Job ID = 6458658 SRX = SRX5360586 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:52:11 prefetch.2.10.7: 1) Downloading 'SRR8559092'... 2020-06-21T12:52:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:17 prefetch.2.10.7: 'SRR8559092' is valid 2020-06-21T12:53:17 prefetch.2.10.7: 1) 'SRR8559092' was downloaded successfully Read 5550088 spots for SRR8559092/SRR8559092.sra Written 5550088 spots for SRR8559092/SRR8559092.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: 00:00:54 5550088 reads; of these: 5550088 (100.00%) were unpaired; of these: 2095895 (37.76%) aligned 0 times 3309906 (59.64%) aligned exactly 1 time 144287 (2.60%) aligned >1 times 62.24% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 3020240 / 3454193 = 0.8744 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 21:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.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 21:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:25: #1 total tags in treatment: 433953 INFO @ Sun, 21 Jun 2020 21:55:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:25: #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 21:55:25: #1 tags after filtering in treatment: 433335 INFO @ Sun, 21 Jun 2020 21:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:25: #2 number of paired peaks: 1757 INFO @ Sun, 21 Jun 2020 21:55:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:25: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:55:25: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:55:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05_model.r INFO @ Sun, 21 Jun 2020 21:55:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.05_summits.bed INFO @ Sun, 21 Jun 2020 21:55:27: Done! pass1 - making usageList (55 chroms): 0 millis pass2 - checking and writing primary data (103 records, 4 fields): 4 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 21:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.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 21:55:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:54: #1 total tags in treatment: 433953 INFO @ Sun, 21 Jun 2020 21:55:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:54: #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 21:55:55: #1 tags after filtering in treatment: 433335 INFO @ Sun, 21 Jun 2020 21:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:55: #2 number of paired peaks: 1757 INFO @ Sun, 21 Jun 2020 21:55:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:55: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:55:55: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10_model.r INFO @ Sun, 21 Jun 2020 21:55:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:57: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (55 records, 4 fields): 1 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 21:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.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 21:56:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:25: #1 total tags in treatment: 433953 INFO @ Sun, 21 Jun 2020 21:56:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:25: #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 21:56:25: #1 tags after filtering in treatment: 433335 INFO @ Sun, 21 Jun 2020 21:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:25: #2 number of paired peaks: 1757 INFO @ Sun, 21 Jun 2020 21:56:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:25: #2 predicted fragment length is 202 bps INFO @ Sun, 21 Jun 2020 21:56:25: #2 alternative fragment length(s) may be 202 bps INFO @ Sun, 21 Jun 2020 21:56:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20_model.r INFO @ Sun, 21 Jun 2020 21:56:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360586/SRX5360586.20_summits.bed INFO @ Sun, 21 Jun 2020 21:56:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling