Job ID = 1295536 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,143,112 reads read : 22,143,112 reads written : 22,143,112 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: 00:06:32 22143112 reads; of these: 22143112 (100.00%) were unpaired; of these: 12027102 (54.32%) aligned 0 times 7425311 (33.53%) aligned exactly 1 time 2690699 (12.15%) aligned >1 times 45.68% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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 8 files... [bam_rmdupse_core] 6920908 / 10116010 = 0.6842 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 14:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.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 14:20:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:20:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.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 14:20:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:20:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.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 14:20:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:20:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:21:09: 1000000 INFO @ Mon, 03 Jun 2019 14:21:11: 1000000 INFO @ Mon, 03 Jun 2019 14:21:12: 1000000 INFO @ Mon, 03 Jun 2019 14:21:19: 2000000 INFO @ Mon, 03 Jun 2019 14:21:24: 2000000 INFO @ Mon, 03 Jun 2019 14:21:25: 2000000 INFO @ Mon, 03 Jun 2019 14:21:30: 3000000 INFO @ Mon, 03 Jun 2019 14:21:31: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:21:31: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:21:31: #1 total tags in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:31: #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 14:21:31: #1 tags after filtering in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:31: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:32: #2 number of paired peaks: 1922 INFO @ Mon, 03 Jun 2019 14:21:32: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:32: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:32: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:32: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:32: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 14:21:32: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 03 Jun 2019 14:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05_model.r WARNING @ Mon, 03 Jun 2019 14:21:32: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:32: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 03 Jun 2019 14:21:32: #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 14:21:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:36: 3000000 INFO @ Mon, 03 Jun 2019 14:21:37: 3000000 INFO @ Mon, 03 Jun 2019 14:21:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:21:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:21:38: #1 total tags in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:38: #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 14:21:38: #1 tags after filtering in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:38: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:38: #2 number of paired peaks: 1922 INFO @ Mon, 03 Jun 2019 14:21:38: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:38: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:38: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:38: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:38: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 14:21:38: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 03 Jun 2019 14:21:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10_model.r WARNING @ Mon, 03 Jun 2019 14:21:38: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:38: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 03 Jun 2019 14:21:38: #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 14:21:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:39: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 14:21:39: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 14:21:39: #1 total tags in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:39: #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 14:21:39: #1 tags after filtering in treatment: 3195102 INFO @ Mon, 03 Jun 2019 14:21:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:39: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:39: #2 number of paired peaks: 1922 INFO @ Mon, 03 Jun 2019 14:21:39: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:39: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:39: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:39: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:39: #2 predicted fragment length is 96 bps INFO @ Mon, 03 Jun 2019 14:21:39: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 03 Jun 2019 14:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20_model.r WARNING @ Mon, 03 Jun 2019 14:21:39: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:39: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 03 Jun 2019 14:21:39: #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 14:21:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.05_summits.bed INFO @ Mon, 03 Jun 2019 14:21:49: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2367 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:21:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:21:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.10_summits.bed INFO @ Mon, 03 Jun 2019 14:21:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:21:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX365702/SRX365702.20_summits.bed INFO @ Mon, 03 Jun 2019 14:21:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (550 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。