Job ID = 1292403 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,138,414 reads read : 10,276,828 reads written : 5,138,414 reads 0-length : 5,138,414 spots read : 5,028,817 reads read : 10,057,634 reads written : 5,028,817 reads 0-length : 5,028,817 spots read : 5,110,379 reads read : 10,220,758 reads written : 5,110,379 reads 0-length : 5,110,379 spots read : 4,982,515 reads read : 9,965,030 reads written : 4,982,515 reads 0-length : 4,982,515 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: 00:08:49 20260125 reads; of these: 20260125 (100.00%) were unpaired; of these: 390433 (1.93%) aligned 0 times 15389485 (75.96%) aligned exactly 1 time 4480207 (22.11%) aligned >1 times 98.07% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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] 12117299 / 19869692 = 0.6098 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 18:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.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 18:44:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:44:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.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 18:44:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:44:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:44:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.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 18:44:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:44:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:44:41: 1000000 INFO @ Sun, 02 Jun 2019 18:44:42: 1000000 INFO @ Sun, 02 Jun 2019 18:44:44: 1000000 INFO @ Sun, 02 Jun 2019 18:44:49: 2000000 INFO @ Sun, 02 Jun 2019 18:44:51: 2000000 INFO @ Sun, 02 Jun 2019 18:44:55: 2000000 INFO @ Sun, 02 Jun 2019 18:44:58: 3000000 INFO @ Sun, 02 Jun 2019 18:45:00: 3000000 INFO @ Sun, 02 Jun 2019 18:45:05: 3000000 INFO @ Sun, 02 Jun 2019 18:45:07: 4000000 INFO @ Sun, 02 Jun 2019 18:45:08: 4000000 INFO @ Sun, 02 Jun 2019 18:45:15: 5000000 INFO @ Sun, 02 Jun 2019 18:45:15: 4000000 INFO @ Sun, 02 Jun 2019 18:45:17: 5000000 INFO @ Sun, 02 Jun 2019 18:45:23: 6000000 INFO @ Sun, 02 Jun 2019 18:45:25: 6000000 INFO @ Sun, 02 Jun 2019 18:45:26: 5000000 INFO @ Sun, 02 Jun 2019 18:45:31: 7000000 INFO @ Sun, 02 Jun 2019 18:45:34: 7000000 INFO @ Sun, 02 Jun 2019 18:45:36: 6000000 INFO @ Sun, 02 Jun 2019 18:45:37: #1 tag size is determined as 55 bps INFO @ Sun, 02 Jun 2019 18:45:37: #1 tag size = 55 INFO @ Sun, 02 Jun 2019 18:45:37: #1 total tags in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:45:37: #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 18:45:37: #1 tags after filtering in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:45:37: #1 finished! INFO @ Sun, 02 Jun 2019 18:45:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:45:38: #2 number of paired peaks: 845 WARNING @ Sun, 02 Jun 2019 18:45:38: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Sun, 02 Jun 2019 18:45:38: start model_add_line... INFO @ Sun, 02 Jun 2019 18:45:38: start X-correlation... INFO @ Sun, 02 Jun 2019 18:45:38: end of X-cor INFO @ Sun, 02 Jun 2019 18:45:38: #2 finished! INFO @ Sun, 02 Jun 2019 18:45:38: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 18:45:38: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 18:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05_model.r WARNING @ Sun, 02 Jun 2019 18:45:38: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:45:38: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 18:45:38: #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 18:45:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:45:40: #1 tag size is determined as 55 bps INFO @ Sun, 02 Jun 2019 18:45:40: #1 tag size = 55 INFO @ Sun, 02 Jun 2019 18:45:40: #1 total tags in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:45:40: #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 18:45:40: #1 tags after filtering in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:45:40: #1 finished! INFO @ Sun, 02 Jun 2019 18:45:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:45:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:45:41: #2 number of paired peaks: 845 WARNING @ Sun, 02 Jun 2019 18:45:41: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Sun, 02 Jun 2019 18:45:41: start model_add_line... INFO @ Sun, 02 Jun 2019 18:45:41: start X-correlation... INFO @ Sun, 02 Jun 2019 18:45:41: end of X-cor INFO @ Sun, 02 Jun 2019 18:45:41: #2 finished! INFO @ Sun, 02 Jun 2019 18:45:41: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 18:45:41: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 18:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10_model.r WARNING @ Sun, 02 Jun 2019 18:45:41: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:45:41: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 18:45:41: #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 18:45:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:45:46: 7000000 INFO @ Sun, 02 Jun 2019 18:45:53: #1 tag size is determined as 55 bps INFO @ Sun, 02 Jun 2019 18:45:53: #1 tag size = 55 INFO @ Sun, 02 Jun 2019 18:45:53: #1 total tags in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:45:53: #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 18:45:54: #1 tags after filtering in treatment: 7752393 INFO @ Sun, 02 Jun 2019 18:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:45:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:45:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:45:54: #2 number of paired peaks: 845 WARNING @ Sun, 02 Jun 2019 18:45:54: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Sun, 02 Jun 2019 18:45:54: start model_add_line... INFO @ Sun, 02 Jun 2019 18:45:54: start X-correlation... INFO @ Sun, 02 Jun 2019 18:45:55: end of X-cor INFO @ Sun, 02 Jun 2019 18:45:55: #2 finished! INFO @ Sun, 02 Jun 2019 18:45:55: #2 predicted fragment length is 69 bps INFO @ Sun, 02 Jun 2019 18:45:55: #2 alternative fragment length(s) may be 4,69 bps INFO @ Sun, 02 Jun 2019 18:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20_model.r WARNING @ Sun, 02 Jun 2019 18:45:55: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:45:55: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Sun, 02 Jun 2019 18:45:55: #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 18:45:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:46:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:46:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.05_summits.bed INFO @ Sun, 02 Jun 2019 18:46:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.10_summits.bed INFO @ Sun, 02 Jun 2019 18:46:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:46:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194185/SRX4194185.20_summits.bed INFO @ Sun, 02 Jun 2019 18:46:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (373 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。