Job ID = 6452366 SRX = SRX013011 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:11 prefetch.2.10.7: 1) Downloading 'SRR030277'... 2020-06-21T08:28:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:08 prefetch.2.10.7: 'SRR030277' is valid 2020-06-21T08:29:08 prefetch.2.10.7: 1) 'SRR030277' was downloaded successfully Read 4199400 spots for SRR030277/SRR030277.sra Written 4199400 spots for SRR030277/SRR030277.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: 00:00:01 Multiseed full-index search: 00:00:40 4199400 reads; of these: 4199400 (100.00%) were unpaired; of these: 1719238 (40.94%) aligned 0 times 2099758 (50.00%) aligned exactly 1 time 380404 (9.06%) aligned >1 times 59.06% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 83489 / 2480162 = 0.0337 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 17:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.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 17:31:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:29: 1000000 INFO @ Sun, 21 Jun 2020 17:31:37: 2000000 INFO @ Sun, 21 Jun 2020 17:31:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:31:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:31:40: #1 total tags in treatment: 2396673 INFO @ Sun, 21 Jun 2020 17:31:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:40: #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 17:31:41: #1 tags after filtering in treatment: 2396460 INFO @ Sun, 21 Jun 2020 17:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:41: #2 number of paired peaks: 1410 INFO @ Sun, 21 Jun 2020 17:31:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:41: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 17:31:41: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 17:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05_model.r INFO @ Sun, 21 Jun 2020 17:31:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:47: #3 Call peaks for each chromosome... 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 17:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.05_summits.bed INFO @ Sun, 21 Jun 2020 17:31:50: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (1661 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.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 17:31:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:59: 1000000 INFO @ Sun, 21 Jun 2020 17:32:07: 2000000 INFO @ Sun, 21 Jun 2020 17:32:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:32:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:32:10: #1 total tags in treatment: 2396673 INFO @ Sun, 21 Jun 2020 17:32:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:10: #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 17:32:11: #1 tags after filtering in treatment: 2396460 INFO @ Sun, 21 Jun 2020 17:32:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:11: #2 number of paired peaks: 1410 INFO @ Sun, 21 Jun 2020 17:32:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:11: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 17:32:11: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 17:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10_model.r INFO @ Sun, 21 Jun 2020 17:32:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:16: #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 17:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.10_summits.bed INFO @ Sun, 21 Jun 2020 17:32:19: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.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 17:32:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:32:29: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:32:37: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:32:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:32:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:32:40: #1 total tags in treatment: 2396673 INFO @ Sun, 21 Jun 2020 17:32:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:40: #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 17:32:40: #1 tags after filtering in treatment: 2396460 INFO @ Sun, 21 Jun 2020 17:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:41: #2 number of paired peaks: 1410 INFO @ Sun, 21 Jun 2020 17:32:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:41: #2 predicted fragment length is 154 bps INFO @ Sun, 21 Jun 2020 17:32:41: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 21 Jun 2020 17:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20_model.r INFO @ Sun, 21 Jun 2020 17:32:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013011/SRX013011.20_summits.bed INFO @ Sun, 21 Jun 2020 17:32:49: Done! pass1 - making usageList (41 chroms): 3 millis pass2 - checking and writing primary data (60 records, 4 fields): 3 millis CompletedMACS2peakCalling