Job ID = 6455568 SRX = SRX287892 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:04:40 prefetch.2.10.7: 1) Downloading 'SRR870081'... 2020-06-21T10:04:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:06:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:06:14 prefetch.2.10.7: 'SRR870081' is valid 2020-06-21T10:06:14 prefetch.2.10.7: 1) 'SRR870081' was downloaded successfully Read 13548301 spots for SRR870081/SRR870081.sra Written 13548301 spots for SRR870081/SRR870081.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: 00:04:11 13548301 reads; of these: 13548301 (100.00%) were unpaired; of these: 740393 (5.46%) aligned 0 times 8686053 (64.11%) aligned exactly 1 time 4121855 (30.42%) aligned >1 times 94.54% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 2780222 / 12807908 = 0.2171 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 19:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.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 19:14:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:46: 1000000 INFO @ Sun, 21 Jun 2020 19:14:51: 2000000 INFO @ Sun, 21 Jun 2020 19:14:56: 3000000 INFO @ Sun, 21 Jun 2020 19:15:01: 4000000 INFO @ Sun, 21 Jun 2020 19:15:06: 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 19:15:10: 6000000 INFO @ Sun, 21 Jun 2020 19:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.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 19:15:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:15: 7000000 INFO @ Sun, 21 Jun 2020 19:15:16: 1000000 INFO @ Sun, 21 Jun 2020 19:15:20: 8000000 INFO @ Sun, 21 Jun 2020 19:15:21: 2000000 INFO @ Sun, 21 Jun 2020 19:15:25: 9000000 INFO @ Sun, 21 Jun 2020 19:15:26: 3000000 INFO @ Sun, 21 Jun 2020 19:15:30: 10000000 INFO @ Sun, 21 Jun 2020 19:15:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:31: #1 total tags in treatment: 10027686 INFO @ Sun, 21 Jun 2020 19:15:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:31: #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 19:15:31: #1 tags after filtering in treatment: 10027685 INFO @ Sun, 21 Jun 2020 19:15:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:31: 4000000 INFO @ Sun, 21 Jun 2020 19:15:32: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 19:15:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:32: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 19:15:32: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 19:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05_model.r INFO @ Sun, 21 Jun 2020 19:15:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:36: 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 19:15:41: 6000000 INFO @ Sun, 21 Jun 2020 19:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.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 19:15:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:15:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:15:46: 7000000 INFO @ Sun, 21 Jun 2020 19:15:46: 1000000 INFO @ Sun, 21 Jun 2020 19:15:51: 2000000 INFO @ Sun, 21 Jun 2020 19:15:51: 8000000 INFO @ Sun, 21 Jun 2020 19:15:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:56: 3000000 INFO @ Sun, 21 Jun 2020 19:15:57: 9000000 INFO @ Sun, 21 Jun 2020 19:16:01: 4000000 INFO @ Sun, 21 Jun 2020 19:16:02: 10000000 INFO @ Sun, 21 Jun 2020 19:16:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:02: #1 total tags in treatment: 10027686 INFO @ Sun, 21 Jun 2020 19:16:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:02: #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 19:16:02: #1 tags after filtering in treatment: 10027685 INFO @ Sun, 21 Jun 2020 19:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:03: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 19:16:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:03: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 19:16:03: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 19:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10_model.r INFO @ Sun, 21 Jun 2020 19:16:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:06: 5000000 INFO @ Sun, 21 Jun 2020 19:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:07: Done! pass1 - making usageList (620 chroms): 2 millis pass2 - checking and writing primary data (4788 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:11: 6000000 INFO @ Sun, 21 Jun 2020 19:16:17: 7000000 INFO @ Sun, 21 Jun 2020 19:16:22: 8000000 INFO @ Sun, 21 Jun 2020 19:16:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:27: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:32: 10000000 INFO @ Sun, 21 Jun 2020 19:16:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:32: #1 total tags in treatment: 10027686 INFO @ Sun, 21 Jun 2020 19:16:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:32: #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 19:16:33: #1 tags after filtering in treatment: 10027685 INFO @ Sun, 21 Jun 2020 19:16:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:34: #2 number of paired peaks: 1630 INFO @ Sun, 21 Jun 2020 19:16:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:34: #2 predicted fragment length is 180 bps INFO @ Sun, 21 Jun 2020 19:16:34: #2 alternative fragment length(s) may be 180 bps INFO @ Sun, 21 Jun 2020 19:16:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20_model.r INFO @ Sun, 21 Jun 2020 19:16:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:36: Done! pass1 - making usageList (527 chroms): 1 millis pass2 - checking and writing primary data (3671 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287892/SRX287892.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:07: Done! pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (2660 records, 4 fields): 15 millis CompletedMACS2peakCalling