Job ID = 6459103 SRX = SRX6386775 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:56:25 prefetch.2.10.7: 1) Downloading 'SRR9624507'... 2020-06-21T12:56:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:10:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:10:34 prefetch.2.10.7: 1) 'SRR9624507' was downloaded successfully Read 62392803 spots for SRR9624507/SRR9624507.sra Written 62392803 spots for SRR9624507/SRR9624507.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: 00:12:30 62392803 reads; of these: 62392803 (100.00%) were unpaired; of these: 41781166 (66.96%) aligned 0 times 12843086 (20.58%) aligned exactly 1 time 7768551 (12.45%) aligned >1 times 33.04% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 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 12 files... [bam_rmdupse_core] 15970540 / 20611637 = 0.7748 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 22:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.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 22:30:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:30:06: 1000000 INFO @ Sun, 21 Jun 2020 22:30:12: 2000000 INFO @ Sun, 21 Jun 2020 22:30:17: 3000000 INFO @ Sun, 21 Jun 2020 22:30:22: 4000000 INFO @ Sun, 21 Jun 2020 22:30:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:30:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:30:26: #1 total tags in treatment: 4641097 INFO @ Sun, 21 Jun 2020 22:30:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:30:26: #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 22:30:26: #1 tags after filtering in treatment: 4641084 INFO @ Sun, 21 Jun 2020 22:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:30:26: #1 finished! INFO @ Sun, 21 Jun 2020 22:30:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:30:27: #2 number of paired peaks: 3295 INFO @ Sun, 21 Jun 2020 22:30:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:30:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:30:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:30:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:30:27: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 22:30:27: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 22:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05_model.r INFO @ Sun, 21 Jun 2020 22:30:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:30:27: #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 22:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.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 22:30:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:30:36: 1000000 INFO @ Sun, 21 Jun 2020 22:30:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:30:42: 2000000 INFO @ Sun, 21 Jun 2020 22:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.05_summits.bed INFO @ Sun, 21 Jun 2020 22:30:43: Done! pass1 - making usageList (924 chroms): 1 millis pass2 - checking and writing primary data (4903 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:30:47: 3000000 INFO @ Sun, 21 Jun 2020 22:30:52: 4000000 INFO @ Sun, 21 Jun 2020 22:30:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:30:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:30:56: #1 total tags in treatment: 4641097 INFO @ Sun, 21 Jun 2020 22:30:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:30:56: #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 22:30:56: #1 tags after filtering in treatment: 4641084 INFO @ Sun, 21 Jun 2020 22:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:30:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:30:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:30:57: #2 number of paired peaks: 3295 INFO @ Sun, 21 Jun 2020 22:30:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:30:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:30:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:30:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:30:57: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 22:30:57: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 22:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10_model.r INFO @ Sun, 21 Jun 2020 22:30:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:30:57: #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 22:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.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 22:31:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:06: 1000000 INFO @ Sun, 21 Jun 2020 22:31:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:11: 2000000 INFO @ Sun, 21 Jun 2020 22:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.10_summits.bed INFO @ Sun, 21 Jun 2020 22:31:13: Done! pass1 - making usageList (775 chroms): 2 millis pass2 - checking and writing primary data (2834 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:31:17: 3000000 INFO @ Sun, 21 Jun 2020 22:31:22: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:31:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:31:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:31:26: #1 total tags in treatment: 4641097 INFO @ Sun, 21 Jun 2020 22:31:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:26: #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 22:31:26: #1 tags after filtering in treatment: 4641084 INFO @ Sun, 21 Jun 2020 22:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:26: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:27: #2 number of paired peaks: 3295 INFO @ Sun, 21 Jun 2020 22:31:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:27: #2 predicted fragment length is 139 bps INFO @ Sun, 21 Jun 2020 22:31:27: #2 alternative fragment length(s) may be 139 bps INFO @ Sun, 21 Jun 2020 22:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20_model.r INFO @ Sun, 21 Jun 2020 22:31:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:31:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386775/SRX6386775.20_summits.bed INFO @ Sun, 21 Jun 2020 22:31:43: Done! pass1 - making usageList (676 chroms): 1 millis pass2 - checking and writing primary data (1744 records, 4 fields): 18 millis CompletedMACS2peakCalling