Job ID = 6455891 SRX = SRX3032295 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:21 prefetch.2.10.7: 1) Downloading 'SRR5863985'... 2020-06-21T10:30:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:12 prefetch.2.10.7: 1) 'SRR5863985' was downloaded successfully 2020-06-21T10:38:12 prefetch.2.10.7: 'SRR5863985' has 0 unresolved dependencies Read 36939698 spots for SRR5863985/SRR5863985.sra Written 36939698 spots for SRR5863985/SRR5863985.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:48 36939698 reads; of these: 36939698 (100.00%) were unpaired; of these: 28451300 (77.02%) aligned 0 times 8174115 (22.13%) aligned exactly 1 time 314283 (0.85%) aligned >1 times 22.98% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 7354216 / 8488398 = 0.8664 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 19:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.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 19:48:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:24: 1000000 INFO @ Sun, 21 Jun 2020 19:48:25: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:48:25: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:48:25: #1 total tags in treatment: 1134182 INFO @ Sun, 21 Jun 2020 19:48:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:25: #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 19:48:25: #1 tags after filtering in treatment: 1133620 INFO @ Sun, 21 Jun 2020 19:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:25: #2 number of paired peaks: 6459 INFO @ Sun, 21 Jun 2020 19:48:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:25: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 19:48:25: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 19:48:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05_model.r INFO @ Sun, 21 Jun 2020 19:48:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.05_summits.bed INFO @ Sun, 21 Jun 2020 19:48:30: Done! pass1 - making usageList (104 chroms): 1 millis pass2 - checking and writing primary data (4218 records, 4 fields): 8 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 19:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.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 19:48:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:53: 1000000 INFO @ Sun, 21 Jun 2020 19:48:54: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:48:54: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:48:54: #1 total tags in treatment: 1134182 INFO @ Sun, 21 Jun 2020 19:48:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:48:54: #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 19:48:54: #1 tags after filtering in treatment: 1133620 INFO @ Sun, 21 Jun 2020 19:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:48:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:48:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:48:54: #2 number of paired peaks: 6459 INFO @ Sun, 21 Jun 2020 19:48:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:48:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:48:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:48:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:48:54: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 19:48:54: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 19:48:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10_model.r INFO @ Sun, 21 Jun 2020 19:48:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:48:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:59: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (2422 records, 4 fields): 4 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 19:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.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 19:49:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:49:16: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:49:23: 1000000 INFO @ Sun, 21 Jun 2020 19:49:23: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 19:49:23: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 19:49:23: #1 total tags in treatment: 1134182 INFO @ Sun, 21 Jun 2020 19:49:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:23: #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 19:49:24: #1 tags after filtering in treatment: 1133620 INFO @ Sun, 21 Jun 2020 19:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:24: #2 number of paired peaks: 6459 INFO @ Sun, 21 Jun 2020 19:49:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:24: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 19:49:24: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 19:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20_model.r INFO @ Sun, 21 Jun 2020 19:49:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:49:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3032295/SRX3032295.20_summits.bed INFO @ Sun, 21 Jun 2020 19:49:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1043 records, 4 fields): 3 millis CompletedMACS2peakCalling