Job ID = 6456072 SRX = SRX3167250 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:35:59 prefetch.2.10.7: 1) Downloading 'SRR6014253'... 2020-06-21T10:35:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:13 prefetch.2.10.7: 'SRR6014253' is valid 2020-06-21T10:38:13 prefetch.2.10.7: 1) 'SRR6014253' was downloaded successfully Read 7760856 spots for SRR6014253/SRR6014253.sra Written 7760856 spots for SRR6014253/SRR6014253.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: 00:01:57 7760856 reads; of these: 7760856 (100.00%) were unpaired; of these: 859192 (11.07%) aligned 0 times 4991799 (64.32%) aligned exactly 1 time 1909865 (24.61%) aligned >1 times 88.93% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 2090920 / 6901664 = 0.3030 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 19:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.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 19:42:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:48: 1000000 INFO @ Sun, 21 Jun 2020 19:42:53: 2000000 INFO @ Sun, 21 Jun 2020 19:42:59: 3000000 INFO @ Sun, 21 Jun 2020 19:43:05: 4000000 INFO @ Sun, 21 Jun 2020 19:43:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:09: #1 total tags in treatment: 4810744 INFO @ Sun, 21 Jun 2020 19:43:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:09: #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 19:43:10: #1 tags after filtering in treatment: 4810581 INFO @ Sun, 21 Jun 2020 19:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:10: #2 number of paired peaks: 3025 INFO @ Sun, 21 Jun 2020 19:43:10: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:10: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:10: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:10: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:10: #2 predicted fragment length is 334 bps INFO @ Sun, 21 Jun 2020 19:43:10: #2 alternative fragment length(s) may be 334 bps INFO @ Sun, 21 Jun 2020 19:43:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05_model.r INFO @ Sun, 21 Jun 2020 19:43:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:10: #3 Pre-compute pvalue-qvalue table... 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 19:43:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.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 19:43:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:19: 1000000 INFO @ Sun, 21 Jun 2020 19:43:26: 2000000 INFO @ Sun, 21 Jun 2020 19:43:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:32: 3000000 INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:33: Done! pass1 - making usageList (535 chroms): 2 millis pass2 - checking and writing primary data (3569 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:39: 4000000 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 19:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.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 19:43:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:45: #1 total tags in treatment: 4810744 INFO @ Sun, 21 Jun 2020 19:43:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:45: #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 19:43:45: #1 tags after filtering in treatment: 4810581 INFO @ Sun, 21 Jun 2020 19:43:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:46: #2 number of paired peaks: 3025 INFO @ Sun, 21 Jun 2020 19:43:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:46: #2 predicted fragment length is 334 bps INFO @ Sun, 21 Jun 2020 19:43:46: #2 alternative fragment length(s) may be 334 bps INFO @ Sun, 21 Jun 2020 19:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10_model.r INFO @ Sun, 21 Jun 2020 19:43:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:50: 1000000 INFO @ Sun, 21 Jun 2020 19:43:57: 2000000 INFO @ Sun, 21 Jun 2020 19:44:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:08: Done! pass1 - making usageList (419 chroms): 1 millis pass2 - checking and writing primary data (2557 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:11: 4000000 INFO @ Sun, 21 Jun 2020 19:44:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:44:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:44:16: #1 total tags in treatment: 4810744 INFO @ Sun, 21 Jun 2020 19:44:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:16: #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 19:44:17: #1 tags after filtering in treatment: 4810581 INFO @ Sun, 21 Jun 2020 19:44:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:17: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:17: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:44:17: #2 number of paired peaks: 3025 INFO @ Sun, 21 Jun 2020 19:44:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:17: #2 predicted fragment length is 334 bps INFO @ Sun, 21 Jun 2020 19:44:17: #2 alternative fragment length(s) may be 334 bps INFO @ Sun, 21 Jun 2020 19:44:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20_model.r INFO @ Sun, 21 Jun 2020 19:44:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167250/SRX3167250.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:40: Done! pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (1674 records, 4 fields): 9 millis CompletedMACS2peakCalling