Job ID = 6456584 SRX = SRX365702 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:00:31 prefetch.2.10.7: 1) Downloading 'SRR1013780'... 2020-06-21T11:00:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:03:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:03:53 prefetch.2.10.7: 1) 'SRR1013780' was downloaded successfully Read 22143112 spots for SRR1013780/SRR1013780.sra Written 22143112 spots for SRR1013780/SRR1013780.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: 00:03:57 22143112 reads; of these: 22143112 (100.00%) were unpaired; of these: 12054008 (54.44%) aligned 0 times 7459386 (33.69%) aligned exactly 1 time 2629718 (11.88%) aligned >1 times 45.56% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 7256261 / 10089104 = 0.7192 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 20:11:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.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 20:11:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:23: 1000000 INFO @ Sun, 21 Jun 2020 20:11:30: 2000000 INFO @ Sun, 21 Jun 2020 20:11:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:11:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:11:36: #1 total tags in treatment: 2832843 INFO @ Sun, 21 Jun 2020 20:11:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:36: #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 20:11:37: #1 tags after filtering in treatment: 2832691 INFO @ Sun, 21 Jun 2020 20:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:37: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:37: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 20:11:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:37: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 20:11:37: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 20:11:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05_model.r INFO @ Sun, 21 Jun 2020 20:11:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:44: #3 Call peaks for each chromosome... 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 20:11:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.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 20:11:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.05_summits.bed INFO @ Sun, 21 Jun 2020 20:11:47: Done! pass1 - making usageList (680 chroms): 2 millis pass2 - checking and writing primary data (2340 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:52: 1000000 INFO @ Sun, 21 Jun 2020 20:11:58: 2000000 INFO @ Sun, 21 Jun 2020 20:12:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:03: #1 total tags in treatment: 2832843 INFO @ Sun, 21 Jun 2020 20:12:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:03: #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 20:12:04: #1 tags after filtering in treatment: 2832691 INFO @ Sun, 21 Jun 2020 20:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:04: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 20:12:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:04: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 20:12:04: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 20:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10_model.r INFO @ Sun, 21 Jun 2020 20:12:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10_peaks.xls BedGraph に変換中... INFO @ Sun, 21 Jun 2020 20:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:14: Done! 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 pass1 - making usageList (560 chroms): 2 millis pass2 - checking and writing primary data (1463 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:12:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.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 20:12:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:23: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:31: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:12:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:12:37: #1 total tags in treatment: 2832843 INFO @ Sun, 21 Jun 2020 20:12:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:37: #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 20:12:38: #1 tags after filtering in treatment: 2832691 INFO @ Sun, 21 Jun 2020 20:12:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:38: #2 number of paired peaks: 3200 INFO @ Sun, 21 Jun 2020 20:12:38: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:38: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:38: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:38: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:38: #2 predicted fragment length is 122 bps INFO @ Sun, 21 Jun 2020 20:12:38: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 21 Jun 2020 20:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20_model.r INFO @ Sun, 21 Jun 2020 20:12:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365702/SRX365702.20_summits.bed INFO @ Sun, 21 Jun 2020 20:12:48: Done! pass1 - making usageList (387 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 11 millis CompletedMACS2peakCalling