Job ID = 5720708 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,880,148 reads read : 1,880,148 reads written : 1,880,148 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:29 1880148 reads; of these: 1880148 (100.00%) were unpaired; of these: 55089 (2.93%) aligned 0 times 1531953 (81.48%) aligned exactly 1 time 293106 (15.59%) aligned >1 times 97.07% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 154944 / 1825059 = 0.0849 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 @ Thu, 16 Apr 2020 00:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.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 @ Thu, 16 Apr 2020 00:59:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:04: 1000000 INFO @ Thu, 16 Apr 2020 01:00:08: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:00:08: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:00:08: #1 total tags in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:00:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:08: #1 tags after filtering in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:00:08: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:08: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:08: #2 number of paired peaks: 3746 INFO @ Thu, 16 Apr 2020 01:00:08: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:08: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:08: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:08: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:08: #2 predicted fragment length is 111 bps INFO @ Thu, 16 Apr 2020 01:00:08: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 16 Apr 2020 01:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05_model.r INFO @ Thu, 16 Apr 2020 01:00:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.05_summits.bed INFO @ Thu, 16 Apr 2020 01:00:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3017 records, 4 fields): 4 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 @ Thu, 16 Apr 2020 01:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.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 @ Thu, 16 Apr 2020 01:00:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:34: 1000000 INFO @ Thu, 16 Apr 2020 01:00:38: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:00:38: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:00:38: #1 total tags in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:00:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:38: #1 tags after filtering in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:38: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:38: #2 number of paired peaks: 3746 INFO @ Thu, 16 Apr 2020 01:00:38: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:38: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:38: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:38: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:38: #2 predicted fragment length is 111 bps INFO @ Thu, 16 Apr 2020 01:00:38: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 16 Apr 2020 01:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10_model.r INFO @ Thu, 16 Apr 2020 01:00:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:00:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.10_summits.bed INFO @ Thu, 16 Apr 2020 01:00:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2061 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.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 @ Thu, 16 Apr 2020 01:00:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:05: 1000000 INFO @ Thu, 16 Apr 2020 01:01:10: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:01:10: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:01:10: #1 total tags in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:01:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:01:10: #1 tags after filtering in treatment: 1670115 INFO @ Thu, 16 Apr 2020 01:01:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:10: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:11: #2 number of paired peaks: 3746 INFO @ Thu, 16 Apr 2020 01:01:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:11: #2 predicted fragment length is 111 bps INFO @ Thu, 16 Apr 2020 01:01:11: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 16 Apr 2020 01:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20_model.r INFO @ Thu, 16 Apr 2020 01:01:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:01:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158172/SRX4158172.20_summits.bed INFO @ Thu, 16 Apr 2020 01:01:18: Done! BigWig に変換しました。 pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1319 records, 4 fields): 3 millis CompletedMACS2peakCalling