Job ID = 6452512 SRX = SRX013112 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:59:53 prefetch.2.10.7: 1) Downloading 'SRR030378'... 2020-06-21T07:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:00:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:00:42 prefetch.2.10.7: 'SRR030378' is valid 2020-06-21T08:00:42 prefetch.2.10.7: 1) 'SRR030378' was downloaded successfully Read 7423467 spots for SRR030378/SRR030378.sra Written 7423467 spots for SRR030378/SRR030378.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: 00:01:18 7423467 reads; of these: 7423467 (100.00%) were unpaired; of these: 532318 (7.17%) aligned 0 times 6393642 (86.13%) aligned exactly 1 time 497507 (6.70%) aligned >1 times 92.83% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 634147 / 6891149 = 0.0920 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 17:04:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.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 17:04:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:18: 1000000 INFO @ Sun, 21 Jun 2020 17:04:23: 2000000 INFO @ Sun, 21 Jun 2020 17:04:29: 3000000 INFO @ Sun, 21 Jun 2020 17:04:35: 4000000 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 17:04:41: 5000000 INFO @ Sun, 21 Jun 2020 17:04:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.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 17:04:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:04:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:04:47: 6000000 INFO @ Sun, 21 Jun 2020 17:04:48: 1000000 INFO @ Sun, 21 Jun 2020 17:04:49: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:04:49: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:04:49: #1 total tags in treatment: 6257002 INFO @ Sun, 21 Jun 2020 17:04:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:04:49: #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 17:04:49: #1 tags after filtering in treatment: 6256727 INFO @ Sun, 21 Jun 2020 17:04:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:04:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:04:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:04:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:04:50: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 17:04:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:04:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:04:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:04:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:04:50: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 17:04:50: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 17:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05_model.r INFO @ Sun, 21 Jun 2020 17:04:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:04:54: 2000000 INFO @ Sun, 21 Jun 2020 17:04:59: 3000000 INFO @ Sun, 21 Jun 2020 17:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:05: 4000000 INFO @ Sun, 21 Jun 2020 17:05:10: 5000000 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 17:05:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.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 17:05:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:05:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.05_summits.bed INFO @ Sun, 21 Jun 2020 17:05:13: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (5270 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:05:16: 6000000 INFO @ Sun, 21 Jun 2020 17:05:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:05:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:05:18: #1 total tags in treatment: 6257002 INFO @ Sun, 21 Jun 2020 17:05:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:18: #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 17:05:18: 1000000 INFO @ Sun, 21 Jun 2020 17:05:18: #1 tags after filtering in treatment: 6256727 INFO @ Sun, 21 Jun 2020 17:05:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:18: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:19: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 17:05:19: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:19: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 17:05:19: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 17:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10_model.r INFO @ Sun, 21 Jun 2020 17:05:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:05:24: 2000000 INFO @ Sun, 21 Jun 2020 17:05:30: 3000000 INFO @ Sun, 21 Jun 2020 17:05:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:05:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:05:41: 5000000 INFO @ Sun, 21 Jun 2020 17:05:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.10_summits.bed INFO @ Sun, 21 Jun 2020 17:05:42: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (2099 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:05:47: 6000000 INFO @ Sun, 21 Jun 2020 17:05:48: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:05:48: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:05:48: #1 total tags in treatment: 6257002 INFO @ Sun, 21 Jun 2020 17:05:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:05:48: #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 17:05:49: #1 tags after filtering in treatment: 6256727 INFO @ Sun, 21 Jun 2020 17:05:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:05:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:05:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:05:49: #2 number of paired peaks: 1031 INFO @ Sun, 21 Jun 2020 17:05:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:05:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:05:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:05:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:05:49: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 17:05:49: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 17:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20_model.r INFO @ Sun, 21 Jun 2020 17:05:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:05:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:06:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013112/SRX013112.20_summits.bed INFO @ Sun, 21 Jun 2020 17:06:12: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (460 records, 4 fields): 23 millis CompletedMACS2peakCalling