Job ID = 1290672 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,676,822 reads read : 12,676,822 reads written : 12,676,822 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: 00:00:01 Multiseed full-index search: 00:02:22 12676822 reads; of these: 12676822 (100.00%) were unpaired; of these: 722624 (5.70%) aligned 0 times 9735291 (76.80%) aligned exactly 1 time 2218907 (17.50%) aligned >1 times 94.30% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 1315950 / 11954198 = 0.1101 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 @ Sat, 01 Jun 2019 22:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.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 @ Sat, 01 Jun 2019 22:00:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.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 @ Sat, 01 Jun 2019 22:00:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.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 @ Sat, 01 Jun 2019 22:00:58: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:00:58: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:05: 1000000 INFO @ Sat, 01 Jun 2019 22:01:05: 1000000 INFO @ Sat, 01 Jun 2019 22:01:06: 1000000 INFO @ Sat, 01 Jun 2019 22:01:12: 2000000 INFO @ Sat, 01 Jun 2019 22:01:13: 2000000 INFO @ Sat, 01 Jun 2019 22:01:14: 2000000 INFO @ Sat, 01 Jun 2019 22:01:18: 3000000 INFO @ Sat, 01 Jun 2019 22:01:20: 3000000 INFO @ Sat, 01 Jun 2019 22:01:22: 3000000 INFO @ Sat, 01 Jun 2019 22:01:25: 4000000 INFO @ Sat, 01 Jun 2019 22:01:27: 4000000 INFO @ Sat, 01 Jun 2019 22:01:30: 4000000 INFO @ Sat, 01 Jun 2019 22:01:31: 5000000 INFO @ Sat, 01 Jun 2019 22:01:34: 5000000 INFO @ Sat, 01 Jun 2019 22:01:38: 6000000 INFO @ Sat, 01 Jun 2019 22:01:38: 5000000 INFO @ Sat, 01 Jun 2019 22:01:41: 6000000 INFO @ Sat, 01 Jun 2019 22:01:44: 7000000 INFO @ Sat, 01 Jun 2019 22:01:46: 6000000 INFO @ Sat, 01 Jun 2019 22:01:48: 7000000 INFO @ Sat, 01 Jun 2019 22:01:51: 8000000 INFO @ Sat, 01 Jun 2019 22:01:53: 7000000 INFO @ Sat, 01 Jun 2019 22:01:55: 8000000 INFO @ Sat, 01 Jun 2019 22:01:57: 9000000 INFO @ Sat, 01 Jun 2019 22:02:01: 8000000 INFO @ Sat, 01 Jun 2019 22:02:02: 9000000 INFO @ Sat, 01 Jun 2019 22:02:04: 10000000 INFO @ Sat, 01 Jun 2019 22:02:08: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:08: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:08: #1 total tags in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:08: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:08: #1 tags after filtering in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:08: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:08: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:09: #2 number of paired peaks: 382 WARNING @ Sat, 01 Jun 2019 22:02:09: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:09: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:09: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:09: 10000000 INFO @ Sat, 01 Jun 2019 22:02:09: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:09: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:09: #2 predicted fragment length is 34 bps INFO @ Sat, 01 Jun 2019 22:02:09: #2 alternative fragment length(s) may be 1,34,574 bps INFO @ Sat, 01 Jun 2019 22:02:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10_model.r WARNING @ Sat, 01 Jun 2019 22:02:09: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:09: #2 You may need to consider one of the other alternative d(s): 1,34,574 WARNING @ Sat, 01 Jun 2019 22:02:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:09: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:09: 9000000 INFO @ Sat, 01 Jun 2019 22:02:14: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:14: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:14: #1 total tags in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:14: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:14: #1 tags after filtering in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:14: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:14: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:15: #2 number of paired peaks: 382 WARNING @ Sat, 01 Jun 2019 22:02:15: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:15: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:15: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:15: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:15: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:15: #2 predicted fragment length is 34 bps INFO @ Sat, 01 Jun 2019 22:02:15: #2 alternative fragment length(s) may be 1,34,574 bps INFO @ Sat, 01 Jun 2019 22:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20_model.r WARNING @ Sat, 01 Jun 2019 22:02:15: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:15: #2 You may need to consider one of the other alternative d(s): 1,34,574 WARNING @ Sat, 01 Jun 2019 22:02:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:15: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:17: 10000000 INFO @ Sat, 01 Jun 2019 22:02:22: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 22:02:22: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 22:02:22: #1 total tags in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:22: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:02:22: #1 tags after filtering in treatment: 10638248 INFO @ Sat, 01 Jun 2019 22:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:22: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:22: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:23: #2 number of paired peaks: 382 WARNING @ Sat, 01 Jun 2019 22:02:23: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sat, 01 Jun 2019 22:02:23: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:23: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:23: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:23: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:23: #2 predicted fragment length is 34 bps INFO @ Sat, 01 Jun 2019 22:02:23: #2 alternative fragment length(s) may be 1,34,574 bps INFO @ Sat, 01 Jun 2019 22:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05_model.r WARNING @ Sat, 01 Jun 2019 22:02:23: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 22:02:23: #2 You may need to consider one of the other alternative d(s): 1,34,574 WARNING @ Sat, 01 Jun 2019 22:02:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 22:02:23: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:37: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:43: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.10_summits.bed INFO @ Sat, 01 Jun 2019 22:02:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:02:51: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:02:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:02:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:02:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.20_summits.bed INFO @ Sat, 01 Jun 2019 22:02:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:03:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX076078/SRX076078.05_summits.bed INFO @ Sat, 01 Jun 2019 22:03:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (682 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。