Job ID = 1307142 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,105,766 reads read : 44,211,532 reads written : 22,105,766 reads 0-length : 22,105,766 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: 00:08:12 22105766 reads; of these: 22105766 (100.00%) were unpaired; of these: 379013 (1.71%) aligned 0 times 19838609 (89.74%) aligned exactly 1 time 1888144 (8.54%) aligned >1 times 98.29% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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_sort_core] merging from 12 files... [bam_rmdupse_core] 11041761 / 21726753 = 0.5082 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 22:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.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 22:28:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.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 22:28:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.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 22:28:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:28:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:28:59: 1000000 INFO @ Mon, 03 Jun 2019 22:29:00: 1000000 INFO @ Mon, 03 Jun 2019 22:29:01: 1000000 INFO @ Mon, 03 Jun 2019 22:29:08: 2000000 INFO @ Mon, 03 Jun 2019 22:29:09: 2000000 INFO @ Mon, 03 Jun 2019 22:29:11: 2000000 INFO @ Mon, 03 Jun 2019 22:29:17: 3000000 INFO @ Mon, 03 Jun 2019 22:29:17: 3000000 INFO @ Mon, 03 Jun 2019 22:29:21: 3000000 INFO @ Mon, 03 Jun 2019 22:29:25: 4000000 INFO @ Mon, 03 Jun 2019 22:29:26: 4000000 INFO @ Mon, 03 Jun 2019 22:29:32: 4000000 INFO @ Mon, 03 Jun 2019 22:29:35: 5000000 INFO @ Mon, 03 Jun 2019 22:29:35: 5000000 INFO @ Mon, 03 Jun 2019 22:29:42: 5000000 INFO @ Mon, 03 Jun 2019 22:29:44: 6000000 INFO @ Mon, 03 Jun 2019 22:29:44: 6000000 INFO @ Mon, 03 Jun 2019 22:29:52: 6000000 INFO @ Mon, 03 Jun 2019 22:29:52: 7000000 INFO @ Mon, 03 Jun 2019 22:29:52: 7000000 INFO @ Mon, 03 Jun 2019 22:30:01: 8000000 INFO @ Mon, 03 Jun 2019 22:30:02: 8000000 INFO @ Mon, 03 Jun 2019 22:30:02: 7000000 INFO @ Mon, 03 Jun 2019 22:30:11: 9000000 INFO @ Mon, 03 Jun 2019 22:30:11: 9000000 INFO @ Mon, 03 Jun 2019 22:30:12: 8000000 INFO @ Mon, 03 Jun 2019 22:30:20: 10000000 INFO @ Mon, 03 Jun 2019 22:30:20: 10000000 INFO @ Mon, 03 Jun 2019 22:30:22: 9000000 INFO @ Mon, 03 Jun 2019 22:30:26: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:30:26: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:30:26: #1 total tags in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:26: #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 22:30:26: #1 tags after filtering in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:26: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:26: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:30:26: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:30:26: #1 total tags in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:26: #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 22:30:26: #1 tags after filtering in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:26: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:28: #2 number of paired peaks: 12653 INFO @ Mon, 03 Jun 2019 22:30:28: start model_add_line... INFO @ Mon, 03 Jun 2019 22:30:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:30:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:30:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:30:29: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:30:29: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10_model.r WARNING @ Mon, 03 Jun 2019 22:30:29: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:30:29: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:30:29: #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 22:30:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:30:29: #2 number of paired peaks: 12653 INFO @ Mon, 03 Jun 2019 22:30:29: start model_add_line... INFO @ Mon, 03 Jun 2019 22:30:29: start X-correlation... INFO @ Mon, 03 Jun 2019 22:30:29: end of X-cor INFO @ Mon, 03 Jun 2019 22:30:29: #2 finished! INFO @ Mon, 03 Jun 2019 22:30:29: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:30:29: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:30:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05_model.r WARNING @ Mon, 03 Jun 2019 22:30:29: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:30:29: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:30:29: #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 22:30:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:30:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:30:31: 10000000 INFO @ Mon, 03 Jun 2019 22:30:38: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:30:38: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:30:38: #1 total tags in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:30:38: #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 22:30:38: #1 tags after filtering in treatment: 10684992 INFO @ Mon, 03 Jun 2019 22:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:30:38: #1 finished! INFO @ Mon, 03 Jun 2019 22:30:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:30:40: #2 number of paired peaks: 12653 INFO @ Mon, 03 Jun 2019 22:30:40: start model_add_line... INFO @ Mon, 03 Jun 2019 22:30:41: start X-correlation... INFO @ Mon, 03 Jun 2019 22:30:41: end of X-cor INFO @ Mon, 03 Jun 2019 22:30:41: #2 finished! INFO @ Mon, 03 Jun 2019 22:30:41: #2 predicted fragment length is 115 bps INFO @ Mon, 03 Jun 2019 22:30:41: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 03 Jun 2019 22:30:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20_model.r WARNING @ Mon, 03 Jun 2019 22:30:41: #2 Since the d (115) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:30:41: #2 You may need to consider one of the other alternative d(s): 115 WARNING @ Mon, 03 Jun 2019 22:30:41: #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 22:30:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:30:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 22:31:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:31:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:31:14: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:31:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:31:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:31:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.10_summits.bed BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 22:31:15: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8937 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:31:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:31:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:31:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.05_summits.bed INFO @ Mon, 03 Jun 2019 22:31:19: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9667 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:31:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:31:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:31:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241026/SRX5241026.20_summits.bed INFO @ Mon, 03 Jun 2019 22:31:26: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7933 records, 4 fields): 13 millis CompletedMACS2peakCalling