Job ID = 6456431 SRX = SRX3404026 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:44:53 prefetch.2.10.7: 1) Downloading 'SRR6303503'... 2020-06-21T10:44:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:46:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:46:55 prefetch.2.10.7: 'SRR6303503' is valid 2020-06-21T10:46:55 prefetch.2.10.7: 1) 'SRR6303503' was downloaded successfully 2020-06-21T10:46:56 prefetch.2.10.7: 'SRR6303503' has 0 unresolved dependencies Read 17869683 spots for SRR6303503/SRR6303503.sra Written 17869683 spots for SRR6303503/SRR6303503.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: 00:05:00 17869683 reads; of these: 17869683 (100.00%) were unpaired; of these: 589822 (3.30%) aligned 0 times 12433513 (69.58%) aligned exactly 1 time 4846348 (27.12%) aligned >1 times 96.70% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 1900082 / 17279861 = 0.1100 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 19:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.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 19:57:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:21: 1000000 INFO @ Sun, 21 Jun 2020 19:57:26: 2000000 INFO @ Sun, 21 Jun 2020 19:57:32: 3000000 INFO @ Sun, 21 Jun 2020 19:57:37: 4000000 INFO @ Sun, 21 Jun 2020 19:57:43: 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 19:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.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 19:57:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:48: 6000000 INFO @ Sun, 21 Jun 2020 19:57:52: 1000000 INFO @ Sun, 21 Jun 2020 19:57:55: 7000000 INFO @ Sun, 21 Jun 2020 19:57:58: 2000000 INFO @ Sun, 21 Jun 2020 19:58:01: 8000000 INFO @ Sun, 21 Jun 2020 19:58:05: 3000000 INFO @ Sun, 21 Jun 2020 19:58:07: 9000000 INFO @ Sun, 21 Jun 2020 19:58:11: 4000000 INFO @ Sun, 21 Jun 2020 19:58:13: 10000000 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 19:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.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 19:58:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:17: 5000000 INFO @ Sun, 21 Jun 2020 19:58:20: 11000000 INFO @ Sun, 21 Jun 2020 19:58:22: 1000000 INFO @ Sun, 21 Jun 2020 19:58:24: 6000000 INFO @ Sun, 21 Jun 2020 19:58:26: 12000000 INFO @ Sun, 21 Jun 2020 19:58:29: 2000000 INFO @ Sun, 21 Jun 2020 19:58:31: 7000000 INFO @ Sun, 21 Jun 2020 19:58:33: 13000000 INFO @ Sun, 21 Jun 2020 19:58:35: 3000000 INFO @ Sun, 21 Jun 2020 19:58:37: 8000000 INFO @ Sun, 21 Jun 2020 19:58:39: 14000000 INFO @ Sun, 21 Jun 2020 19:58:42: 4000000 INFO @ Sun, 21 Jun 2020 19:58:43: 9000000 INFO @ Sun, 21 Jun 2020 19:58:46: 15000000 INFO @ Sun, 21 Jun 2020 19:58:48: 5000000 INFO @ Sun, 21 Jun 2020 19:58:49: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:58:49: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:58:49: #1 total tags in treatment: 15379779 INFO @ Sun, 21 Jun 2020 19:58:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:49: #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 19:58:49: #1 tags after filtering in treatment: 15379702 INFO @ Sun, 21 Jun 2020 19:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:50: 10000000 INFO @ Sun, 21 Jun 2020 19:58:50: #2 number of paired peaks: 1192 INFO @ Sun, 21 Jun 2020 19:58:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:51: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:58:51: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 19:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05_model.r INFO @ Sun, 21 Jun 2020 19:58:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:54: 6000000 INFO @ Sun, 21 Jun 2020 19:58:56: 11000000 INFO @ Sun, 21 Jun 2020 19:59:01: 7000000 INFO @ Sun, 21 Jun 2020 19:59:02: 12000000 INFO @ Sun, 21 Jun 2020 19:59:07: 8000000 INFO @ Sun, 21 Jun 2020 19:59:09: 13000000 INFO @ Sun, 21 Jun 2020 19:59:13: 9000000 INFO @ Sun, 21 Jun 2020 19:59:15: 14000000 INFO @ Sun, 21 Jun 2020 19:59:20: 10000000 INFO @ Sun, 21 Jun 2020 19:59:21: 15000000 INFO @ Sun, 21 Jun 2020 19:59:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:59:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:59:24: #1 total tags in treatment: 15379779 INFO @ Sun, 21 Jun 2020 19:59:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:24: #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 19:59:24: #1 tags after filtering in treatment: 15379702 INFO @ Sun, 21 Jun 2020 19:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:26: 11000000 INFO @ Sun, 21 Jun 2020 19:59:26: #2 number of paired peaks: 1192 INFO @ Sun, 21 Jun 2020 19:59:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:26: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:59:26: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 19:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10_model.r INFO @ Sun, 21 Jun 2020 19:59:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:31: 12000000 INFO @ Sun, 21 Jun 2020 19:59:37: 13000000 INFO @ Sun, 21 Jun 2020 19:59:43: 14000000 INFO @ Sun, 21 Jun 2020 19:59:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.05_summits.bed INFO @ Sun, 21 Jun 2020 19:59:44: Done! pass1 - making usageList (604 chroms): 3 millis pass2 - checking and writing primary data (4167 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:59:49: 15000000 INFO @ Sun, 21 Jun 2020 19:59:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:59:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:59:51: #1 total tags in treatment: 15379779 INFO @ Sun, 21 Jun 2020 19:59:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:51: #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 19:59:52: #1 tags after filtering in treatment: 15379702 INFO @ Sun, 21 Jun 2020 19:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:53: #2 number of paired peaks: 1192 INFO @ Sun, 21 Jun 2020 19:59:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:53: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 19:59:53: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 19:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20_model.r INFO @ Sun, 21 Jun 2020 19:59:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.10_summits.bed INFO @ Sun, 21 Jun 2020 20:00:18: Done! pass1 - making usageList (487 chroms): 1 millis pass2 - checking and writing primary data (2852 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:00:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404026/SRX3404026.20_summits.bed INFO @ Sun, 21 Jun 2020 20:00:46: Done! pass1 - making usageList (292 chroms): 1 millis pass2 - checking and writing primary data (1635 records, 4 fields): 12 millis CompletedMACS2peakCalling