Job ID = 6454235 SRX = SRX193314 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:12:25 prefetch.2.10.7: 1) Downloading 'SRR585047'... 2020-06-21T09:12:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:15:00 prefetch.2.10.7: 'SRR585047' is valid 2020-06-21T09:15:00 prefetch.2.10.7: 1) 'SRR585047' was downloaded successfully Read 13661717 spots for SRR585047/SRR585047.sra Written 13661717 spots for SRR585047/SRR585047.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: 00:03:26 13661717 reads; of these: 13661717 (100.00%) were unpaired; of these: 1686814 (12.35%) aligned 0 times 8818798 (64.55%) aligned exactly 1 time 3156105 (23.10%) aligned >1 times 87.65% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3030769 / 11974903 = 0.2531 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 18:22:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.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 18:22:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:22: 1000000 INFO @ Sun, 21 Jun 2020 18:22:28: 2000000 INFO @ Sun, 21 Jun 2020 18:22:34: 3000000 INFO @ Sun, 21 Jun 2020 18:22:40: 4000000 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 18:22:46: 5000000 INFO @ Sun, 21 Jun 2020 18:22:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.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 18:22:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:52: 6000000 INFO @ Sun, 21 Jun 2020 18:22:53: 1000000 INFO @ Sun, 21 Jun 2020 18:22:59: 7000000 INFO @ Sun, 21 Jun 2020 18:22:59: 2000000 INFO @ Sun, 21 Jun 2020 18:23:06: 3000000 INFO @ Sun, 21 Jun 2020 18:23:06: 8000000 INFO @ Sun, 21 Jun 2020 18:23:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:23:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:23:12: #1 total tags in treatment: 8944134 INFO @ Sun, 21 Jun 2020 18:23:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:12: #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 18:23:12: 4000000 INFO @ Sun, 21 Jun 2020 18:23:13: #1 tags after filtering in treatment: 8944010 INFO @ Sun, 21 Jun 2020 18:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:13: #2 number of paired peaks: 1589 INFO @ Sun, 21 Jun 2020 18:23:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:14: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:23:14: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05_model.r INFO @ Sun, 21 Jun 2020 18:23:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:14: #3 Pre-compute pvalue-qvalue table... 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 18:23:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.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 18:23:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:19: 5000000 INFO @ Sun, 21 Jun 2020 18:23:23: 1000000 INFO @ Sun, 21 Jun 2020 18:23:26: 6000000 INFO @ Sun, 21 Jun 2020 18:23:30: 2000000 INFO @ Sun, 21 Jun 2020 18:23:32: 7000000 INFO @ Sun, 21 Jun 2020 18:23:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:36: 3000000 INFO @ Sun, 21 Jun 2020 18:23:39: 8000000 INFO @ Sun, 21 Jun 2020 18:23:43: 4000000 INFO @ Sun, 21 Jun 2020 18:23:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:23:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:23:46: #1 total tags in treatment: 8944134 INFO @ Sun, 21 Jun 2020 18:23:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:46: #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 18:23:46: #1 tags after filtering in treatment: 8944010 INFO @ Sun, 21 Jun 2020 18:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:47: Done! INFO @ Sun, 21 Jun 2020 18:23:47: #2 number of paired peaks: 1589 INFO @ Sun, 21 Jun 2020 18:23:47: start model_add_line... pass1 - making usageList (599 chroms): 1 millis pass2 - checking and writing primary data (6280 records, 4 fields): 23 millis INFO @ Sun, 21 Jun 2020 18:23:47: start X-correlation... CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:47: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:23:47: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10_model.r INFO @ Sun, 21 Jun 2020 18:23:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:49: 5000000 INFO @ Sun, 21 Jun 2020 18:23:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:24:02: 7000000 INFO @ Sun, 21 Jun 2020 18:24:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:09: 8000000 INFO @ Sun, 21 Jun 2020 18:24:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:24:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:24:15: #1 total tags in treatment: 8944134 INFO @ Sun, 21 Jun 2020 18:24:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:15: #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 18:24:15: #1 tags after filtering in treatment: 8944010 INFO @ Sun, 21 Jun 2020 18:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:16: #2 number of paired peaks: 1589 INFO @ Sun, 21 Jun 2020 18:24:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:16: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:24:16: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20_model.r INFO @ Sun, 21 Jun 2020 18:24:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:19: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (3676 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193314/SRX193314.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:49: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (1931 records, 4 fields): 10 millis CompletedMACS2peakCalling