Job ID = 6455685 SRX = SRX287986 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:21 prefetch.2.10.7: 1) Downloading 'SRR870175'... 2020-06-21T10:23:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:54 prefetch.2.10.7: 'SRR870175' is valid 2020-06-21T10:25:54 prefetch.2.10.7: 1) 'SRR870175' was downloaded successfully Read 14005474 spots for SRR870175/SRR870175.sra Written 14005474 spots for SRR870175/SRR870175.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: 00:02:50 14005474 reads; of these: 14005474 (100.00%) were unpaired; of these: 1151455 (8.22%) aligned 0 times 11955741 (85.36%) aligned exactly 1 time 898278 (6.41%) aligned >1 times 91.78% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 2224597 / 12854019 = 0.1731 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 19:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.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 19:32:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:57: 1000000 INFO @ Sun, 21 Jun 2020 19:33:02: 2000000 INFO @ Sun, 21 Jun 2020 19:33:07: 3000000 INFO @ Sun, 21 Jun 2020 19:33:12: 4000000 INFO @ Sun, 21 Jun 2020 19:33:16: 5000000 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 19:33:21: 6000000 INFO @ Sun, 21 Jun 2020 19:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.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 19:33:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:26: 7000000 INFO @ Sun, 21 Jun 2020 19:33:27: 1000000 INFO @ Sun, 21 Jun 2020 19:33:31: 8000000 INFO @ Sun, 21 Jun 2020 19:33:32: 2000000 INFO @ Sun, 21 Jun 2020 19:33:36: 9000000 INFO @ Sun, 21 Jun 2020 19:33:38: 3000000 INFO @ Sun, 21 Jun 2020 19:33:41: 10000000 INFO @ Sun, 21 Jun 2020 19:33:42: 4000000 INFO @ Sun, 21 Jun 2020 19:33:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:45: #1 total tags in treatment: 10629422 INFO @ Sun, 21 Jun 2020 19:33:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:45: #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 19:33:45: #1 tags after filtering in treatment: 10629118 INFO @ Sun, 21 Jun 2020 19:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:46: #2 number of paired peaks: 5979 INFO @ Sun, 21 Jun 2020 19:33:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:46: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 19:33:46: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 19:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05_model.r INFO @ Sun, 21 Jun 2020 19:33:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:47: 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 19:33:52: 6000000 INFO @ Sun, 21 Jun 2020 19:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.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 19:33:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:57: 7000000 INFO @ Sun, 21 Jun 2020 19:33:57: 1000000 INFO @ Sun, 21 Jun 2020 19:34:02: 8000000 INFO @ Sun, 21 Jun 2020 19:34:02: 2000000 INFO @ Sun, 21 Jun 2020 19:34:07: 9000000 INFO @ Sun, 21 Jun 2020 19:34:08: 3000000 INFO @ Sun, 21 Jun 2020 19:34:12: 4000000 INFO @ Sun, 21 Jun 2020 19:34:13: 10000000 INFO @ Sun, 21 Jun 2020 19:34:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:16: #1 total tags in treatment: 10629422 INFO @ Sun, 21 Jun 2020 19:34:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:16: #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 19:34:16: #1 tags after filtering in treatment: 10629118 INFO @ Sun, 21 Jun 2020 19:34:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:17: 5000000 INFO @ Sun, 21 Jun 2020 19:34:18: #2 number of paired peaks: 5979 INFO @ Sun, 21 Jun 2020 19:34:18: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:18: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:18: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:18: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:18: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 19:34:18: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 19:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10_model.r INFO @ Sun, 21 Jun 2020 19:34:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:22: 6000000 INFO @ Sun, 21 Jun 2020 19:34:27: 7000000 INFO @ Sun, 21 Jun 2020 19:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:29: Done! pass1 - making usageList (65 chroms): 3 millis pass2 - checking and writing primary data (17746 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:32: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:37: 9000000 INFO @ Sun, 21 Jun 2020 19:34:42: 10000000 INFO @ Sun, 21 Jun 2020 19:34:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:45: #1 total tags in treatment: 10629422 INFO @ Sun, 21 Jun 2020 19:34:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:45: #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 19:34:46: #1 tags after filtering in treatment: 10629118 INFO @ Sun, 21 Jun 2020 19:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:47: #2 number of paired peaks: 5979 INFO @ Sun, 21 Jun 2020 19:34:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:47: #2 predicted fragment length is 251 bps INFO @ Sun, 21 Jun 2020 19:34:47: #2 alternative fragment length(s) may be 251 bps INFO @ Sun, 21 Jun 2020 19:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20_model.r INFO @ Sun, 21 Jun 2020 19:34:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:01: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (11375 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287986/SRX287986.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:29: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (5822 records, 4 fields): 7 millis CompletedMACS2peakCalling