Job ID = 6452508 SRX = SRX013108 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:01:53 prefetch.2.10.7: 1) Downloading 'SRR030374'... 2020-06-21T08:01:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:17 prefetch.2.10.7: 'SRR030374' is valid 2020-06-21T08:04:17 prefetch.2.10.7: 1) 'SRR030374' was downloaded successfully Read 8604186 spots for SRR030374/SRR030374.sra Written 8604186 spots for SRR030374/SRR030374.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: 00:00:41 8604186 reads; of these: 8604186 (100.00%) were unpaired; of these: 6419294 (74.61%) aligned 0 times 1973891 (22.94%) aligned exactly 1 time 211001 (2.45%) aligned >1 times 25.39% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 1459394 / 2184892 = 0.6679 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 17:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.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 17:06:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:22: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:06:22: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:06:22: #1 total tags in treatment: 725498 INFO @ Sun, 21 Jun 2020 17:06:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:22: #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 17:06:22: #1 tags after filtering in treatment: 724949 INFO @ Sun, 21 Jun 2020 17:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:22: #2 number of paired peaks: 1654 INFO @ Sun, 21 Jun 2020 17:06:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:22: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 17:06:22: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 17:06:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05_model.r INFO @ Sun, 21 Jun 2020 17:06:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:06:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.05_summits.bed INFO @ Sun, 21 Jun 2020 17:06:25: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (153 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 17:06:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.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 17:06:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:06:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:06:52: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:06:52: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:06:52: #1 total tags in treatment: 725498 INFO @ Sun, 21 Jun 2020 17:06:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:06:52: #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 17:06:52: #1 tags after filtering in treatment: 724949 INFO @ Sun, 21 Jun 2020 17:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:06:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:06:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:06:53: #2 number of paired peaks: 1654 INFO @ Sun, 21 Jun 2020 17:06:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:06:53: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 17:06:53: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 17:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10_model.r INFO @ Sun, 21 Jun 2020 17:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:06:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.10_summits.bed INFO @ Sun, 21 Jun 2020 17:06:56: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 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 17:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.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 17:07:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:18: #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 17:07:22: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:07:22: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:07:22: #1 total tags in treatment: 725498 INFO @ Sun, 21 Jun 2020 17:07:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:07:22: #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 17:07:22: #1 tags after filtering in treatment: 724949 INFO @ Sun, 21 Jun 2020 17:07:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:07:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:07:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:07:23: #2 number of paired peaks: 1654 INFO @ Sun, 21 Jun 2020 17:07:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:07:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:07:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:07:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:07:23: #2 predicted fragment length is 115 bps INFO @ Sun, 21 Jun 2020 17:07:23: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 21 Jun 2020 17:07:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20_model.r INFO @ Sun, 21 Jun 2020 17:07:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:07:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:07:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013108/SRX013108.20_summits.bed INFO @ Sun, 21 Jun 2020 17:07:26: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling