Job ID = 6453856 SRX = SRX1531760 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:49:19 prefetch.2.10.7: 1) Downloading 'SRR3102818'... 2020-06-21T08:49:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:08 prefetch.2.10.7: 'SRR3102818' is valid 2020-06-21T08:51:08 prefetch.2.10.7: 1) 'SRR3102818' was downloaded successfully Read 22460845 spots for SRR3102818/SRR3102818.sra Written 22460845 spots for SRR3102818/SRR3102818.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: 00:01:04 22460845 reads; of these: 22460845 (100.00%) were unpaired; of these: 22317952 (99.36%) aligned 0 times 120722 (0.54%) aligned exactly 1 time 22171 (0.10%) aligned >1 times 0.64% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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_rmdupse_core] 20345 / 142893 = 0.1424 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 17:53:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.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 17:53:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:51: #1 total tags in treatment: 122548 INFO @ Sun, 21 Jun 2020 17:53:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:51: #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 17:53:51: #1 tags after filtering in treatment: 121857 INFO @ Sun, 21 Jun 2020 17:53:51: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 17:53:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:51: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 17:53:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:51: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:53:51: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 17:53:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05_model.r INFO @ Sun, 21 Jun 2020 17:53:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.05_summits.bed INFO @ Sun, 21 Jun 2020 17:53:52: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 2 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 17:54:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.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 17:54:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:21: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:54:21: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:54:21: #1 total tags in treatment: 122548 INFO @ Sun, 21 Jun 2020 17:54:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:21: #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 17:54:21: #1 tags after filtering in treatment: 121857 INFO @ Sun, 21 Jun 2020 17:54:21: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 17:54:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:21: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 17:54:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:21: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:54:21: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 17:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10_model.r INFO @ Sun, 21 Jun 2020 17:54:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.10_summits.bed INFO @ Sun, 21 Jun 2020 17:54:22: Done! pass1 - making usageList (26 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.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 17:54:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:54:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:54:51: #1 total tags in treatment: 122548 INFO @ Sun, 21 Jun 2020 17:54:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:51: #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 17:54:51: #1 tags after filtering in treatment: 121857 INFO @ Sun, 21 Jun 2020 17:54:51: #1 Redundant rate of treatment: 0.01 INFO @ Sun, 21 Jun 2020 17:54:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:51: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 17:54:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:51: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 17:54:51: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 17:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20_model.r INFO @ Sun, 21 Jun 2020 17:54:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1531760/SRX1531760.20_summits.bed INFO @ Sun, 21 Jun 2020 17:54:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 2 millis CompletedMACS2peakCalling