Job ID = 6454652 SRX = SRX2433660 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:15 prefetch.2.10.7: 1) Downloading 'SRR5118379'... 2020-06-21T09:31:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:18 prefetch.2.10.7: 1) 'SRR5118379' was downloaded successfully Read 54395805 spots for SRR5118379/SRR5118379.sra Written 54395805 spots for SRR5118379/SRR5118379.sra 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:37 54395805 reads; of these: 54395805 (100.00%) were unpaired; of these: 50236093 (92.35%) aligned 0 times 2915365 (5.36%) aligned exactly 1 time 1244347 (2.29%) aligned >1 times 7.65% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2868379 / 4159712 = 0.6896 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.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 @ Sun, 21 Jun 2020 18:52:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:14: 1000000 INFO @ Sun, 21 Jun 2020 18:52:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:15: #1 total tags in treatment: 1291333 INFO @ Sun, 21 Jun 2020 18:52:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:52:16: #1 tags after filtering in treatment: 1291010 INFO @ Sun, 21 Jun 2020 18:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:16: #2 number of paired peaks: 1028 INFO @ Sun, 21 Jun 2020 18:52:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:16: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:52:16: #2 alternative fragment length(s) may be 47,186,402,442,493,560 bps INFO @ Sun, 21 Jun 2020 18:52:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05_model.r WARNING @ Sun, 21 Jun 2020 18:52:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:16: #2 You may need to consider one of the other alternative d(s): 47,186,402,442,493,560 WARNING @ Sun, 21 Jun 2020 18:52:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:52:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:21: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 7 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.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 @ Sun, 21 Jun 2020 18:52:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:52:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:52:43: 1000000 INFO @ Sun, 21 Jun 2020 18:52:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:52:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:52:45: #1 total tags in treatment: 1291333 INFO @ Sun, 21 Jun 2020 18:52:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:52:45: #1 tags after filtering in treatment: 1291010 INFO @ Sun, 21 Jun 2020 18:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:46: #2 number of paired peaks: 1028 INFO @ Sun, 21 Jun 2020 18:52:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:46: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:52:46: #2 alternative fragment length(s) may be 47,186,402,442,493,560 bps INFO @ Sun, 21 Jun 2020 18:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:46: #2 You may need to consider one of the other alternative d(s): 47,186,402,442,493,560 WARNING @ Sun, 21 Jun 2020 18:52:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:52:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.10_summits.bed INFO @ Sun, 21 Jun 2020 18:52:51: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.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 @ Sun, 21 Jun 2020 18:53:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:53:13: 1000000 INFO @ Sun, 21 Jun 2020 18:53:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:15: #1 total tags in treatment: 1291333 INFO @ Sun, 21 Jun 2020 18:53:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:53:15: #1 tags after filtering in treatment: 1291010 INFO @ Sun, 21 Jun 2020 18:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:16: #2 number of paired peaks: 1028 INFO @ Sun, 21 Jun 2020 18:53:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:16: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:53:16: #2 alternative fragment length(s) may be 47,186,402,442,493,560 bps INFO @ Sun, 21 Jun 2020 18:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20_model.r WARNING @ Sun, 21 Jun 2020 18:53:16: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:16: #2 You may need to consider one of the other alternative d(s): 47,186,402,442,493,560 WARNING @ Sun, 21 Jun 2020 18:53:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:53:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:53:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2433660/SRX2433660.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:21: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 4 millis CompletedMACS2peakCalling