Job ID = 6453867 SRX = SRX1537616 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:48:04 prefetch.2.10.7: 1) Downloading 'SRR3109311'... 2020-06-21T08:48:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:42 prefetch.2.10.7: 'SRR3109311' is valid 2020-06-21T08:51:42 prefetch.2.10.7: 1) 'SRR3109311' was downloaded successfully Read 9945723 spots for SRR3109311/SRR3109311.sra Written 9945723 spots for SRR3109311/SRR3109311.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: 00:01:53 9945723 reads; of these: 9945723 (100.00%) were unpaired; of these: 6884407 (69.22%) aligned 0 times 1955943 (19.67%) aligned exactly 1 time 1105373 (11.11%) aligned >1 times 30.78% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 1600490 / 3061316 = 0.5228 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 17:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.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 17:55:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:24: 1000000 INFO @ Sun, 21 Jun 2020 17:55:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:27: #1 total tags in treatment: 1460826 INFO @ Sun, 21 Jun 2020 17:55:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:27: #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 17:55:27: #1 tags after filtering in treatment: 1460744 INFO @ Sun, 21 Jun 2020 17:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:27: #2 number of paired peaks: 1579 INFO @ Sun, 21 Jun 2020 17:55:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:27: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 17:55:27: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 17:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05_model.r INFO @ Sun, 21 Jun 2020 17:55:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.05_summits.bed INFO @ Sun, 21 Jun 2020 17:55:33: Done! pass1 - making usageList (547 chroms): 1 millis pass2 - checking and writing primary data (1588 records, 4 fields): 19 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 17:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.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 17:55:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:53: 1000000 INFO @ Sun, 21 Jun 2020 17:55:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:55:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:55:56: #1 total tags in treatment: 1460826 INFO @ Sun, 21 Jun 2020 17:55:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:56: #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 17:55:57: #1 tags after filtering in treatment: 1460744 INFO @ Sun, 21 Jun 2020 17:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:57: #2 number of paired peaks: 1579 INFO @ Sun, 21 Jun 2020 17:55:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:57: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 17:55:57: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 17:55:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10_model.r INFO @ Sun, 21 Jun 2020 17:55:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:03: Done! pass1 - making usageList (393 chroms): 2 millis pass2 - checking and writing primary data (977 records, 4 fields): 14 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 17:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.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 17:56:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:17: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:56:23: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:56:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:56:26: #1 total tags in treatment: 1460826 INFO @ Sun, 21 Jun 2020 17:56:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:26: #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 17:56:27: #1 tags after filtering in treatment: 1460744 INFO @ Sun, 21 Jun 2020 17:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:27: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:27: #2 number of paired peaks: 1579 INFO @ Sun, 21 Jun 2020 17:56:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:27: #2 predicted fragment length is 111 bps INFO @ Sun, 21 Jun 2020 17:56:27: #2 alternative fragment length(s) may be 111 bps INFO @ Sun, 21 Jun 2020 17:56:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20_model.r INFO @ Sun, 21 Jun 2020 17:56:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537616/SRX1537616.20_summits.bed INFO @ Sun, 21 Jun 2020 17:56:33: Done! pass1 - making usageList (160 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 8 millis CompletedMACS2peakCalling