Job ID = 6455926 SRX = SRX3068965 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:38:14 prefetch.2.10.7: 1) Downloading 'SRR5907441'... 2020-06-21T10:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:19 prefetch.2.10.7: 'SRR5907441' is valid 2020-06-21T10:40:19 prefetch.2.10.7: 1) 'SRR5907441' was downloaded successfully Read 9272991 spots for SRR5907441/SRR5907441.sra Written 9272991 spots for SRR5907441/SRR5907441.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: 00:01:16 9272991 reads; of these: 9272991 (100.00%) were unpaired; of these: 5603658 (60.43%) aligned 0 times 3122061 (33.67%) aligned exactly 1 time 547272 (5.90%) aligned >1 times 39.57% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 1779282 / 3669333 = 0.4849 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 19:43:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.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 19:43:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:31: 1000000 INFO @ Sun, 21 Jun 2020 19:43:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:43:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:43:38: #1 total tags in treatment: 1890051 INFO @ Sun, 21 Jun 2020 19:43:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:38: #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 19:43:38: #1 tags after filtering in treatment: 1889774 INFO @ Sun, 21 Jun 2020 19:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:38: #2 number of paired peaks: 1703 INFO @ Sun, 21 Jun 2020 19:43:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:39: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 19:43:39: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 19:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05_model.r INFO @ Sun, 21 Jun 2020 19:43:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:46: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (1851 records, 4 fields): 13 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 19:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.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 19:43:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:01: 1000000 INFO @ Sun, 21 Jun 2020 19:44:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:44:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:44:07: #1 total tags in treatment: 1890051 INFO @ Sun, 21 Jun 2020 19:44:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:07: #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 19:44:08: #1 tags after filtering in treatment: 1889774 INFO @ Sun, 21 Jun 2020 19:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:08: #2 number of paired peaks: 1703 INFO @ Sun, 21 Jun 2020 19:44:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:08: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 19:44:08: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 19:44:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10_model.r INFO @ Sun, 21 Jun 2020 19:44:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:15: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (869 records, 4 fields): 10 millis CompletedMACS2peakCalling 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 19:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.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 19:44:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:30: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:44:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:44:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:44:37: #1 total tags in treatment: 1890051 INFO @ Sun, 21 Jun 2020 19:44:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:44:37: #1 tags after filtering in treatment: 1889774 INFO @ Sun, 21 Jun 2020 19:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:37: #2 number of paired peaks: 1703 INFO @ Sun, 21 Jun 2020 19:44:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:37: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 19:44:37: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 19:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20_model.r INFO @ Sun, 21 Jun 2020 19:44:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:44:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068965/SRX3068965.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:44: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 6 millis CompletedMACS2peakCalling