Job ID = 6453090 SRX = SRX1032399 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:01:08 prefetch.2.10.7: 1) Downloading 'SRR2031900'... 2020-06-21T08:01:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:38 prefetch.2.10.7: 1) 'SRR2031900' was downloaded successfully Read 23414513 spots for SRR2031900/SRR2031900.sra Written 23414513 spots for SRR2031900/SRR2031900.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: 00:06:31 23414513 reads; of these: 23414513 (100.00%) were unpaired; of these: 1160953 (4.96%) aligned 0 times 16531361 (70.60%) aligned exactly 1 time 5722199 (24.44%) aligned >1 times 95.04% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 12251815 / 22253560 = 0.5506 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 17:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.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 17:21:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:13: 1000000 INFO @ Sun, 21 Jun 2020 17:21:19: 2000000 INFO @ Sun, 21 Jun 2020 17:21:26: 3000000 INFO @ Sun, 21 Jun 2020 17:21:31: 4000000 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 17:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.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 17:21:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:38: 5000000 INFO @ Sun, 21 Jun 2020 17:21:44: 1000000 INFO @ Sun, 21 Jun 2020 17:21:45: 6000000 INFO @ Sun, 21 Jun 2020 17:21:52: 2000000 INFO @ Sun, 21 Jun 2020 17:21:52: 7000000 INFO @ Sun, 21 Jun 2020 17:22:00: 3000000 INFO @ Sun, 21 Jun 2020 17:22:00: 8000000 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 17:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.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 17:22:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:07: 9000000 INFO @ Sun, 21 Jun 2020 17:22:08: 4000000 INFO @ Sun, 21 Jun 2020 17:22:14: 10000000 INFO @ Sun, 21 Jun 2020 17:22:14: 1000000 INFO @ Sun, 21 Jun 2020 17:22:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:22:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:22:14: #1 total tags in treatment: 10001745 INFO @ Sun, 21 Jun 2020 17:22:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:14: #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 17:22:15: #1 tags after filtering in treatment: 10001744 INFO @ Sun, 21 Jun 2020 17:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:16: 5000000 INFO @ Sun, 21 Jun 2020 17:22:16: #2 number of paired peaks: 1867 INFO @ Sun, 21 Jun 2020 17:22:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:16: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:22:16: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 17:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05_model.r INFO @ Sun, 21 Jun 2020 17:22:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:22: 2000000 INFO @ Sun, 21 Jun 2020 17:22:24: 6000000 INFO @ Sun, 21 Jun 2020 17:22:30: 3000000 INFO @ Sun, 21 Jun 2020 17:22:31: 7000000 INFO @ Sun, 21 Jun 2020 17:22:38: 4000000 INFO @ Sun, 21 Jun 2020 17:22:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:40: 8000000 INFO @ Sun, 21 Jun 2020 17:22:46: 5000000 INFO @ Sun, 21 Jun 2020 17:22:48: 9000000 INFO @ Sun, 21 Jun 2020 17:22:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.05_summits.bed INFO @ Sun, 21 Jun 2020 17:22:51: Done! pass1 - making usageList (779 chroms): 2 millis pass2 - checking and writing primary data (9365 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:22:54: 6000000 INFO @ Sun, 21 Jun 2020 17:22:56: 10000000 INFO @ Sun, 21 Jun 2020 17:22:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:22:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:22:56: #1 total tags in treatment: 10001745 INFO @ Sun, 21 Jun 2020 17:22:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:56: #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 17:22:56: #1 tags after filtering in treatment: 10001744 INFO @ Sun, 21 Jun 2020 17:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:57: #2 number of paired peaks: 1867 INFO @ Sun, 21 Jun 2020 17:22:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:57: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:22:57: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 17:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10_model.r INFO @ Sun, 21 Jun 2020 17:22:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:57: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:23:01: 7000000 INFO @ Sun, 21 Jun 2020 17:23:09: 8000000 INFO @ Sun, 21 Jun 2020 17:23:16: 9000000 INFO @ Sun, 21 Jun 2020 17:23:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:23:23: 10000000 INFO @ Sun, 21 Jun 2020 17:23:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:23:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:23:23: #1 total tags in treatment: 10001745 INFO @ Sun, 21 Jun 2020 17:23:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:23: #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 17:23:23: #1 tags after filtering in treatment: 10001744 INFO @ Sun, 21 Jun 2020 17:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:24: #2 number of paired peaks: 1867 INFO @ Sun, 21 Jun 2020 17:23:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:24: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 17:23:24: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 17:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20_model.r INFO @ Sun, 21 Jun 2020 17:23:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.10_summits.bed INFO @ Sun, 21 Jun 2020 17:23:30: Done! pass1 - making usageList (646 chroms): 1 millis pass2 - checking and writing primary data (5883 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1032399/SRX1032399.20_summits.bed INFO @ Sun, 21 Jun 2020 17:23:58: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (3102 records, 4 fields): 15 millis CompletedMACS2peakCalling