Job ID = 6457796 SRX = SRX4798832 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:14:52 prefetch.2.10.7: 1) Downloading 'SRR7965237'... 2020-06-21T12:14:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:15:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:15:53 prefetch.2.10.7: 'SRR7965237' is valid 2020-06-21T12:15:53 prefetch.2.10.7: 1) 'SRR7965237' was downloaded successfully Read 6592596 spots for SRR7965237/SRR7965237.sra Written 6592596 spots for SRR7965237/SRR7965237.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: 00:01:37 6592596 reads; of these: 6592596 (100.00%) were unpaired; of these: 602832 (9.14%) aligned 0 times 5152576 (78.16%) aligned exactly 1 time 837188 (12.70%) aligned >1 times 90.86% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 781170 / 5989764 = 0.1304 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 21:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.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 21:19:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:56: 1000000 INFO @ Sun, 21 Jun 2020 21:20:01: 2000000 INFO @ Sun, 21 Jun 2020 21:20:06: 3000000 INFO @ Sun, 21 Jun 2020 21:20:11: 4000000 INFO @ Sun, 21 Jun 2020 21:20:16: 5000000 INFO @ Sun, 21 Jun 2020 21:20:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:20:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:20:18: #1 total tags in treatment: 5208594 INFO @ Sun, 21 Jun 2020 21:20:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:18: #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 21:20:18: #1 tags after filtering in treatment: 5208381 INFO @ Sun, 21 Jun 2020 21:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:18: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 21:20:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:18: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:20:18: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05_model.r INFO @ Sun, 21 Jun 2020 21:20:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:18: #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 21:20:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.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 21:20:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:26: 1000000 INFO @ Sun, 21 Jun 2020 21:20:31: 2000000 INFO @ Sun, 21 Jun 2020 21:20:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:20:36: 3000000 INFO @ Sun, 21 Jun 2020 21:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.05_summits.bed INFO @ Sun, 21 Jun 2020 21:20:38: Done! pass1 - making usageList (301 chroms): 2 millis pass2 - checking and writing primary data (4593 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:20:41: 4000000 INFO @ Sun, 21 Jun 2020 21:20:47: 5000000 INFO @ Sun, 21 Jun 2020 21:20:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:20:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:20:48: #1 total tags in treatment: 5208594 INFO @ Sun, 21 Jun 2020 21:20:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:48: #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 21:20:48: #1 tags after filtering in treatment: 5208381 INFO @ Sun, 21 Jun 2020 21:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:49: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 21:20:49: start model_add_line... BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:20:49: start X-correlation... 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 21:20:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:49: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:20:49: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10_model.r INFO @ Sun, 21 Jun 2020 21:20:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.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 21:20:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:56: 1000000 INFO @ Sun, 21 Jun 2020 21:21:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:01: 2000000 INFO @ Sun, 21 Jun 2020 21:21:06: 3000000 INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:07: Done! pass1 - making usageList (212 chroms): 1 millis pass2 - checking and writing primary data (1474 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:21:17: 5000000 INFO @ Sun, 21 Jun 2020 21:21:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:21:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:21:18: #1 total tags in treatment: 5208594 INFO @ Sun, 21 Jun 2020 21:21:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:18: #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 21:21:18: #1 tags after filtering in treatment: 5208381 INFO @ Sun, 21 Jun 2020 21:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:19: #2 number of paired peaks: 2276 INFO @ Sun, 21 Jun 2020 21:21:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:19: #2 predicted fragment length is 194 bps INFO @ Sun, 21 Jun 2020 21:21:19: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 21 Jun 2020 21:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20_model.r INFO @ Sun, 21 Jun 2020 21:21:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:21:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798832/SRX4798832.20_summits.bed INFO @ Sun, 21 Jun 2020 21:21:38: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (386 records, 4 fields): 4 millis CompletedMACS2peakCalling