Job ID = 6455804 SRX = SRX3009512 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:14:51 prefetch.2.10.7: 1) Downloading 'SRR5832213'... 2020-06-21T10:14:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:08 prefetch.2.10.7: 1) 'SRR5832213' was downloaded successfully Read 22010851 spots for SRR5832213/SRR5832213.sra Written 22010851 spots for SRR5832213/SRR5832213.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: 00:02:51 22010851 reads; of these: 22010851 (100.00%) were unpaired; of these: 16484742 (74.89%) aligned 0 times 4563249 (20.73%) aligned exactly 1 time 962860 (4.37%) aligned >1 times 25.11% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 2810021 / 5526109 = 0.5085 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 19:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.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 19:24:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:46: 1000000 INFO @ Sun, 21 Jun 2020 19:24:51: 2000000 INFO @ Sun, 21 Jun 2020 19:24:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:24:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:24:55: #1 total tags in treatment: 2716088 INFO @ Sun, 21 Jun 2020 19:24:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:55: #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 19:24:55: #1 tags after filtering in treatment: 2715794 INFO @ Sun, 21 Jun 2020 19:24:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:56: #2 number of paired peaks: 5953 INFO @ Sun, 21 Jun 2020 19:24:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:56: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 19:24:56: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 19:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05_model.r INFO @ Sun, 21 Jun 2020 19:24:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.05_summits.bed INFO @ Sun, 21 Jun 2020 19:25:08: Done! pass1 - making usageList (171 chroms): 2 millis pass2 - checking and writing primary data (6603 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 19:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.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 19:25:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:17: 1000000 INFO @ Sun, 21 Jun 2020 19:25:23: 2000000 INFO @ Sun, 21 Jun 2020 19:25:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:25:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:25:27: #1 total tags in treatment: 2716088 INFO @ Sun, 21 Jun 2020 19:25:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:27: #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 19:25:27: #1 tags after filtering in treatment: 2715794 INFO @ Sun, 21 Jun 2020 19:25:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:28: #2 number of paired peaks: 5953 INFO @ Sun, 21 Jun 2020 19:25:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:28: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 19:25:28: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 19:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10_model.r INFO @ Sun, 21 Jun 2020 19:25:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:36: #3 Call peaks for each chromosome... 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 19:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:40: Done! pass1 - making usageList (132 chroms): 2 millis pass2 - checking and writing primary data (5422 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.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 19:25:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:47: 1000000 INFO @ Sun, 21 Jun 2020 19:25:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:25:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:25:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:25:55: #1 total tags in treatment: 2716088 INFO @ Sun, 21 Jun 2020 19:25:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:55: #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 19:25:56: #1 tags after filtering in treatment: 2715794 INFO @ Sun, 21 Jun 2020 19:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:56: #2 number of paired peaks: 5953 INFO @ Sun, 21 Jun 2020 19:25:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:56: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 19:25:56: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 19:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20_model.r INFO @ Sun, 21 Jun 2020 19:25:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:26:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009512/SRX3009512.20_summits.bed INFO @ Sun, 21 Jun 2020 19:26:07: Done! pass1 - making usageList (94 chroms): 2 millis pass2 - checking and writing primary data (3969 records, 4 fields): 7 millis CompletedMACS2peakCalling