Job ID = 6457817 SRX = SRX4798860 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:54:04 prefetch.2.10.7: 1) Downloading 'SRR7965209'... 2020-06-21T11:54:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:56:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:56:49 prefetch.2.10.7: 'SRR7965209' is valid 2020-06-21T11:56:49 prefetch.2.10.7: 1) 'SRR7965209' was downloaded successfully Read 14074673 spots for SRR7965209/SRR7965209.sra Written 14074673 spots for SRR7965209/SRR7965209.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: 00:01:05 14074673 reads; of these: 14074673 (100.00%) were unpaired; of these: 11929192 (84.76%) aligned 0 times 2012130 (14.30%) aligned exactly 1 time 133351 (0.95%) aligned >1 times 15.24% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 481844 / 2145481 = 0.2246 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 20:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.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 20:59:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:59:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:42: 1000000 INFO @ Sun, 21 Jun 2020 20:59:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:59:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:59:46: #1 total tags in treatment: 1663637 INFO @ Sun, 21 Jun 2020 20:59:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:46: #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 20:59:46: #1 tags after filtering in treatment: 1663070 INFO @ Sun, 21 Jun 2020 20:59:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:46: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:46: #2 number of paired peaks: 4577 INFO @ Sun, 21 Jun 2020 20:59:46: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:46: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:46: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:46: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:46: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 20:59:46: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 20:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05_model.r INFO @ Sun, 21 Jun 2020 20:59:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.05_summits.bed INFO @ Sun, 21 Jun 2020 20:59:53: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (3872 records, 4 fields): 6 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 21:00:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.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 21:00:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:12: 1000000 INFO @ Sun, 21 Jun 2020 21:00:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:00:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:00:16: #1 total tags in treatment: 1663637 INFO @ Sun, 21 Jun 2020 21:00:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:16: #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 21:00:16: #1 tags after filtering in treatment: 1663070 INFO @ Sun, 21 Jun 2020 21:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:00:16: #2 number of paired peaks: 4577 INFO @ Sun, 21 Jun 2020 21:00:16: start model_add_line... INFO @ Sun, 21 Jun 2020 21:00:16: start X-correlation... INFO @ Sun, 21 Jun 2020 21:00:16: end of X-cor INFO @ Sun, 21 Jun 2020 21:00:16: #2 finished! INFO @ Sun, 21 Jun 2020 21:00:16: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:00:16: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 21:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10_model.r INFO @ Sun, 21 Jun 2020 21:00:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:00:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.10_summits.bed INFO @ Sun, 21 Jun 2020 21:00:23: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1969 records, 4 fields): 4 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 21:00:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.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 21:00:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:00:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:00:42: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:00:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:00:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:00:46: #1 total tags in treatment: 1663637 INFO @ Sun, 21 Jun 2020 21:00:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:46: #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 21:00:46: #1 tags after filtering in treatment: 1663070 INFO @ Sun, 21 Jun 2020 21:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:00:46: #2 number of paired peaks: 4577 INFO @ Sun, 21 Jun 2020 21:00:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:00:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:00:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:00:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:00:46: #2 predicted fragment length is 168 bps INFO @ Sun, 21 Jun 2020 21:00:46: #2 alternative fragment length(s) may be 168 bps INFO @ Sun, 21 Jun 2020 21:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20_model.r INFO @ Sun, 21 Jun 2020 21:00:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:00:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:00:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4798860/SRX4798860.20_summits.bed INFO @ Sun, 21 Jun 2020 21:00:53: Done! pass1 - making usageList (24 chroms): 0 millis pass2 - checking and writing primary data (776 records, 4 fields): 11 millis CompletedMACS2peakCalling