Job ID = 6453252 SRX = SRX110770 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:16:18 prefetch.2.10.7: 1) Downloading 'SRR388352'... 2020-06-21T08:16:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:17:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:17:19 prefetch.2.10.7: 'SRR388352' is valid 2020-06-21T08:17:19 prefetch.2.10.7: 1) 'SRR388352' was downloaded successfully Read 17135472 spots for SRR388352/SRR388352.sra Written 17135472 spots for SRR388352/SRR388352.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:02 17135472 reads; of these: 17135472 (100.00%) were unpaired; of these: 3921460 (22.89%) aligned 0 times 7412414 (43.26%) aligned exactly 1 time 5801598 (33.86%) aligned >1 times 77.11% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 6914196 / 13214012 = 0.5232 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 17:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.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 17:25:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:26: 1000000 INFO @ Sun, 21 Jun 2020 17:25:30: 2000000 INFO @ Sun, 21 Jun 2020 17:25:34: 3000000 INFO @ Sun, 21 Jun 2020 17:25:38: 4000000 INFO @ Sun, 21 Jun 2020 17:25:42: 5000000 INFO @ Sun, 21 Jun 2020 17:25:47: 6000000 INFO @ Sun, 21 Jun 2020 17:25:48: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:25:48: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:25:48: #1 total tags in treatment: 6299816 INFO @ Sun, 21 Jun 2020 17:25:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:48: #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 17:25:48: #1 tags after filtering in treatment: 6299813 INFO @ Sun, 21 Jun 2020 17:25:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:49: #2 number of paired peaks: 3908 INFO @ Sun, 21 Jun 2020 17:25:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:49: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 17:25:49: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 17:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05_model.r INFO @ Sun, 21 Jun 2020 17:25:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:49: #3 Pre-compute pvalue-qvalue table... 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 17:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.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 17:25:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:56: 1000000 INFO @ Sun, 21 Jun 2020 17:26:01: 2000000 INFO @ Sun, 21 Jun 2020 17:26:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:06: 3000000 INFO @ Sun, 21 Jun 2020 17:26:11: 4000000 INFO @ Sun, 21 Jun 2020 17:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.05_summits.bed INFO @ Sun, 21 Jun 2020 17:26:13: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (7511 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:16: 5000000 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 17:26:21: 6000000 INFO @ Sun, 21 Jun 2020 17:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.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 17:26:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:26:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:26:22: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:26:22: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:26:22: #1 total tags in treatment: 6299816 INFO @ Sun, 21 Jun 2020 17:26:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:22: #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 17:26:23: #1 tags after filtering in treatment: 6299813 INFO @ Sun, 21 Jun 2020 17:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:23: #2 number of paired peaks: 3908 INFO @ Sun, 21 Jun 2020 17:26:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:23: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 17:26:23: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 17:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10_model.r INFO @ Sun, 21 Jun 2020 17:26:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:26: 1000000 INFO @ Sun, 21 Jun 2020 17:26:30: 2000000 INFO @ Sun, 21 Jun 2020 17:26:34: 3000000 INFO @ Sun, 21 Jun 2020 17:26:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:39: 4000000 INFO @ Sun, 21 Jun 2020 17:26:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:26:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.10_summits.bed INFO @ Sun, 21 Jun 2020 17:26:45: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (5705 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:47: 6000000 INFO @ Sun, 21 Jun 2020 17:26:49: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:26:49: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:26:49: #1 total tags in treatment: 6299816 INFO @ Sun, 21 Jun 2020 17:26:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:49: #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 17:26:49: #1 tags after filtering in treatment: 6299813 INFO @ Sun, 21 Jun 2020 17:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:50: #2 number of paired peaks: 3908 INFO @ Sun, 21 Jun 2020 17:26:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:50: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 17:26:50: #2 alternative fragment length(s) may be 90 bps INFO @ Sun, 21 Jun 2020 17:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20_model.r INFO @ Sun, 21 Jun 2020 17:26:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:27:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110770/SRX110770.20_summits.bed INFO @ Sun, 21 Jun 2020 17:27:12: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (4076 records, 4 fields): 7 millis CompletedMACS2peakCalling