Job ID = 6458951 SRX = SRX5827820 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:11 prefetch.2.10.7: 1) Downloading 'SRR9051571'... 2020-06-21T12:53:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:58:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:58:06 prefetch.2.10.7: 1) 'SRR9051571' was downloaded successfully 2020-06-21T12:58:07 prefetch.2.10.7: 'SRR9051571' has 0 unresolved dependencies Read 37931333 spots for SRR9051571/SRR9051571.sra Written 37931333 spots for SRR9051571/SRR9051571.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: 00:09:02 37931333 reads; of these: 37931333 (100.00%) were unpaired; of these: 4095119 (10.80%) aligned 0 times 29035690 (76.55%) aligned exactly 1 time 4800524 (12.66%) aligned >1 times 89.20% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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_sort_core] merging from 16 files... [bam_rmdupse_core] 18352526 / 33836214 = 0.5424 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 22:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.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 22:17:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:18: 1000000 INFO @ Sun, 21 Jun 2020 22:17:23: 2000000 INFO @ Sun, 21 Jun 2020 22:17:28: 3000000 INFO @ Sun, 21 Jun 2020 22:17:33: 4000000 INFO @ Sun, 21 Jun 2020 22:17:39: 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 22:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.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 22:17:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:44: 6000000 INFO @ Sun, 21 Jun 2020 22:17:48: 1000000 INFO @ Sun, 21 Jun 2020 22:17:49: 7000000 INFO @ Sun, 21 Jun 2020 22:17:53: 2000000 INFO @ Sun, 21 Jun 2020 22:17:54: 8000000 INFO @ Sun, 21 Jun 2020 22:17:58: 3000000 INFO @ Sun, 21 Jun 2020 22:17:59: 9000000 INFO @ Sun, 21 Jun 2020 22:18:03: 4000000 INFO @ Sun, 21 Jun 2020 22:18:04: 10000000 INFO @ Sun, 21 Jun 2020 22:18:09: 5000000 INFO @ Sun, 21 Jun 2020 22:18:09: 11000000 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 22:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.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 22:18:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:14: 6000000 INFO @ Sun, 21 Jun 2020 22:18:14: 12000000 INFO @ Sun, 21 Jun 2020 22:18:18: 1000000 INFO @ Sun, 21 Jun 2020 22:18:19: 7000000 INFO @ Sun, 21 Jun 2020 22:18:20: 13000000 INFO @ Sun, 21 Jun 2020 22:18:23: 2000000 INFO @ Sun, 21 Jun 2020 22:18:24: 8000000 INFO @ Sun, 21 Jun 2020 22:18:25: 14000000 INFO @ Sun, 21 Jun 2020 22:18:29: 3000000 INFO @ Sun, 21 Jun 2020 22:18:29: 9000000 INFO @ Sun, 21 Jun 2020 22:18:30: 15000000 INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:33: #1 total tags in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:18:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:33: #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 22:18:34: 4000000 INFO @ Sun, 21 Jun 2020 22:18:34: #1 tags after filtering in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:34: 10000000 INFO @ Sun, 21 Jun 2020 22:18:35: #2 number of paired peaks: 1645 INFO @ Sun, 21 Jun 2020 22:18:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:35: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:18:35: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05_model.r INFO @ Sun, 21 Jun 2020 22:18:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:39: 5000000 INFO @ Sun, 21 Jun 2020 22:18:39: 11000000 INFO @ Sun, 21 Jun 2020 22:18:44: 6000000 INFO @ Sun, 21 Jun 2020 22:18:44: 12000000 INFO @ Sun, 21 Jun 2020 22:18:49: 7000000 INFO @ Sun, 21 Jun 2020 22:18:50: 13000000 INFO @ Sun, 21 Jun 2020 22:18:54: 8000000 INFO @ Sun, 21 Jun 2020 22:18:55: 14000000 INFO @ Sun, 21 Jun 2020 22:18:59: 9000000 INFO @ Sun, 21 Jun 2020 22:19:00: 15000000 INFO @ Sun, 21 Jun 2020 22:19:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:03: #1 total tags in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:19:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:03: #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 22:19:03: #1 tags after filtering in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:04: 10000000 INFO @ Sun, 21 Jun 2020 22:19:05: #2 number of paired peaks: 1645 INFO @ Sun, 21 Jun 2020 22:19:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:05: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:05: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:05: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:05: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:19:05: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10_model.r INFO @ Sun, 21 Jun 2020 22:19:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:09: 11000000 INFO @ Sun, 21 Jun 2020 22:19:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:14: 12000000 INFO @ Sun, 21 Jun 2020 22:19:20: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:25: 14000000 INFO @ Sun, 21 Jun 2020 22:19:30: 15000000 INFO @ Sun, 21 Jun 2020 22:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.05_summits.bed INFO @ Sun, 21 Jun 2020 22:19:30: Done! pass1 - making usageList (543 chroms): 2 millis pass2 - checking and writing primary data (4248 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:19:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:33: #1 total tags in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:19:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:33: #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 22:19:33: #1 tags after filtering in treatment: 15483688 INFO @ Sun, 21 Jun 2020 22:19:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:35: #2 number of paired peaks: 1645 INFO @ Sun, 21 Jun 2020 22:19:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:35: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:35: #2 predicted fragment length is 155 bps INFO @ Sun, 21 Jun 2020 22:19:35: #2 alternative fragment length(s) may be 155 bps INFO @ Sun, 21 Jun 2020 22:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20_model.r INFO @ Sun, 21 Jun 2020 22:19:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:20:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.10_summits.bed INFO @ Sun, 21 Jun 2020 22:20:01: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (2775 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827820/SRX5827820.20_summits.bed INFO @ Sun, 21 Jun 2020 22:20:32: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (1599 records, 4 fields): 10 millis CompletedMACS2peakCalling