Job ID = 1292329 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,809,537 reads read : 13,809,537 reads written : 13,809,537 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:02:37 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2269437 (16.43%) aligned 0 times 9709655 (70.31%) aligned exactly 1 time 1830445 (13.25%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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_rmdupse_core] 1987779 / 11540100 = 0.1722 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 @ Sun, 02 Jun 2019 18:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.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 @ Sun, 02 Jun 2019 18:09:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:09:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.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 @ Sun, 02 Jun 2019 18:09:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:09:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:09:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.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 @ Sun, 02 Jun 2019 18:09:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:09:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:09:08: 1000000 INFO @ Sun, 02 Jun 2019 18:09:09: 1000000 INFO @ Sun, 02 Jun 2019 18:09:10: 1000000 INFO @ Sun, 02 Jun 2019 18:09:15: 2000000 INFO @ Sun, 02 Jun 2019 18:09:16: 2000000 INFO @ Sun, 02 Jun 2019 18:09:18: 2000000 INFO @ Sun, 02 Jun 2019 18:09:21: 3000000 INFO @ Sun, 02 Jun 2019 18:09:23: 3000000 INFO @ Sun, 02 Jun 2019 18:09:25: 3000000 INFO @ Sun, 02 Jun 2019 18:09:28: 4000000 INFO @ Sun, 02 Jun 2019 18:09:30: 4000000 INFO @ Sun, 02 Jun 2019 18:09:33: 4000000 INFO @ Sun, 02 Jun 2019 18:09:34: 5000000 INFO @ Sun, 02 Jun 2019 18:09:37: 5000000 INFO @ Sun, 02 Jun 2019 18:09:40: 6000000 INFO @ Sun, 02 Jun 2019 18:09:41: 5000000 INFO @ Sun, 02 Jun 2019 18:09:44: 6000000 INFO @ Sun, 02 Jun 2019 18:09:47: 7000000 INFO @ Sun, 02 Jun 2019 18:09:48: 6000000 INFO @ Sun, 02 Jun 2019 18:09:51: 7000000 INFO @ Sun, 02 Jun 2019 18:09:53: 8000000 INFO @ Sun, 02 Jun 2019 18:09:55: 7000000 INFO @ Sun, 02 Jun 2019 18:09:57: 8000000 INFO @ Sun, 02 Jun 2019 18:09:59: 9000000 INFO @ Sun, 02 Jun 2019 18:10:03: 8000000 INFO @ Sun, 02 Jun 2019 18:10:03: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:10:03: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:10:03: #1 total tags in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:10:03: #1 tags after filtering in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:10:03: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:04: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 18:10:04: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 18:10:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:04: 9000000 INFO @ Sun, 02 Jun 2019 18:10:04: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:04: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:04: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:04: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:10:04: #2 alternative fragment length(s) may be 2,44,102,533,571 bps INFO @ Sun, 02 Jun 2019 18:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10_model.r WARNING @ Sun, 02 Jun 2019 18:10:04: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:10:04: #2 You may need to consider one of the other alternative d(s): 2,44,102,533,571 WARNING @ Sun, 02 Jun 2019 18:10:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:10:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:10:08: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:10:08: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:10:08: #1 total tags in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:10:08: #1 tags after filtering in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:10:08: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:09: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 18:10:09: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 18:10:09: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:09: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:09: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:09: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:09: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:10:09: #2 alternative fragment length(s) may be 2,44,102,533,571 bps INFO @ Sun, 02 Jun 2019 18:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20_model.r WARNING @ Sun, 02 Jun 2019 18:10:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:10:09: #2 You may need to consider one of the other alternative d(s): 2,44,102,533,571 WARNING @ Sun, 02 Jun 2019 18:10:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:10:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:10:10: 9000000 INFO @ Sun, 02 Jun 2019 18:10:15: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:10:15: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:10:15: #1 total tags in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 18:10:15: #1 tags after filtering in treatment: 9552321 INFO @ Sun, 02 Jun 2019 18:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:10:15: #1 finished! INFO @ Sun, 02 Jun 2019 18:10:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:10:16: #2 number of paired peaks: 277 WARNING @ Sun, 02 Jun 2019 18:10:16: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sun, 02 Jun 2019 18:10:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:10:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:10:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:10:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:10:16: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:10:16: #2 alternative fragment length(s) may be 2,44,102,533,571 bps INFO @ Sun, 02 Jun 2019 18:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05_model.r WARNING @ Sun, 02 Jun 2019 18:10:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:10:16: #2 You may need to consider one of the other alternative d(s): 2,44,102,533,571 WARNING @ Sun, 02 Jun 2019 18:10:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 18:10:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:10:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:10:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:10:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.10_summits.bed INFO @ Sun, 02 Jun 2019 18:10:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.20_summits.bed INFO @ Sun, 02 Jun 2019 18:10:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331353/SRX331353.05_summits.bed INFO @ Sun, 02 Jun 2019 18:10:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。