Job ID = 6455209 SRX = SRX2832104 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:55 prefetch.2.10.7: 1) Downloading 'SRR5573768'... 2020-06-21T09:48:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:37 prefetch.2.10.7: 'SRR5573768' is valid 2020-06-21T09:50:37 prefetch.2.10.7: 1) 'SRR5573768' was downloaded successfully Read 12923525 spots for SRR5573768/SRR5573768.sra Written 12923525 spots for SRR5573768/SRR5573768.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: 00:04:03 12923525 reads; of these: 12923525 (100.00%) were unpaired; of these: 714360 (5.53%) aligned 0 times 8704909 (67.36%) aligned exactly 1 time 3504256 (27.12%) aligned >1 times 94.47% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2465573 / 12209165 = 0.2019 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 18:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.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 18:58:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:58: 1000000 INFO @ Sun, 21 Jun 2020 18:59:03: 2000000 INFO @ Sun, 21 Jun 2020 18:59:08: 3000000 INFO @ Sun, 21 Jun 2020 18:59:14: 4000000 INFO @ Sun, 21 Jun 2020 18:59:19: 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 18:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.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 18:59:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:24: 6000000 INFO @ Sun, 21 Jun 2020 18:59:28: 1000000 INFO @ Sun, 21 Jun 2020 18:59:29: 7000000 INFO @ Sun, 21 Jun 2020 18:59:33: 2000000 INFO @ Sun, 21 Jun 2020 18:59:35: 8000000 INFO @ Sun, 21 Jun 2020 18:59:38: 3000000 INFO @ Sun, 21 Jun 2020 18:59:41: 9000000 INFO @ Sun, 21 Jun 2020 18:59:44: 4000000 INFO @ Sun, 21 Jun 2020 18:59:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:45: #1 total tags in treatment: 9743592 INFO @ Sun, 21 Jun 2020 18:59:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:45: #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 18:59:45: #1 tags after filtering in treatment: 9743460 INFO @ Sun, 21 Jun 2020 18:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:46: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 18:59:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:46: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 18:59:46: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 18:59:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05_model.r INFO @ Sun, 21 Jun 2020 18:59:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:49: 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 18:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.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 18:59:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:55: 6000000 INFO @ Sun, 21 Jun 2020 18:59:58: 1000000 INFO @ Sun, 21 Jun 2020 19:00:00: 7000000 INFO @ Sun, 21 Jun 2020 19:00:04: 2000000 INFO @ Sun, 21 Jun 2020 19:00:06: 8000000 INFO @ Sun, 21 Jun 2020 19:00:09: 3000000 INFO @ Sun, 21 Jun 2020 19:00:12: 9000000 INFO @ Sun, 21 Jun 2020 19:00:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:15: 4000000 INFO @ Sun, 21 Jun 2020 19:00:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:16: #1 total tags in treatment: 9743592 INFO @ Sun, 21 Jun 2020 19:00:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:16: #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 19:00:16: #1 tags after filtering in treatment: 9743460 INFO @ Sun, 21 Jun 2020 19:00:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:17: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 19:00:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:17: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 19:00:17: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 19:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10_model.r INFO @ Sun, 21 Jun 2020 19:00:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:21: 5000000 INFO @ Sun, 21 Jun 2020 19:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.05_summits.bed INFO @ Sun, 21 Jun 2020 19:00:24: Done! pass1 - making usageList (613 chroms): 2 millis pass2 - checking and writing primary data (5557 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:00:26: 6000000 INFO @ Sun, 21 Jun 2020 19:00:31: 7000000 INFO @ Sun, 21 Jun 2020 19:00:37: 8000000 INFO @ Sun, 21 Jun 2020 19:00:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:43: 9000000 INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:47: #1 total tags in treatment: 9743592 INFO @ Sun, 21 Jun 2020 19:00:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:47: #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 19:00:47: #1 tags after filtering in treatment: 9743460 INFO @ Sun, 21 Jun 2020 19:00:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:47: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:00:48: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 19:00:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:48: #2 predicted fragment length is 210 bps INFO @ Sun, 21 Jun 2020 19:00:48: #2 alternative fragment length(s) may be 210 bps INFO @ Sun, 21 Jun 2020 19:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20_model.r INFO @ Sun, 21 Jun 2020 19:00:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.10_summits.bed INFO @ Sun, 21 Jun 2020 19:00:53: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:01:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2832104/SRX2832104.20_summits.bed INFO @ Sun, 21 Jun 2020 19:01:25: Done! pass1 - making usageList (400 chroms): 2 millis pass2 - checking and writing primary data (952 records, 4 fields): 12 millis CompletedMACS2peakCalling