Job ID = 6455018 SRX = SRX2638365 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:47:10 prefetch.2.10.7: 1) Downloading 'SRR5341691'... 2020-06-21T09:47:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:30 prefetch.2.10.7: 1) 'SRR5341691' was downloaded successfully Read 24108154 spots for SRR5341691/SRR5341691.sra Written 24108154 spots for SRR5341691/SRR5341691.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: 00:07:17 24108154 reads; of these: 24108154 (100.00%) were unpaired; of these: 11544893 (47.89%) aligned 0 times 3831267 (15.89%) aligned exactly 1 time 8731994 (36.22%) aligned >1 times 52.11% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 11148400 / 12563261 = 0.8874 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 19:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.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 19:01:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:27: 1000000 INFO @ Sun, 21 Jun 2020 19:01:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:01:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:01:29: #1 total tags in treatment: 1414861 INFO @ Sun, 21 Jun 2020 19:01:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:29: #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 19:01:30: #1 tags after filtering in treatment: 1414613 INFO @ Sun, 21 Jun 2020 19:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:30: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:01:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:30: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 19:01:30: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 19:01:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05_model.r INFO @ Sun, 21 Jun 2020 19:01:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:36: Done! pass1 - making usageList (616 chroms): 1 millis pass2 - checking and writing primary data (2188 records, 4 fields): 20 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 19:01:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.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 19:01:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:57: 1000000 INFO @ Sun, 21 Jun 2020 19:02:00: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:02:00: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:02:00: #1 total tags in treatment: 1414861 INFO @ Sun, 21 Jun 2020 19:02:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:00: #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 19:02:00: #1 tags after filtering in treatment: 1414613 INFO @ Sun, 21 Jun 2020 19:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:00: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:02:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:00: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 19:02:00: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 19:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10_model.r INFO @ Sun, 21 Jun 2020 19:02:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.10_summits.bed INFO @ Sun, 21 Jun 2020 19:02:06: Done! pass1 - making usageList (411 chroms): 2 millis pass2 - checking and writing primary data (1043 records, 4 fields): 13 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 @ Sun, 21 Jun 2020 19:02:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.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 19:02:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:02:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:02:29: #1 total tags in treatment: 1414861 INFO @ Sun, 21 Jun 2020 19:02:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:29: #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 19:02:30: #1 tags after filtering in treatment: 1414613 INFO @ Sun, 21 Jun 2020 19:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:30: #2 number of paired peaks: 3115 INFO @ Sun, 21 Jun 2020 19:02:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:30: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 19:02:30: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 19:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20_model.r INFO @ Sun, 21 Jun 2020 19:02:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638365/SRX2638365.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:36: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 6 millis CompletedMACS2peakCalling