Job ID = 6453871 SRX = SRX1550608 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:42:47 prefetch.2.10.7: 1) Downloading 'SRR3130847'... 2020-06-21T08:42:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:29 prefetch.2.10.7: 'SRR3130847' is valid 2020-06-21T08:43:29 prefetch.2.10.7: 1) 'SRR3130847' was downloaded successfully Read 1526261 spots for SRR3130847/SRR3130847.sra Written 1526261 spots for SRR3130847/SRR3130847.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: 00:00:14 1526261 reads; of these: 1526261 (100.00%) were unpaired; of these: 982335 (64.36%) aligned 0 times 430860 (28.23%) aligned exactly 1 time 113066 (7.41%) aligned >1 times 35.64% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 113191 / 543926 = 0.2081 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 17:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.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 17:44:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:44:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:44:31: #1 total tags in treatment: 430735 INFO @ Sun, 21 Jun 2020 17:44:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:31: #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 17:44:31: #1 tags after filtering in treatment: 430079 INFO @ Sun, 21 Jun 2020 17:44:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:32: #2 number of paired peaks: 2108 INFO @ Sun, 21 Jun 2020 17:44:32: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:32: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:44:32: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05_model.r INFO @ Sun, 21 Jun 2020 17:44:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:44:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.05_summits.bed INFO @ Sun, 21 Jun 2020 17:44:34: Done! pass1 - making usageList (122 chroms): 1 millis pass2 - checking and writing primary data (838 records, 4 fields): 6 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 17:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.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 17:45:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:03: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:45:03: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:45:03: #1 total tags in treatment: 430735 INFO @ Sun, 21 Jun 2020 17:45:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:03: #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 17:45:03: #1 tags after filtering in treatment: 430079 INFO @ Sun, 21 Jun 2020 17:45:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #2 number of paired peaks: 2108 INFO @ Sun, 21 Jun 2020 17:45:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:03: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10_model.r INFO @ Sun, 21 Jun 2020 17:45:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.10_summits.bed INFO @ Sun, 21 Jun 2020 17:45:05: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 5 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 17:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.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 17:45:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:29: #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 17:45:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:45:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:45:31: #1 total tags in treatment: 430735 INFO @ Sun, 21 Jun 2020 17:45:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:31: #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 17:45:31: #1 tags after filtering in treatment: 430079 INFO @ Sun, 21 Jun 2020 17:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:32: #2 number of paired peaks: 2108 INFO @ Sun, 21 Jun 2020 17:45:32: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:32: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:32: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:32: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:32: #2 predicted fragment length is 125 bps INFO @ Sun, 21 Jun 2020 17:45:32: #2 alternative fragment length(s) may be 125 bps INFO @ Sun, 21 Jun 2020 17:45:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20_model.r INFO @ Sun, 21 Jun 2020 17:45:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550608/SRX1550608.20_summits.bed INFO @ Sun, 21 Jun 2020 17:45:34: Done! pass1 - making usageList (41 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling