Job ID = 1295342 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,173,126 reads read : 16,173,126 reads written : 16,173,126 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: 00:07:25 16173126 reads; of these: 16173126 (100.00%) were unpaired; of these: 7277204 (45.00%) aligned 0 times 2564075 (15.85%) aligned exactly 1 time 6331847 (39.15%) aligned >1 times 55.00% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 3963057 / 8895922 = 0.4455 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 13:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.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 13:27:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:27:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.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 13:27:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:27:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:27:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.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 13:27:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:27:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:27:38: 1000000 INFO @ Mon, 03 Jun 2019 13:27:38: 1000000 INFO @ Mon, 03 Jun 2019 13:27:41: 1000000 INFO @ Mon, 03 Jun 2019 13:27:46: 2000000 INFO @ Mon, 03 Jun 2019 13:27:46: 2000000 INFO @ Mon, 03 Jun 2019 13:27:51: 2000000 INFO @ Mon, 03 Jun 2019 13:27:54: 3000000 INFO @ Mon, 03 Jun 2019 13:27:54: 3000000 INFO @ Mon, 03 Jun 2019 13:28:01: 3000000 INFO @ Mon, 03 Jun 2019 13:28:02: 4000000 INFO @ Mon, 03 Jun 2019 13:28:02: 4000000 INFO @ Mon, 03 Jun 2019 13:28:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:28:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:28:08: #1 total tags in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:28:08: #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 13:28:09: #1 tags after filtering in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:28:09: #1 finished! INFO @ Mon, 03 Jun 2019 13:28:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:28:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:28:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:28:09: #1 total tags in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:28:09: #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 13:28:09: #1 tags after filtering in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:28:09: #1 finished! INFO @ Mon, 03 Jun 2019 13:28:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:28:09: #2 number of paired peaks: 1651 INFO @ Mon, 03 Jun 2019 13:28:09: start model_add_line... INFO @ Mon, 03 Jun 2019 13:28:09: start X-correlation... INFO @ Mon, 03 Jun 2019 13:28:09: end of X-cor INFO @ Mon, 03 Jun 2019 13:28:09: #2 finished! INFO @ Mon, 03 Jun 2019 13:28:09: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:28:09: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20_model.r WARNING @ Mon, 03 Jun 2019 13:28:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:28:09: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:28:09: #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 13:28:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:28:09: #2 number of paired peaks: 1651 INFO @ Mon, 03 Jun 2019 13:28:09: start model_add_line... INFO @ Mon, 03 Jun 2019 13:28:09: start X-correlation... INFO @ Mon, 03 Jun 2019 13:28:09: end of X-cor INFO @ Mon, 03 Jun 2019 13:28:09: #2 finished! INFO @ Mon, 03 Jun 2019 13:28:09: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:28:09: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05_model.r WARNING @ Mon, 03 Jun 2019 13:28:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:28:09: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:28:09: #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 13:28:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:28:10: 4000000 INFO @ Mon, 03 Jun 2019 13:28:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:28:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:28:18: #1 total tags in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:28:18: #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 13:28:18: #1 tags after filtering in treatment: 4932865 INFO @ Mon, 03 Jun 2019 13:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:28:18: #1 finished! INFO @ Mon, 03 Jun 2019 13:28:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:28:18: #2 number of paired peaks: 1651 INFO @ Mon, 03 Jun 2019 13:28:18: start model_add_line... INFO @ Mon, 03 Jun 2019 13:28:19: start X-correlation... INFO @ Mon, 03 Jun 2019 13:28:19: end of X-cor INFO @ Mon, 03 Jun 2019 13:28:19: #2 finished! INFO @ Mon, 03 Jun 2019 13:28:19: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 13:28:19: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 13:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10_model.r WARNING @ Mon, 03 Jun 2019 13:28:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 13:28:19: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 13:28:19: #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 13:28:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:28:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:28:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.20_summits.bed INFO @ Mon, 03 Jun 2019 13:28:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (634 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.05_summits.bed INFO @ Mon, 03 Jun 2019 13:28:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2567 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:28:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335496/SRX335496.10_summits.bed INFO @ Mon, 03 Jun 2019 13:28:41: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1192 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。