Job ID = 6454289 SRX = SRX197563 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:58:04 prefetch.2.10.7: 1) Downloading 'SRR596991'... 2020-06-21T08:58:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:00:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:00:13 prefetch.2.10.7: 'SRR596991' is valid 2020-06-21T09:00:13 prefetch.2.10.7: 1) 'SRR596991' was downloaded successfully Read 14265915 spots for SRR596991/SRR596991.sra Written 14265915 spots for SRR596991/SRR596991.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: 00:02:42 14265915 reads; of these: 14265915 (100.00%) were unpaired; of these: 2382156 (16.70%) aligned 0 times 9207445 (64.54%) aligned exactly 1 time 2676314 (18.76%) aligned >1 times 83.30% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 2195074 / 11883759 = 0.1847 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 18:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.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 18:06:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:29: 1000000 INFO @ Sun, 21 Jun 2020 18:06:35: 2000000 INFO @ Sun, 21 Jun 2020 18:06:40: 3000000 INFO @ Sun, 21 Jun 2020 18:06:45: 4000000 INFO @ Sun, 21 Jun 2020 18:06:50: 5000000 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 18:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.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 18:06:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:56: 6000000 INFO @ Sun, 21 Jun 2020 18:07:00: 1000000 INFO @ Sun, 21 Jun 2020 18:07:01: 7000000 INFO @ Sun, 21 Jun 2020 18:07:06: 2000000 INFO @ Sun, 21 Jun 2020 18:07:07: 8000000 INFO @ Sun, 21 Jun 2020 18:07:11: 3000000 INFO @ Sun, 21 Jun 2020 18:07:13: 9000000 INFO @ Sun, 21 Jun 2020 18:07:17: 4000000 INFO @ Sun, 21 Jun 2020 18:07:17: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:07:17: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:07:17: #1 total tags in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:07:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:17: #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 18:07:18: #1 tags after filtering in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:19: #2 number of paired peaks: 1669 INFO @ Sun, 21 Jun 2020 18:07:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:19: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:07:19: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05_model.r INFO @ Sun, 21 Jun 2020 18:07:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:19: #3 Pre-compute pvalue-qvalue table... 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 18:07:22: 5000000 INFO @ Sun, 21 Jun 2020 18:07:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.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 18:07:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:28: 6000000 INFO @ Sun, 21 Jun 2020 18:07:30: 1000000 INFO @ Sun, 21 Jun 2020 18:07:33: 7000000 INFO @ Sun, 21 Jun 2020 18:07:35: 2000000 INFO @ Sun, 21 Jun 2020 18:07:39: 8000000 INFO @ Sun, 21 Jun 2020 18:07:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:41: 3000000 INFO @ Sun, 21 Jun 2020 18:07:45: 9000000 INFO @ Sun, 21 Jun 2020 18:07:47: 4000000 INFO @ Sun, 21 Jun 2020 18:07:49: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:07:49: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:07:49: #1 total tags in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:07:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:49: #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 18:07:50: #1 tags after filtering in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:07:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:50: #2 number of paired peaks: 1669 INFO @ Sun, 21 Jun 2020 18:07:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:50: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:07:50: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:07:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10_model.r INFO @ Sun, 21 Jun 2020 18:07:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:50: Done! pass1 - making usageList (487 chroms): 2 millis pass2 - checking and writing primary data (5779 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:52: 5000000 INFO @ Sun, 21 Jun 2020 18:07:57: 6000000 INFO @ Sun, 21 Jun 2020 18:08:02: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:08: 8000000 INFO @ Sun, 21 Jun 2020 18:08:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:13: 9000000 INFO @ Sun, 21 Jun 2020 18:08:17: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:08:17: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:08:17: #1 total tags in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:08:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:17: #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 18:08:17: #1 tags after filtering in treatment: 9688685 INFO @ Sun, 21 Jun 2020 18:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:18: #2 number of paired peaks: 1669 INFO @ Sun, 21 Jun 2020 18:08:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:18: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:08:18: #2 alternative fragment length(s) may be 96 bps INFO @ Sun, 21 Jun 2020 18:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20_model.r INFO @ Sun, 21 Jun 2020 18:08:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:22: Done! pass1 - making usageList (419 chroms): 2 millis pass2 - checking and writing primary data (4340 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197563/SRX197563.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:51: Done! pass1 - making usageList (214 chroms): 1 millis pass2 - checking and writing primary data (2067 records, 4 fields): 8 millis CompletedMACS2peakCalling