Job ID = 6454273 SRX = SRX193630 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:04:54 prefetch.2.10.7: 1) Downloading 'SRR586008'... 2020-06-21T09:04:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:08:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:17 prefetch.2.10.7: 1) 'SRR586008' was downloaded successfully Read 19377235 spots for SRR586008/SRR586008.sra Written 19377235 spots for SRR586008/SRR586008.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: 00:03:12 19377235 reads; of these: 19377235 (100.00%) were unpaired; of these: 15155249 (78.21%) aligned 0 times 2878407 (14.85%) aligned exactly 1 time 1343579 (6.93%) aligned >1 times 21.79% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 2166039 / 4221986 = 0.5130 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 18:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.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 18:13:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:01: 1000000 INFO @ Sun, 21 Jun 2020 18:14:07: 2000000 INFO @ Sun, 21 Jun 2020 18:14:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:14:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:14:08: #1 total tags in treatment: 2055947 INFO @ Sun, 21 Jun 2020 18:14:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:08: #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 18:14:08: #1 tags after filtering in treatment: 2055615 INFO @ Sun, 21 Jun 2020 18:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:08: #2 number of paired peaks: 1612 INFO @ Sun, 21 Jun 2020 18:14:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:08: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:14:08: #2 alternative fragment length(s) may be 55,135,207 bps INFO @ Sun, 21 Jun 2020 18:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05_model.r INFO @ Sun, 21 Jun 2020 18:14:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:17: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (902 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 18:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.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 18:14:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:31: 1000000 INFO @ Sun, 21 Jun 2020 18:14:38: 2000000 INFO @ Sun, 21 Jun 2020 18:14:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:14:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:14:38: #1 total tags in treatment: 2055947 INFO @ Sun, 21 Jun 2020 18:14:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:38: #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 18:14:38: #1 tags after filtering in treatment: 2055615 INFO @ Sun, 21 Jun 2020 18:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:39: #2 number of paired peaks: 1612 INFO @ Sun, 21 Jun 2020 18:14:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:39: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:14:39: #2 alternative fragment length(s) may be 55,135,207 bps INFO @ Sun, 21 Jun 2020 18:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10_model.r INFO @ Sun, 21 Jun 2020 18:14:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.10_summits.bed INFO @ Sun, 21 Jun 2020 18:14:47: Done! pass1 - making usageList (155 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 18:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.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 18:14:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:15:01: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:15:08: 2000000 INFO @ Sun, 21 Jun 2020 18:15:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:15:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:15:08: #1 total tags in treatment: 2055947 INFO @ Sun, 21 Jun 2020 18:15:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:15:08: #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 18:15:08: #1 tags after filtering in treatment: 2055615 INFO @ Sun, 21 Jun 2020 18:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:15:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:15:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:15:09: #2 number of paired peaks: 1612 INFO @ Sun, 21 Jun 2020 18:15:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:15:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:15:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:15:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:15:09: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 18:15:09: #2 alternative fragment length(s) may be 55,135,207 bps INFO @ Sun, 21 Jun 2020 18:15:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20_model.r INFO @ Sun, 21 Jun 2020 18:15:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:15:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:15:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193630/SRX193630.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:17: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 5 millis CompletedMACS2peakCalling