Job ID = 6456583 SRX = SRX365701 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:55:01 prefetch.2.10.7: 1) Downloading 'SRR1013779'... 2020-06-21T10:55:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:37 prefetch.2.10.7: 1) 'SRR1013779' was downloaded successfully Read 25412489 spots for SRR1013779/SRR1013779.sra Written 25412489 spots for SRR1013779/SRR1013779.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: 00:05:13 25412489 reads; of these: 25412489 (100.00%) were unpaired; of these: 9979676 (39.27%) aligned 0 times 11492646 (45.22%) aligned exactly 1 time 3940167 (15.50%) aligned >1 times 60.73% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 12877043 / 15432813 = 0.8344 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 20:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.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 20:09:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:26: 1000000 INFO @ Sun, 21 Jun 2020 20:09:32: 2000000 INFO @ Sun, 21 Jun 2020 20:09:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:09:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:09:35: #1 total tags in treatment: 2555770 INFO @ Sun, 21 Jun 2020 20:09:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:35: #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 20:09:35: #1 tags after filtering in treatment: 2555651 INFO @ Sun, 21 Jun 2020 20:09:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:36: #2 number of paired peaks: 4230 INFO @ Sun, 21 Jun 2020 20:09:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:36: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:09:36: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05_model.r INFO @ Sun, 21 Jun 2020 20:09:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.05_summits.bed INFO @ Sun, 21 Jun 2020 20:09:46: Done! pass1 - making usageList (753 chroms): 1 millis pass2 - checking and writing primary data (2734 records, 4 fields): 22 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 20:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.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 20:09:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:56: 1000000 INFO @ Sun, 21 Jun 2020 20:10:03: 2000000 INFO @ Sun, 21 Jun 2020 20:10:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:07: #1 total tags in treatment: 2555770 INFO @ Sun, 21 Jun 2020 20:10:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:07: #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 20:10:08: #1 tags after filtering in treatment: 2555651 INFO @ Sun, 21 Jun 2020 20:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #2 number of paired peaks: 4230 INFO @ Sun, 21 Jun 2020 20:10:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:08: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10_model.r INFO @ Sun, 21 Jun 2020 20:10:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:15: #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 20:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.10_summits.bed INFO @ Sun, 21 Jun 2020 20:10:18: Done! pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (1705 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.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 20:10:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:26: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:10:32: 2000000 INFO @ Sun, 21 Jun 2020 20:10:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:10:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:10:35: #1 total tags in treatment: 2555770 INFO @ Sun, 21 Jun 2020 20:10:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:35: #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 20:10:36: #1 tags after filtering in treatment: 2555651 INFO @ Sun, 21 Jun 2020 20:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:36: #2 number of paired peaks: 4230 INFO @ Sun, 21 Jun 2020 20:10:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:36: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:10:36: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:10:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20_model.r INFO @ Sun, 21 Jun 2020 20:10:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:10:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX365701/SRX365701.20_summits.bed INFO @ Sun, 21 Jun 2020 20:10:46: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (906 records, 4 fields): 15 millis CompletedMACS2peakCalling