Job ID = 6455126 SRX = SRX2748310 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:10 prefetch.2.10.7: 1) Downloading 'SRR5460297'... 2020-06-21T09:40:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:44 prefetch.2.10.7: 'SRR5460297' is valid 2020-06-21T09:40:44 prefetch.2.10.7: 1) 'SRR5460297' was downloaded successfully Read 5817621 spots for SRR5460297/SRR5460297.sra Written 5817621 spots for SRR5460297/SRR5460297.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: 00:00:57 5817621 reads; of these: 5817621 (100.00%) were unpaired; of these: 1374018 (23.62%) aligned 0 times 3762745 (64.68%) aligned exactly 1 time 680858 (11.70%) aligned >1 times 76.38% overall alignment rate Time searching: 00:00:57 Overall time: 00:00:57 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] 1885923 / 4443603 = 0.4244 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 18:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.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 18:43:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:11: 1000000 INFO @ Sun, 21 Jun 2020 18:43:16: 2000000 INFO @ Sun, 21 Jun 2020 18:43:19: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:43:19: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:43:19: #1 total tags in treatment: 2557680 INFO @ Sun, 21 Jun 2020 18:43:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:19: #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 18:43:19: #1 tags after filtering in treatment: 2557581 INFO @ Sun, 21 Jun 2020 18:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:19: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:20: #2 number of paired peaks: 8027 INFO @ Sun, 21 Jun 2020 18:43:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:20: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 18:43:20: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 18:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05_model.r INFO @ Sun, 21 Jun 2020 18:43:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.05_summits.bed INFO @ Sun, 21 Jun 2020 18:43:30: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (6762 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 18:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.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 18:43:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:47: 1000000 INFO @ Sun, 21 Jun 2020 18:43:52: 2000000 INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:43:55: #1 total tags in treatment: 2557680 INFO @ Sun, 21 Jun 2020 18:43:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:55: #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 18:43:56: #1 tags after filtering in treatment: 2557581 INFO @ Sun, 21 Jun 2020 18:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:56: #2 number of paired peaks: 8027 INFO @ Sun, 21 Jun 2020 18:43:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:56: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 18:43:56: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 18:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10_model.r INFO @ Sun, 21 Jun 2020 18:43:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:04: #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 18:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.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 18:44:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:07: Done! pass1 - making usageList (143 chroms): 1 millis pass2 - checking and writing primary data (5140 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:11: 1000000 INFO @ Sun, 21 Jun 2020 18:44:16: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:20: #1 tag size is determined as 25 bps INFO @ Sun, 21 Jun 2020 18:44:20: #1 tag size = 25 INFO @ Sun, 21 Jun 2020 18:44:20: #1 total tags in treatment: 2557680 INFO @ Sun, 21 Jun 2020 18:44:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:20: #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 18:44:20: #1 tags after filtering in treatment: 2557581 INFO @ Sun, 21 Jun 2020 18:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:21: #2 number of paired peaks: 8027 INFO @ Sun, 21 Jun 2020 18:44:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:21: #2 predicted fragment length is 156 bps INFO @ Sun, 21 Jun 2020 18:44:21: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 21 Jun 2020 18:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20_model.r INFO @ Sun, 21 Jun 2020 18:44:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:44:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2748310/SRX2748310.20_summits.bed INFO @ Sun, 21 Jun 2020 18:44:31: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (2906 records, 4 fields): 7 millis CompletedMACS2peakCalling