Job ID = 1292322 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,858,982 reads read : 22,858,982 reads written : 22,858,982 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: 00:06:02 22858982 reads; of these: 22858982 (100.00%) were unpaired; of these: 654805 (2.86%) aligned 0 times 18698111 (81.80%) aligned exactly 1 time 3506066 (15.34%) aligned >1 times 97.14% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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 12 files... [bam_rmdupse_core] 8947675 / 22204177 = 0.4030 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 18:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.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 18:13:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.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 18:13:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.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 18:13:36: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:36: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:46: 1000000 INFO @ Sun, 02 Jun 2019 18:13:47: 1000000 INFO @ Sun, 02 Jun 2019 18:13:48: 1000000 INFO @ Sun, 02 Jun 2019 18:13:57: 2000000 INFO @ Sun, 02 Jun 2019 18:13:58: 2000000 INFO @ Sun, 02 Jun 2019 18:13:59: 2000000 INFO @ Sun, 02 Jun 2019 18:14:07: 3000000 INFO @ Sun, 02 Jun 2019 18:14:08: 3000000 INFO @ Sun, 02 Jun 2019 18:14:10: 3000000 INFO @ Sun, 02 Jun 2019 18:14:16: 4000000 INFO @ Sun, 02 Jun 2019 18:14:18: 4000000 INFO @ Sun, 02 Jun 2019 18:14:21: 4000000 INFO @ Sun, 02 Jun 2019 18:14:26: 5000000 INFO @ Sun, 02 Jun 2019 18:14:29: 5000000 INFO @ Sun, 02 Jun 2019 18:14:32: 5000000 INFO @ Sun, 02 Jun 2019 18:14:36: 6000000 INFO @ Sun, 02 Jun 2019 18:14:39: 6000000 INFO @ Sun, 02 Jun 2019 18:14:43: 6000000 INFO @ Sun, 02 Jun 2019 18:14:46: 7000000 INFO @ Sun, 02 Jun 2019 18:14:49: 7000000 INFO @ Sun, 02 Jun 2019 18:14:54: 7000000 INFO @ Sun, 02 Jun 2019 18:14:56: 8000000 INFO @ Sun, 02 Jun 2019 18:15:00: 8000000 INFO @ Sun, 02 Jun 2019 18:15:05: 8000000 INFO @ Sun, 02 Jun 2019 18:15:06: 9000000 INFO @ Sun, 02 Jun 2019 18:15:10: 9000000 INFO @ Sun, 02 Jun 2019 18:15:16: 9000000 INFO @ Sun, 02 Jun 2019 18:15:16: 10000000 INFO @ Sun, 02 Jun 2019 18:15:20: 10000000 INFO @ Sun, 02 Jun 2019 18:15:26: 11000000 INFO @ Sun, 02 Jun 2019 18:15:27: 10000000 INFO @ Sun, 02 Jun 2019 18:15:31: 11000000 INFO @ Sun, 02 Jun 2019 18:15:37: 12000000 INFO @ Sun, 02 Jun 2019 18:15:38: 11000000 INFO @ Sun, 02 Jun 2019 18:15:41: 12000000 INFO @ Sun, 02 Jun 2019 18:15:47: 13000000 INFO @ Sun, 02 Jun 2019 18:15:49: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:15:49: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:15:49: #1 total tags in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:15:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:49: #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 18:15:49: 12000000 INFO @ Sun, 02 Jun 2019 18:15:49: #1 tags after filtering in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:15:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:15:49: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:51: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 18:15:51: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 18:15:51: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:51: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:51: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:51: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:51: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:15:51: #2 alternative fragment length(s) may be 2,44,574 bps INFO @ Sun, 02 Jun 2019 18:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20_model.r WARNING @ Sun, 02 Jun 2019 18:15:51: #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 18:15:51: #2 You may need to consider one of the other alternative d(s): 2,44,574 WARNING @ Sun, 02 Jun 2019 18:15:51: #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 18:15:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:15:52: 13000000 INFO @ Sun, 02 Jun 2019 18:15:54: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:15:54: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:15:54: #1 total tags in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:15:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:54: #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 18:15:54: #1 tags after filtering in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:15:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:56: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 18:15:56: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 18:15:56: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:56: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:56: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:56: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:56: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:15:56: #2 alternative fragment length(s) may be 2,44,574 bps INFO @ Sun, 02 Jun 2019 18:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10_model.r WARNING @ Sun, 02 Jun 2019 18:15:56: #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 18:15:56: #2 You may need to consider one of the other alternative d(s): 2,44,574 WARNING @ Sun, 02 Jun 2019 18:15:56: #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 18:15:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:16:00: 13000000 INFO @ Sun, 02 Jun 2019 18:16:03: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:16:03: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:16:03: #1 total tags in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:16:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:16:03: #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 18:16:03: #1 tags after filtering in treatment: 13256502 INFO @ Sun, 02 Jun 2019 18:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:16:03: #1 finished! INFO @ Sun, 02 Jun 2019 18:16:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:16:04: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 18:16:04: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 18:16:04: start model_add_line... INFO @ Sun, 02 Jun 2019 18:16:05: start X-correlation... INFO @ Sun, 02 Jun 2019 18:16:05: end of X-cor INFO @ Sun, 02 Jun 2019 18:16:05: #2 finished! INFO @ Sun, 02 Jun 2019 18:16:05: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:16:05: #2 alternative fragment length(s) may be 2,44,574 bps INFO @ Sun, 02 Jun 2019 18:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05_model.r WARNING @ Sun, 02 Jun 2019 18:16:05: #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 18:16:05: #2 You may need to consider one of the other alternative d(s): 2,44,574 WARNING @ Sun, 02 Jun 2019 18:16:05: #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 18:16:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:16:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.20_summits.bed INFO @ Sun, 02 Jun 2019 18:16:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:16:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.10_summits.bed INFO @ Sun, 02 Jun 2019 18:16:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:16:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331346/SRX331346.05_summits.bed INFO @ Sun, 02 Jun 2019 18:16:55: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (763 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。