dec 2019 00:46:50: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:50: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:00: 1000000 INFO @ Thu, 12 Dec 2019 00:47:09: 2000000 INFO @ Thu, 12 Dec 2019 00:47:19: 3000000 INFO @ Thu, 12 Dec 2019 00:47:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.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 @ Thu, 12 Dec 2019 00:47:19: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:19: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:29: 1000000 INFO @ Thu, 12 Dec 2019 00:47:30: 4000000 INFO @ Thu, 12 Dec 2019 00:47:39: 2000000 INFO @ Thu, 12 Dec 2019 00:47:41: 5000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:47:48: 3000000 INFO @ Thu, 12 Dec 2019 00:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.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 @ Thu, 12 Dec 2019 00:47:49: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:49: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:51: 6000000 INFO @ Thu, 12 Dec 2019 00:47:57: 4000000 INFO @ Thu, 12 Dec 2019 00:47:58: 1000000 INFO @ Thu, 12 Dec 2019 00:48:02: 7000000 INFO @ Thu, 12 Dec 2019 00:48:06: 5000000 INFO @ Thu, 12 Dec 2019 00:48:06: 2000000 INFO @ Thu, 12 Dec 2019 00:48:12: 8000000 INFO @ Thu, 12 Dec 2019 00:48:14: 3000000 INFO @ Thu, 12 Dec 2019 00:48:15: 6000000 INFO @ Thu, 12 Dec 2019 00:48:21: 4000000 INFO @ Thu, 12 Dec 2019 00:48:24: 9000000 INFO @ Thu, 12 Dec 2019 00:48:24: 7000000 INFO @ Thu, 12 Dec 2019 00:48:29: 5000000 INFO @ Thu, 12 Dec 2019 00:48:32: 8000000 INFO @ Thu, 12 Dec 2019 00:48:35: 10000000 INFO @ Thu, 12 Dec 2019 00:48:37: 6000000 INFO @ Thu, 12 Dec 2019 00:48:41: 9000000 INFO @ Thu, 12 Dec 2019 00:48:45: 7000000 INFO @ Thu, 12 Dec 2019 00:48:46: 11000000 INFO @ Thu, 12 Dec 2019 00:48:49: 10000000 INFO @ Thu, 12 Dec 2019 00:48:52: 8000000 INFO @ Thu, 12 Dec 2019 00:48:57: 12000000 INFO @ Thu, 12 Dec 2019 00:48:57: 11000000 INFO @ Thu, 12 Dec 2019 00:49:00: 9000000 INFO @ Thu, 12 Dec 2019 00:49:05: 12000000 INFO @ Thu, 12 Dec 2019 00:49:07: 13000000 INFO @ Thu, 12 Dec 2019 00:49:07: 10000000 INFO @ Thu, 12 Dec 2019 00:49:14: 13000000 INFO @ Thu, 12 Dec 2019 00:49:15: 11000000 INFO @ Thu, 12 Dec 2019 00:49:17: 14000000 INFO @ Thu, 12 Dec 2019 00:49:22: 14000000 INFO @ Thu, 12 Dec 2019 00:49:22: 12000000 INFO @ Thu, 12 Dec 2019 00:49:27: 15000000 INFO @ Thu, 12 Dec 2019 00:49:30: 13000000 INFO @ Thu, 12 Dec 2019 00:49:30: 15000000 INFO @ Thu, 12 Dec 2019 00:49:36: 16000000 INFO @ Thu, 12 Dec 2019 00:49:37: 14000000 INFO @ Thu, 12 Dec 2019 00:49:38: 16000000 INFO @ Thu, 12 Dec 2019 00:49:45: 15000000 INFO @ Thu, 12 Dec 2019 00:49:47: 17000000 INFO @ Thu, 12 Dec 2019 00:49:47: 17000000 INFO @ Thu, 12 Dec 2019 00:49:51: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:49:51: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:49:51: #1 total tags in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:49:51: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:49:51: #1 tags after filtering in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:49:51: #1 finished! INFO @ Thu, 12 Dec 2019 00:49:51: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:49:52: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:49:52: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:49:52: #1 total tags in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:49:52: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:49:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:49:52: #1 tags after filtering in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:49:52: #1 finished! INFO @ Thu, 12 Dec 2019 00:49:52: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:49:53: #2 number of paired peaks: 168 WARNING @ Thu, 12 Dec 2019 00:49:53: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Thu, 12 Dec 2019 00:49:53: start model_add_line... INFO @ Thu, 12 Dec 2019 00:49:53: start X-correlation... INFO @ Thu, 12 Dec 2019 00:49:53: 16000000 INFO @ Thu, 12 Dec 2019 00:49:53: end of X-cor INFO @ Thu, 12 Dec 2019 00:49:53: #2 finished! INFO @ Thu, 12 Dec 2019 00:49:53: #2 predicted fragment length is 2 bps INFO @ Thu, 12 Dec 2019 00:49:53: #2 alternative fragment length(s) may be 2,24,36,522,596 bps INFO @ Thu, 12 Dec 2019 00:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10_model.r WARNING @ Thu, 12 Dec 2019 00:49:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:49:53: #2 You may need to consider one of the other alternative d(s): 2,24,36,522,596 WARNING @ Thu, 12 Dec 2019 00:49:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:49:53: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:49:54: #2 number of paired peaks: 168 WARNING @ Thu, 12 Dec 2019 00:49:54: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Thu, 12 Dec 2019 00:49:54: start model_add_line... INFO @ Thu, 12 Dec 2019 00:49:54: start X-correlation... INFO @ Thu, 12 Dec 2019 00:49:54: end of X-cor INFO @ Thu, 12 Dec 2019 00:49:54: #2 finished! INFO @ Thu, 12 Dec 2019 00:49:54: #2 predicted fragment length is 2 bps INFO @ Thu, 12 Dec 2019 00:49:54: #2 alternative fragment length(s) may be 2,24,36,522,596 bps INFO @ Thu, 12 Dec 2019 00:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05_model.r WARNING @ Thu, 12 Dec 2019 00:49:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:49:54: #2 You may need to consider one of the other alternative d(s): 2,24,36,522,596 WARNING @ Thu, 12 Dec 2019 00:49:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:49:54: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:50:00: 17000000 INFO @ Thu, 12 Dec 2019 00:50:04: #1 tag size is determined as 42 bps INFO @ Thu, 12 Dec 2019 00:50:04: #1 tag size = 42 INFO @ Thu, 12 Dec 2019 00:50:04: #1 total tags in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:50:04: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:50:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:50:04: #1 tags after filtering in treatment: 17506362 INFO @ Thu, 12 Dec 2019 00:50:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:50:04: #1 finished! INFO @ Thu, 12 Dec 2019 00:50:04: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:50:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:50:06: #2 number of paired peaks: 168 WARNING @ Thu, 12 Dec 2019 00:50:06: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Thu, 12 Dec 2019 00:50:06: start model_add_line... INFO @ Thu, 12 Dec 2019 00:50:06: start X-correlation... INFO @ Thu, 12 Dec 2019 00:50:06: end of X-cor INFO @ Thu, 12 Dec 2019 00:50:06: #2 finished! INFO @ Thu, 12 Dec 2019 00:50:06: #2 predicted fragment length is 2 bps INFO @ Thu, 12 Dec 2019 00:50:06: #2 alternative fragment length(s) may be 2,24,36,522,596 bps INFO @ Thu, 12 Dec 2019 00:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20_model.r WARNING @ Thu, 12 Dec 2019 00:50:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:50:06: #2 You may need to consider one of the other alternative d(s): 2,24,36,522,596 WARNING @ Thu, 12 Dec 2019 00:50:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:50:06: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:50:33: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:50:33: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:50:46: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.10_summits.bed INFO @ Thu, 12 Dec 2019 00:50:53: Done! INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05_peaks.narrowPeak pass1 - making usageList (0 chroms): 3 millis INFO @ Thu, 12 Dec 2019 00:50:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.05_summits.bed INFO @ Thu, 12 Dec 2019 00:50:53: Done! needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:51:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:51:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:51:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529207/SRX529207.20_summits.bed INFO @ Thu, 12 Dec 2019 00:51:06: 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。