Job ID = 6458341 SRX = SRX5011087 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:27:07 prefetch.2.10.7: 1) Downloading 'SRR8191536'... 2020-06-21T12:27:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:30:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:30:39 prefetch.2.10.7: 1) 'SRR8191536' was downloaded successfully Read 22788335 spots for SRR8191536/SRR8191536.sra Written 22788335 spots for SRR8191536/SRR8191536.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: 00:04:31 22788335 reads; of these: 22788335 (100.00%) were unpaired; of these: 5509407 (24.18%) aligned 0 times 14085708 (61.81%) aligned exactly 1 time 3193220 (14.01%) aligned >1 times 75.82% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 8726606 / 17278928 = 0.5050 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 21:39:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.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 21:39:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:45: 1000000 INFO @ Sun, 21 Jun 2020 21:39:52: 2000000 INFO @ Sun, 21 Jun 2020 21:39:59: 3000000 INFO @ Sun, 21 Jun 2020 21:40:06: 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 21:40:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.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 21:40:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:13: 5000000 INFO @ Sun, 21 Jun 2020 21:40:15: 1000000 INFO @ Sun, 21 Jun 2020 21:40:21: 6000000 INFO @ Sun, 21 Jun 2020 21:40:22: 2000000 INFO @ Sun, 21 Jun 2020 21:40:29: 7000000 INFO @ Sun, 21 Jun 2020 21:40:29: 3000000 INFO @ Sun, 21 Jun 2020 21:40:35: 4000000 INFO @ Sun, 21 Jun 2020 21:40:36: 8000000 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 21:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.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 21:40:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:40:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:40:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:40:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:40:40: #1 total tags in treatment: 8552322 INFO @ Sun, 21 Jun 2020 21:40:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:40: #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 21:40:40: #1 tags after filtering in treatment: 8552198 INFO @ Sun, 21 Jun 2020 21:40:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:41: #2 number of paired peaks: 4376 INFO @ Sun, 21 Jun 2020 21:40:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:41: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 21:40:41: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 21:40:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05_model.r INFO @ Sun, 21 Jun 2020 21:40:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:40:42: 5000000 INFO @ Sun, 21 Jun 2020 21:40:46: 1000000 INFO @ Sun, 21 Jun 2020 21:40:49: 6000000 INFO @ Sun, 21 Jun 2020 21:40:54: 2000000 INFO @ Sun, 21 Jun 2020 21:40:56: 7000000 INFO @ Sun, 21 Jun 2020 21:41:02: 3000000 INFO @ Sun, 21 Jun 2020 21:41:03: 8000000 INFO @ Sun, 21 Jun 2020 21:41:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:07: #1 total tags in treatment: 8552322 INFO @ Sun, 21 Jun 2020 21:41:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:07: #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 21:41:07: #1 tags after filtering in treatment: 8552198 INFO @ Sun, 21 Jun 2020 21:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:08: #2 number of paired peaks: 4376 INFO @ Sun, 21 Jun 2020 21:41:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:08: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 21:41:08: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 21:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10_model.r INFO @ Sun, 21 Jun 2020 21:41:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:09: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:16: Done! pass1 - making usageList (369 chroms): 2 millis pass2 - checking and writing primary data (10290 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:17: 5000000 INFO @ Sun, 21 Jun 2020 21:41:24: 6000000 INFO @ Sun, 21 Jun 2020 21:41:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:32: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:41:38: 8000000 INFO @ Sun, 21 Jun 2020 21:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:41: Done! pass1 - making usageList (287 chroms): 2 millis pass2 - checking and writing primary data (7343 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:41:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:41:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:41:42: #1 total tags in treatment: 8552322 INFO @ Sun, 21 Jun 2020 21:41:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:42: #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 21:41:43: #1 tags after filtering in treatment: 8552198 INFO @ Sun, 21 Jun 2020 21:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:44: #2 number of paired peaks: 4376 INFO @ Sun, 21 Jun 2020 21:41:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:44: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 21:41:44: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 21:41:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20_model.r INFO @ Sun, 21 Jun 2020 21:41:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011087/SRX5011087.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:18: Done! pass1 - making usageList (170 chroms): 1 millis pass2 - checking and writing primary data (4216 records, 4 fields): 10 millis CompletedMACS2peakCalling