Job ID = 6454613 SRX = SRX2399658 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:11:09 prefetch.2.10.7: 1) Downloading 'SRR5081492'... 2020-06-21T09:11:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:12:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:12:37 prefetch.2.10.7: 'SRR5081492' is valid 2020-06-21T09:12:37 prefetch.2.10.7: 1) 'SRR5081492' was downloaded successfully 2020-06-21T09:12:37 prefetch.2.10.7: 'SRR5081492' has 0 unresolved dependencies Read 13448762 spots for SRR5081492/SRR5081492.sra Written 13448762 spots for SRR5081492/SRR5081492.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:13 13448762 reads; of these: 13448762 (100.00%) were unpaired; of these: 1047107 (7.79%) aligned 0 times 8537820 (63.48%) aligned exactly 1 time 3863835 (28.73%) aligned >1 times 92.21% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 3175346 / 12401655 = 0.2560 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 18:21:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.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 18:21:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:21:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:04: 1000000 INFO @ Sun, 21 Jun 2020 18:22:12: 2000000 INFO @ Sun, 21 Jun 2020 18:22:19: 3000000 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 18:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.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 18:22:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:27: 4000000 INFO @ Sun, 21 Jun 2020 18:22:34: 1000000 INFO @ Sun, 21 Jun 2020 18:22:37: 5000000 INFO @ Sun, 21 Jun 2020 18:22:42: 2000000 INFO @ Sun, 21 Jun 2020 18:22:45: 6000000 INFO @ Sun, 21 Jun 2020 18:22:50: 3000000 INFO @ Sun, 21 Jun 2020 18:22:53: 7000000 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 18:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.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 18:22:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:58: 4000000 INFO @ Sun, 21 Jun 2020 18:23:02: 8000000 INFO @ Sun, 21 Jun 2020 18:23:05: 1000000 INFO @ Sun, 21 Jun 2020 18:23:07: 5000000 INFO @ Sun, 21 Jun 2020 18:23:10: 9000000 INFO @ Sun, 21 Jun 2020 18:23:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:23:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:23:12: #1 total tags in treatment: 9226309 INFO @ Sun, 21 Jun 2020 18:23:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:12: #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 18:23:13: #1 tags after filtering in treatment: 9226307 INFO @ Sun, 21 Jun 2020 18:23:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:13: 2000000 INFO @ Sun, 21 Jun 2020 18:23:14: #2 number of paired peaks: 8545 INFO @ Sun, 21 Jun 2020 18:23:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:14: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:23:14: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05_model.r INFO @ Sun, 21 Jun 2020 18:23:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:16: 6000000 INFO @ Sun, 21 Jun 2020 18:23:22: 3000000 INFO @ Sun, 21 Jun 2020 18:23:25: 7000000 INFO @ Sun, 21 Jun 2020 18:23:31: 4000000 INFO @ Sun, 21 Jun 2020 18:23:34: 8000000 INFO @ Sun, 21 Jun 2020 18:23:40: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:23:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:43: 9000000 INFO @ Sun, 21 Jun 2020 18:23:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:23:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:23:45: #1 total tags in treatment: 9226309 INFO @ Sun, 21 Jun 2020 18:23:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:45: #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 18:23:46: #1 tags after filtering in treatment: 9226307 INFO @ Sun, 21 Jun 2020 18:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:47: #2 number of paired peaks: 8545 INFO @ Sun, 21 Jun 2020 18:23:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:47: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:23:47: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10_model.r INFO @ Sun, 21 Jun 2020 18:23:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:48: 6000000 INFO @ Sun, 21 Jun 2020 18:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:56: 7000000 INFO @ Sun, 21 Jun 2020 18:23:56: Done! pass1 - making usageList (701 chroms): 3 millis pass2 - checking and writing primary data (9432 records, 4 fields): 50 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:04: 8000000 INFO @ Sun, 21 Jun 2020 18:24:13: 9000000 INFO @ Sun, 21 Jun 2020 18:24:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:24:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:24:14: #1 total tags in treatment: 9226309 INFO @ Sun, 21 Jun 2020 18:24:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:14: #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 18:24:15: #1 tags after filtering in treatment: 9226307 INFO @ Sun, 21 Jun 2020 18:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:16: #2 number of paired peaks: 8545 INFO @ Sun, 21 Jun 2020 18:24:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:17: #2 predicted fragment length is 186 bps INFO @ Sun, 21 Jun 2020 18:24:17: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 21 Jun 2020 18:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20_model.r INFO @ Sun, 21 Jun 2020 18:24:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:27: Done! pass1 - making usageList (498 chroms): 2 millis pass2 - checking and writing primary data (7939 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2399658/SRX2399658.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:56: Done! pass1 - making usageList (325 chroms): 2 millis pass2 - checking and writing primary data (6553 records, 4 fields): 26 millis CompletedMACS2peakCalling