Job ID = 1295042 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,226,746 reads read : 8,453,492 reads written : 4,226,746 reads 0-length : 4,226,746 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: 00:02:56 4226746 reads; of these: 4226746 (100.00%) were unpaired; of these: 994060 (23.52%) aligned 0 times 2579026 (61.02%) aligned exactly 1 time 653660 (15.46%) aligned >1 times 76.48% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 545754 / 3232686 = 0.1688 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 11:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.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 11:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.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 11:29:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.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 11:29:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:29:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:29:58: 1000000 INFO @ Mon, 03 Jun 2019 11:30:01: 1000000 INFO @ Mon, 03 Jun 2019 11:30:01: 1000000 INFO @ Mon, 03 Jun 2019 11:30:11: 2000000 INFO @ Mon, 03 Jun 2019 11:30:17: 2000000 INFO @ Mon, 03 Jun 2019 11:30:17: 2000000 INFO @ Mon, 03 Jun 2019 11:30:20: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:30:20: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:30:20: #1 total tags in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:30:20: #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 11:30:20: #1 tags after filtering in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:30:20: #1 finished! INFO @ Mon, 03 Jun 2019 11:30:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:30:20: #2 number of paired peaks: 4935 INFO @ Mon, 03 Jun 2019 11:30:20: start model_add_line... INFO @ Mon, 03 Jun 2019 11:30:20: start X-correlation... INFO @ Mon, 03 Jun 2019 11:30:20: end of X-cor INFO @ Mon, 03 Jun 2019 11:30:20: #2 finished! INFO @ Mon, 03 Jun 2019 11:30:20: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:30:20: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20_model.r WARNING @ Mon, 03 Jun 2019 11:30:20: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:30:20: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Mon, 03 Jun 2019 11:30:20: #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 11:30:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:27: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:30:27: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:30:27: #1 total tags in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:30:27: #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 11:30:27: #1 tags after filtering in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:30:27: #1 finished! INFO @ Mon, 03 Jun 2019 11:30:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:30:27: #2 number of paired peaks: 4935 INFO @ Mon, 03 Jun 2019 11:30:27: start model_add_line... INFO @ Mon, 03 Jun 2019 11:30:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:30:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:30:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:30:27: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:30:27: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10_model.r WARNING @ Mon, 03 Jun 2019 11:30:27: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:30:27: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Mon, 03 Jun 2019 11:30:27: #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 11:30:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:28: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 11:30:28: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 11:30:28: #1 total tags in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:30:28: #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 11:30:28: #1 tags after filtering in treatment: 2686932 INFO @ Mon, 03 Jun 2019 11:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:30:28: #1 finished! INFO @ Mon, 03 Jun 2019 11:30:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:30:28: #2 number of paired peaks: 4935 INFO @ Mon, 03 Jun 2019 11:30:28: start model_add_line... INFO @ Mon, 03 Jun 2019 11:30:28: start X-correlation... INFO @ Mon, 03 Jun 2019 11:30:28: end of X-cor INFO @ Mon, 03 Jun 2019 11:30:28: #2 finished! INFO @ Mon, 03 Jun 2019 11:30:28: #2 predicted fragment length is 192 bps INFO @ Mon, 03 Jun 2019 11:30:28: #2 alternative fragment length(s) may be 192 bps INFO @ Mon, 03 Jun 2019 11:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05_model.r WARNING @ Mon, 03 Jun 2019 11:30:28: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:30:28: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Mon, 03 Jun 2019 11:30:28: #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 11:30:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:30:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.20_summits.bed INFO @ Mon, 03 Jun 2019 11:30:35: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3017 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:30:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:30:39: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 11:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.10_summits.bed INFO @ Mon, 03 Jun 2019 11:30:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4271 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX315134/SRX315134.05_summits.bed INFO @ Mon, 03 Jun 2019 11:30:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5491 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。