Job ID = 1295819 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,708,598 reads read : 8,708,598 reads written : 8,708,598 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: 00:04:26 8708598 reads; of these: 8708598 (100.00%) were unpaired; of these: 502931 (5.78%) aligned 0 times 6127403 (70.36%) aligned exactly 1 time 2078264 (23.86%) aligned >1 times 94.22% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 4950854 / 8205667 = 0.6033 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 @ Mon, 03 Jun 2019 15:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:51:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:51:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 15:51:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:51:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:51:41: 1000000 INFO @ Mon, 03 Jun 2019 15:51:41: 1000000 INFO @ Mon, 03 Jun 2019 15:51:43: 1000000 INFO @ Mon, 03 Jun 2019 15:51:51: 2000000 INFO @ Mon, 03 Jun 2019 15:51:51: 2000000 INFO @ Mon, 03 Jun 2019 15:51:55: 2000000 INFO @ Mon, 03 Jun 2019 15:51:59: 3000000 INFO @ Mon, 03 Jun 2019 15:52:01: 3000000 INFO @ Mon, 03 Jun 2019 15:52:02: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:52:02: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:52:02: #1 total tags in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:52:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:52:02: #1 tags after filtering in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:52:02: #1 finished! INFO @ Mon, 03 Jun 2019 15:52:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:52:02: #2 number of paired peaks: 2100 INFO @ Mon, 03 Jun 2019 15:52:02: start model_add_line... INFO @ Mon, 03 Jun 2019 15:52:02: start X-correlation... INFO @ Mon, 03 Jun 2019 15:52:02: end of X-cor INFO @ Mon, 03 Jun 2019 15:52:02: #2 finished! INFO @ Mon, 03 Jun 2019 15:52:02: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 15:52:02: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 15:52:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10_model.r WARNING @ Mon, 03 Jun 2019 15:52:02: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:52:02: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 15:52:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:52:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:52:04: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:52:04: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:52:04: #1 total tags in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:52:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:52:04: #1 tags after filtering in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:52:04: #1 finished! INFO @ Mon, 03 Jun 2019 15:52:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:52:05: #2 number of paired peaks: 2100 INFO @ Mon, 03 Jun 2019 15:52:05: start model_add_line... INFO @ Mon, 03 Jun 2019 15:52:05: start X-correlation... INFO @ Mon, 03 Jun 2019 15:52:05: end of X-cor INFO @ Mon, 03 Jun 2019 15:52:05: #2 finished! INFO @ Mon, 03 Jun 2019 15:52:05: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 15:52:05: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 15:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05_model.r WARNING @ Mon, 03 Jun 2019 15:52:05: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:52:05: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 15:52:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:52:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:52:06: 3000000 INFO @ Mon, 03 Jun 2019 15:52:09: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:52:09: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:52:09: #1 total tags in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:52:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:52:09: #1 tags after filtering in treatment: 3254813 INFO @ Mon, 03 Jun 2019 15:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:52:09: #1 finished! INFO @ Mon, 03 Jun 2019 15:52:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:52:09: #2 number of paired peaks: 2100 INFO @ Mon, 03 Jun 2019 15:52:09: start model_add_line... INFO @ Mon, 03 Jun 2019 15:52:09: start X-correlation... INFO @ Mon, 03 Jun 2019 15:52:09: end of X-cor INFO @ Mon, 03 Jun 2019 15:52:09: #2 finished! INFO @ Mon, 03 Jun 2019 15:52:09: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 15:52:09: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 15:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20_model.r WARNING @ Mon, 03 Jun 2019 15:52:09: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:52:09: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Mon, 03 Jun 2019 15:52:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:52:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:52:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.10_summits.bed INFO @ Mon, 03 Jun 2019 15:52:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.05_summits.bed INFO @ Mon, 03 Jun 2019 15:52:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2330 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4563534/SRX4563534.20_summits.bed INFO @ Mon, 03 Jun 2019 15:52:26: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (691 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。