Job ID = 6456064 SRX = SRX3167243 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:34:07 prefetch.2.10.7: 1) Downloading 'SRR6014246'... 2020-06-21T10:34:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:30 prefetch.2.10.7: 'SRR6014246' is valid 2020-06-21T10:36:30 prefetch.2.10.7: 1) 'SRR6014246' was downloaded successfully Read 6818737 spots for SRR6014246/SRR6014246.sra Written 6818737 spots for SRR6014246/SRR6014246.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: 00:01:46 6818737 reads; of these: 6818737 (100.00%) were unpaired; of these: 1551065 (22.75%) aligned 0 times 4027013 (59.06%) aligned exactly 1 time 1240659 (18.19%) aligned >1 times 77.25% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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_rmdupse_core] 2331494 / 5267672 = 0.4426 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 19:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.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 19:40:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:24: 1000000 INFO @ Sun, 21 Jun 2020 19:40:30: 2000000 INFO @ Sun, 21 Jun 2020 19:40:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:40:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:40:36: #1 total tags in treatment: 2936178 INFO @ Sun, 21 Jun 2020 19:40:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:40:36: #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 19:40:37: #1 tags after filtering in treatment: 2935933 INFO @ Sun, 21 Jun 2020 19:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:40:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:40:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:40:37: #2 number of paired peaks: 4261 INFO @ Sun, 21 Jun 2020 19:40:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:40:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:40:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:40:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:40:37: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 19:40:37: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 19:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05_model.r INFO @ Sun, 21 Jun 2020 19:40:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:40:37: #3 Pre-compute pvalue-qvalue table... 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 19:40:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:40:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.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 19:40:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:40:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.05_summits.bed INFO @ Sun, 21 Jun 2020 19:40:51: Done! pass1 - making usageList (451 chroms): 2 millis pass2 - checking and writing primary data (4732 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:40:55: 1000000 INFO @ Sun, 21 Jun 2020 19:41:03: 2000000 INFO @ Sun, 21 Jun 2020 19:41:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:41:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:41:10: #1 total tags in treatment: 2936178 INFO @ Sun, 21 Jun 2020 19:41:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:10: #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 19:41:10: #1 tags after filtering in treatment: 2935933 INFO @ Sun, 21 Jun 2020 19:41:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:10: #2 number of paired peaks: 4261 INFO @ Sun, 21 Jun 2020 19:41:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:10: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 19:41:10: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 19:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10_model.r INFO @ Sun, 21 Jun 2020 19:41:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:10: #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 19:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.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 19:41:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.10_summits.bed INFO @ Sun, 21 Jun 2020 19:41:24: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (3291 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:41:25: 1000000 INFO @ Sun, 21 Jun 2020 19:41:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:41:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:41:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:41:37: #1 total tags in treatment: 2936178 INFO @ Sun, 21 Jun 2020 19:41:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:41:37: #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 19:41:38: #1 tags after filtering in treatment: 2935933 INFO @ Sun, 21 Jun 2020 19:41:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:41:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:41:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:41:38: #2 number of paired peaks: 4261 INFO @ Sun, 21 Jun 2020 19:41:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:41:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:41:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:41:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:41:38: #2 predicted fragment length is 219 bps INFO @ Sun, 21 Jun 2020 19:41:38: #2 alternative fragment length(s) may be 219 bps INFO @ Sun, 21 Jun 2020 19:41:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20_model.r INFO @ Sun, 21 Jun 2020 19:41:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:41:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:41:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:41:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:41:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:41:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167243/SRX3167243.20_summits.bed INFO @ Sun, 21 Jun 2020 19:41:51: Done! pass1 - making usageList (123 chroms): 2 millis pass2 - checking and writing primary data (2236 records, 4 fields): 6 millis CompletedMACS2peakCalling