Job ID = 1292765 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,338,445 reads read : 13,338,445 reads written : 13,338,445 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: 00:02:59 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 89011 (0.67%) aligned 0 times 10992351 (82.41%) aligned exactly 1 time 2257083 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 2113802 / 13249434 = 0.1595 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 20:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.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 20:26:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:26:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.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 20:26:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:26:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.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 20:26:38: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:26:38: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:26:46: 1000000 INFO @ Sun, 02 Jun 2019 20:26:46: 1000000 INFO @ Sun, 02 Jun 2019 20:26:47: 1000000 INFO @ Sun, 02 Jun 2019 20:26:55: 2000000 INFO @ Sun, 02 Jun 2019 20:26:55: 2000000 INFO @ Sun, 02 Jun 2019 20:26:55: 2000000 INFO @ Sun, 02 Jun 2019 20:27:03: 3000000 INFO @ Sun, 02 Jun 2019 20:27:03: 3000000 INFO @ Sun, 02 Jun 2019 20:27:04: 3000000 INFO @ Sun, 02 Jun 2019 20:27:11: 4000000 INFO @ Sun, 02 Jun 2019 20:27:12: 4000000 INFO @ Sun, 02 Jun 2019 20:27:13: 4000000 INFO @ Sun, 02 Jun 2019 20:27:20: 5000000 INFO @ Sun, 02 Jun 2019 20:27:21: 5000000 INFO @ Sun, 02 Jun 2019 20:27:21: 5000000 INFO @ Sun, 02 Jun 2019 20:27:28: 6000000 INFO @ Sun, 02 Jun 2019 20:27:29: 6000000 INFO @ Sun, 02 Jun 2019 20:27:30: 6000000 INFO @ Sun, 02 Jun 2019 20:27:36: 7000000 INFO @ Sun, 02 Jun 2019 20:27:36: 7000000 INFO @ Sun, 02 Jun 2019 20:27:39: 7000000 INFO @ Sun, 02 Jun 2019 20:27:44: 8000000 INFO @ Sun, 02 Jun 2019 20:27:44: 8000000 INFO @ Sun, 02 Jun 2019 20:27:48: 8000000 INFO @ Sun, 02 Jun 2019 20:27:52: 9000000 INFO @ Sun, 02 Jun 2019 20:27:52: 9000000 INFO @ Sun, 02 Jun 2019 20:27:57: 9000000 INFO @ Sun, 02 Jun 2019 20:28:00: 10000000 INFO @ Sun, 02 Jun 2019 20:28:00: 10000000 INFO @ Sun, 02 Jun 2019 20:28:06: 10000000 INFO @ Sun, 02 Jun 2019 20:28:08: 11000000 INFO @ Sun, 02 Jun 2019 20:28:08: 11000000 INFO @ Sun, 02 Jun 2019 20:28:09: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:09: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:09: #1 total tags in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:09: #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 20:28:09: #1 tags after filtering in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:09: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:10: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:10: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:10: #1 total tags in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:10: #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 20:28:10: #1 tags after filtering in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:10: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:10: #2 number of paired peaks: 371 WARNING @ Sun, 02 Jun 2019 20:28:10: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sun, 02 Jun 2019 20:28:10: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:10: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:10: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:10: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:10: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:28:10: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 20:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20_model.r WARNING @ Sun, 02 Jun 2019 20:28:10: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:28:10: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 20:28:10: #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 20:28:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:28:11: #2 number of paired peaks: 371 WARNING @ Sun, 02 Jun 2019 20:28:11: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sun, 02 Jun 2019 20:28:11: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:11: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:11: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:11: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:11: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:28:11: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 20:28:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10_model.r WARNING @ Sun, 02 Jun 2019 20:28:11: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:28:11: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 20:28:11: #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 20:28:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:28:15: 11000000 INFO @ Sun, 02 Jun 2019 20:28:16: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:16: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:16: #1 total tags in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:16: #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 20:28:16: #1 tags after filtering in treatment: 11135632 INFO @ Sun, 02 Jun 2019 20:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:16: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:17: #2 number of paired peaks: 371 WARNING @ Sun, 02 Jun 2019 20:28:17: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Sun, 02 Jun 2019 20:28:17: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:17: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:17: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:17: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:17: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 20:28:17: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 20:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05_model.r WARNING @ Sun, 02 Jun 2019 20:28:17: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:28:17: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 20:28:17: #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 20:28:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:28:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:28:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:28:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.20_summits.bed INFO @ Sun, 02 Jun 2019 20:28:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (133 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:28:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:28:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:28:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.10_summits.bed INFO @ Sun, 02 Jun 2019 20:28:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494990/SRX494990.05_summits.bed INFO @ Sun, 02 Jun 2019 20:29:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (958 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。