Job ID = 6454208 SRX = SRX187588 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:54 prefetch.2.10.7: 1) Downloading 'SRR572652'... 2020-06-21T09:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:10:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:10:18 prefetch.2.10.7: 1) 'SRR572652' was downloaded successfully Read 35702391 spots for SRR572652/SRR572652.sra Written 35702391 spots for SRR572652/SRR572652.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:04 35702391 reads; of these: 35702391 (100.00%) were unpaired; of these: 29550674 (82.77%) aligned 0 times 4893120 (13.71%) aligned exactly 1 time 1258597 (3.53%) aligned >1 times 17.23% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 4385537 / 6151717 = 0.7129 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 18:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.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 18:16:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:29: 1000000 INFO @ Sun, 21 Jun 2020 18:16:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:16:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:16:34: #1 total tags in treatment: 1766180 INFO @ Sun, 21 Jun 2020 18:16:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:16:34: #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 18:16:34: #1 tags after filtering in treatment: 1766117 INFO @ Sun, 21 Jun 2020 18:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:16:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:16:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:16:34: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 18:16:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:16:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:16:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:16:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:16:34: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:16:34: #2 alternative fragment length(s) may be 168,191 bps INFO @ Sun, 21 Jun 2020 18:16:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05_model.r INFO @ Sun, 21 Jun 2020 18:16:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:16:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:16:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:16:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:16:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.05_summits.bed INFO @ Sun, 21 Jun 2020 18:16:41: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (998 records, 4 fields): 15 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 18:16:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.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 18:16:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:58: 1000000 INFO @ Sun, 21 Jun 2020 18:17:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:17:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:17:04: #1 total tags in treatment: 1766180 INFO @ Sun, 21 Jun 2020 18:17:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:04: #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 18:17:04: #1 tags after filtering in treatment: 1766117 INFO @ Sun, 21 Jun 2020 18:17:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:04: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 18:17:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:04: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:17:04: #2 alternative fragment length(s) may be 168,191 bps INFO @ Sun, 21 Jun 2020 18:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10_model.r INFO @ Sun, 21 Jun 2020 18:17:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:10: Done! pass1 - making usageList (403 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 11 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 18:17:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.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 18:17:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:29: 1000000 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 18:17:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:17:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:17:34: #1 total tags in treatment: 1766180 INFO @ Sun, 21 Jun 2020 18:17:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:34: #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 18:17:34: #1 tags after filtering in treatment: 1766117 INFO @ Sun, 21 Jun 2020 18:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:34: #2 number of paired peaks: 1534 INFO @ Sun, 21 Jun 2020 18:17:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:34: #2 predicted fragment length is 191 bps INFO @ Sun, 21 Jun 2020 18:17:34: #2 alternative fragment length(s) may be 168,191 bps INFO @ Sun, 21 Jun 2020 18:17:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20_model.r INFO @ Sun, 21 Jun 2020 18:17:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX187588/SRX187588.20_summits.bed INFO @ Sun, 21 Jun 2020 18:17:41: Done! pass1 - making usageList (164 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 5 millis CompletedMACS2peakCalling