Job ID = 6456906 SRX = SRX4053333 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:15:54 prefetch.2.10.7: 1) Downloading 'SRR7132380'... 2020-06-21T11:15:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:46 prefetch.2.10.7: 'SRR7132380' is valid 2020-06-21T11:16:46 prefetch.2.10.7: 1) 'SRR7132380' was downloaded successfully 2020-06-21T11:16:46 prefetch.2.10.7: 'SRR7132380' has 0 unresolved dependencies Read 5387630 spots for SRR7132380/SRR7132380.sra Written 5387630 spots for SRR7132380/SRR7132380.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: 00:01:05 5387630 reads; of these: 5387630 (100.00%) were unpaired; of these: 646463 (12.00%) aligned 0 times 4394722 (81.57%) aligned exactly 1 time 346445 (6.43%) aligned >1 times 88.00% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1182815 / 4741167 = 0.2495 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 20:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.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 20:19:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:19:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:49: 1000000 INFO @ Sun, 21 Jun 2020 20:19:55: 2000000 INFO @ Sun, 21 Jun 2020 20:20:00: 3000000 INFO @ Sun, 21 Jun 2020 20:20:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:04: #1 total tags in treatment: 3558352 INFO @ Sun, 21 Jun 2020 20:20:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:04: #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 20:20:04: #1 tags after filtering in treatment: 3557960 INFO @ Sun, 21 Jun 2020 20:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:05: #2 number of paired peaks: 9730 INFO @ Sun, 21 Jun 2020 20:20:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:05: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:20:05: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05_model.r INFO @ Sun, 21 Jun 2020 20:20:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:05: #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 20:20:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.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 20:20:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:20:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:20:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:20: 1000000 INFO @ Sun, 21 Jun 2020 20:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.05_summits.bed INFO @ Sun, 21 Jun 2020 20:20:20: Done! pass1 - making usageList (71 chroms): 2 millis pass2 - checking and writing primary data (5790 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:25: 2000000 INFO @ Sun, 21 Jun 2020 20:20:31: 3000000 INFO @ Sun, 21 Jun 2020 20:20:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:20:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:20:34: #1 total tags in treatment: 3558352 INFO @ Sun, 21 Jun 2020 20:20:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:20:34: #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 20:20:34: #1 tags after filtering in treatment: 3557960 INFO @ Sun, 21 Jun 2020 20:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:20:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:20:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:20:35: #2 number of paired peaks: 9730 INFO @ Sun, 21 Jun 2020 20:20:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:20:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:20:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:20:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:20:35: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:20:35: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10_model.r INFO @ Sun, 21 Jun 2020 20:20:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:20:35: #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 20:20:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.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 20:20:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:20:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:20:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:20:50: 1000000 INFO @ Sun, 21 Jun 2020 20:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.10_summits.bed INFO @ Sun, 21 Jun 2020 20:20:50: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (5517 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:20:55: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:21:01: 3000000 INFO @ Sun, 21 Jun 2020 20:21:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:21:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:21:04: #1 total tags in treatment: 3558352 INFO @ Sun, 21 Jun 2020 20:21:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:21:04: #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 20:21:04: #1 tags after filtering in treatment: 3557960 INFO @ Sun, 21 Jun 2020 20:21:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:21:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:21:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:21:05: #2 number of paired peaks: 9730 INFO @ Sun, 21 Jun 2020 20:21:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:21:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:21:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:21:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:21:05: #2 predicted fragment length is 171 bps INFO @ Sun, 21 Jun 2020 20:21:05: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 21 Jun 2020 20:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20_model.r INFO @ Sun, 21 Jun 2020 20:21:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:21:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:21:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:21:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053333/SRX4053333.20_summits.bed INFO @ Sun, 21 Jun 2020 20:21:20: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (4878 records, 4 fields): 10 millis CompletedMACS2peakCalling