Job ID = 1292453 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,643,898 reads read : 13,643,898 reads written : 13,643,898 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: 00:02:56 13643898 reads; of these: 13643898 (100.00%) were unpaired; of these: 1182089 (8.66%) aligned 0 times 10405120 (76.26%) aligned exactly 1 time 2056689 (15.07%) aligned >1 times 91.34% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 7967714 / 12461809 = 0.6394 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 18:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.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 18:59:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:59:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.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 18:59:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:59:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.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 18:59:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:59:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:59:33: 1000000 INFO @ Sun, 02 Jun 2019 18:59:34: 1000000 INFO @ Sun, 02 Jun 2019 18:59:35: 1000000 INFO @ Sun, 02 Jun 2019 18:59:40: 2000000 INFO @ Sun, 02 Jun 2019 18:59:42: 2000000 INFO @ Sun, 02 Jun 2019 18:59:43: 2000000 INFO @ Sun, 02 Jun 2019 18:59:46: 3000000 INFO @ Sun, 02 Jun 2019 18:59:49: 3000000 INFO @ Sun, 02 Jun 2019 18:59:51: 3000000 INFO @ Sun, 02 Jun 2019 18:59:53: 4000000 INFO @ Sun, 02 Jun 2019 18:59:56: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 18:59:56: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 18:59:56: #1 total tags in treatment: 4494095 INFO @ Sun, 02 Jun 2019 18:59:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:56: #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 18:59:56: #1 tags after filtering in treatment: 4494095 INFO @ Sun, 02 Jun 2019 18:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:56: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:56: 4000000 INFO @ Sun, 02 Jun 2019 18:59:57: #2 number of paired peaks: 730 WARNING @ Sun, 02 Jun 2019 18:59:57: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:57: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:57: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:57: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:57: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:57: #2 predicted fragment length is 38 bps INFO @ Sun, 02 Jun 2019 18:59:57: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Sun, 02 Jun 2019 18:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20_model.r WARNING @ Sun, 02 Jun 2019 18:59:57: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:57: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Sun, 02 Jun 2019 18:59:57: #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 18:59:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:59: 4000000 INFO @ Sun, 02 Jun 2019 19:00:00: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:00:00: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:00:00: #1 total tags in treatment: 4494095 INFO @ Sun, 02 Jun 2019 19:00:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:00: #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 19:00:00: #1 tags after filtering in treatment: 4494095 INFO @ Sun, 02 Jun 2019 19:00:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:00: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:01: #2 number of paired peaks: 730 WARNING @ Sun, 02 Jun 2019 19:00:01: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:01: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:01: #2 predicted fragment length is 38 bps INFO @ Sun, 02 Jun 2019 19:00:01: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Sun, 02 Jun 2019 19:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10_model.r WARNING @ Sun, 02 Jun 2019 19:00:01: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:00:01: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Sun, 02 Jun 2019 19:00:01: #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 19:00:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:02: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:00:02: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:00:02: #1 total tags in treatment: 4494095 INFO @ Sun, 02 Jun 2019 19:00:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:02: #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 19:00:02: #1 tags after filtering in treatment: 4494095 INFO @ Sun, 02 Jun 2019 19:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:02: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:03: #2 number of paired peaks: 730 WARNING @ Sun, 02 Jun 2019 19:00:03: Fewer paired peaks (730) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 730 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:03: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:03: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:03: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:03: #2 predicted fragment length is 38 bps INFO @ Sun, 02 Jun 2019 19:00:03: #2 alternative fragment length(s) may be 3,38,513,582 bps INFO @ Sun, 02 Jun 2019 19:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05_model.r WARNING @ Sun, 02 Jun 2019 19:00:03: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:00:03: #2 You may need to consider one of the other alternative d(s): 3,38,513,582 WARNING @ Sun, 02 Jun 2019 19:00:03: #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 19:00:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.20_summits.bed INFO @ Sun, 02 Jun 2019 19:00:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.10_summits.bed INFO @ Sun, 02 Jun 2019 19:00:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626828/SRX4626828.05_summits.bed INFO @ Sun, 02 Jun 2019 19:00:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (891 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。