Job ID = 6456359 SRX = SRX3380803 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:56:31 prefetch.2.10.7: 1) Downloading 'SRR6278166'... 2020-06-21T10:56:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:02:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:02:11 prefetch.2.10.7: 1) 'SRR6278166' was downloaded successfully Read 30487113 spots for SRR6278166/SRR6278166.sra Written 30487113 spots for SRR6278166/SRR6278166.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: 00:06:45 30487113 reads; of these: 30487113 (100.00%) were unpaired; of these: 1654309 (5.43%) aligned 0 times 26147101 (85.76%) aligned exactly 1 time 2685703 (8.81%) aligned >1 times 94.57% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 25983179 / 28832804 = 0.9012 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 20:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.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 20:14:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:25: 1000000 INFO @ Sun, 21 Jun 2020 20:14:30: 2000000 INFO @ Sun, 21 Jun 2020 20:14:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:14:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:14:35: #1 total tags in treatment: 2849625 INFO @ Sun, 21 Jun 2020 20:14:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:14:35: #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 20:14:35: #1 tags after filtering in treatment: 2849493 INFO @ Sun, 21 Jun 2020 20:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:14:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:14:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:14:36: #2 number of paired peaks: 7016 INFO @ Sun, 21 Jun 2020 20:14:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:14:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:14:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:14:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:14:36: #2 predicted fragment length is 252 bps INFO @ Sun, 21 Jun 2020 20:14:36: #2 alternative fragment length(s) may be 252 bps INFO @ Sun, 21 Jun 2020 20:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05_model.r INFO @ Sun, 21 Jun 2020 20:14:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:14:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:14:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:14:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:14:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.05_summits.bed INFO @ Sun, 21 Jun 2020 20:14:47: Done! pass1 - making usageList (580 chroms): 2 millis pass2 - checking and writing primary data (6709 records, 4 fields): 21 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 20:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.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 20:14:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:14:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:14:55: 1000000 INFO @ Sun, 21 Jun 2020 20:15:00: 2000000 INFO @ Sun, 21 Jun 2020 20:15:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:15:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:15:05: #1 total tags in treatment: 2849625 INFO @ Sun, 21 Jun 2020 20:15:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:05: #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 20:15:06: #1 tags after filtering in treatment: 2849493 INFO @ Sun, 21 Jun 2020 20:15:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:06: #2 number of paired peaks: 7016 INFO @ Sun, 21 Jun 2020 20:15:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:06: #2 predicted fragment length is 252 bps INFO @ Sun, 21 Jun 2020 20:15:06: #2 alternative fragment length(s) may be 252 bps INFO @ Sun, 21 Jun 2020 20:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10_model.r INFO @ Sun, 21 Jun 2020 20:15:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:15:15: #3 Call peaks for each chromosome... 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 20:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.10_summits.bed INFO @ Sun, 21 Jun 2020 20:15:18: Done! pass1 - making usageList (516 chroms): 1 millis pass2 - checking and writing primary data (4308 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:15:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.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 20:15:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:15:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:15:25: 1000000 INFO @ Sun, 21 Jun 2020 20:15:30: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:15:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:15:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:15:35: #1 total tags in treatment: 2849625 INFO @ Sun, 21 Jun 2020 20:15:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:15:35: #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 20:15:36: #1 tags after filtering in treatment: 2849493 INFO @ Sun, 21 Jun 2020 20:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:15:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:15:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:15:36: #2 number of paired peaks: 7016 INFO @ Sun, 21 Jun 2020 20:15:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:15:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:15:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:15:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:15:36: #2 predicted fragment length is 252 bps INFO @ Sun, 21 Jun 2020 20:15:36: #2 alternative fragment length(s) may be 252 bps INFO @ Sun, 21 Jun 2020 20:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20_model.r INFO @ Sun, 21 Jun 2020 20:15:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:15:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:15:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:15:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:15:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:15:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380803/SRX3380803.20_summits.bed INFO @ Sun, 21 Jun 2020 20:15:48: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (2107 records, 4 fields): 12 millis CompletedMACS2peakCalling