Job ID = 6454668 SRX = SRX2458929 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:32:29 prefetch.2.10.7: 1) Downloading 'SRR5140278'... 2020-06-21T09:32:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:31 prefetch.2.10.7: 'SRR5140278' is valid 2020-06-21T09:33:31 prefetch.2.10.7: 1) 'SRR5140278' was downloaded successfully 2020-06-21T09:33:31 prefetch.2.10.7: 'SRR5140278' has 0 unresolved dependencies Read 11305060 spots for SRR5140278/SRR5140278.sra Written 11305060 spots for SRR5140278/SRR5140278.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: 00:02:51 11305060 reads; of these: 11305060 (100.00%) were unpaired; of these: 580587 (5.14%) aligned 0 times 8007297 (70.83%) aligned exactly 1 time 2717176 (24.04%) aligned >1 times 94.86% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 7160066 / 10724473 = 0.6676 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 18:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.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 18:38:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:01: 1000000 INFO @ Sun, 21 Jun 2020 18:39:06: 2000000 INFO @ Sun, 21 Jun 2020 18:39:12: 3000000 INFO @ Sun, 21 Jun 2020 18:39:15: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:39:15: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:39:15: #1 total tags in treatment: 3564407 INFO @ Sun, 21 Jun 2020 18:39:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:15: #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 18:39:15: #1 tags after filtering in treatment: 3564230 INFO @ Sun, 21 Jun 2020 18:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:16: #2 number of paired peaks: 2479 INFO @ Sun, 21 Jun 2020 18:39:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:16: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 18:39:16: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 18:39:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05_model.r INFO @ Sun, 21 Jun 2020 18:39:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:16: #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 18:39:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.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 18:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:28: Done! pass1 - making usageList (650 chroms): 1 millis pass2 - checking and writing primary data (2016 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:31: 1000000 INFO @ Sun, 21 Jun 2020 18:39:37: 2000000 INFO @ Sun, 21 Jun 2020 18:39:42: 3000000 INFO @ Sun, 21 Jun 2020 18:39:45: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:39:45: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:39:45: #1 total tags in treatment: 3564407 INFO @ Sun, 21 Jun 2020 18:39:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:45: #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 18:39:46: #1 tags after filtering in treatment: 3564230 INFO @ Sun, 21 Jun 2020 18:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:46: #2 number of paired peaks: 2479 INFO @ Sun, 21 Jun 2020 18:39:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:46: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 18:39:46: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 18:39:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10_model.r INFO @ Sun, 21 Jun 2020 18:39:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:46: #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 18:39:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.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 18:39:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:59: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:01: 1000000 INFO @ Sun, 21 Jun 2020 18:40:06: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:12: 3000000 INFO @ Sun, 21 Jun 2020 18:40:15: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:40:15: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:40:15: #1 total tags in treatment: 3564407 INFO @ Sun, 21 Jun 2020 18:40:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:15: #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 18:40:15: #1 tags after filtering in treatment: 3564230 INFO @ Sun, 21 Jun 2020 18:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:15: #2 number of paired peaks: 2479 INFO @ Sun, 21 Jun 2020 18:40:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:15: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 18:40:15: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 18:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20_model.r INFO @ Sun, 21 Jun 2020 18:40:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458929/SRX2458929.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:28: Done! pass1 - making usageList (209 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 7 millis CompletedMACS2peakCalling