Job ID = 6365858 SRX = SRX003824 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:24:29 prefetch.2.10.7: 1) Downloading 'SRR015064'... 2020-06-15T22:24:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:35:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:35:28 prefetch.2.10.7: 1) 'SRR015064' was downloaded successfully Read 14069076 spots for SRR015064/SRR015064.sra Written 14069076 spots for SRR015064/SRR015064.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: 00:01:30 14069076 reads; of these: 14069076 (100.00%) were unpaired; of these: 7705645 (54.77%) aligned 0 times 5267740 (37.44%) aligned exactly 1 time 1095691 (7.79%) aligned >1 times 45.23% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 874238 / 6363431 = 0.1374 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 @ Tue, 16 Jun 2020 07:40:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:40:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:59: 1000000 INFO @ Tue, 16 Jun 2020 07:41:04: 2000000 INFO @ Tue, 16 Jun 2020 07:41:09: 3000000 INFO @ Tue, 16 Jun 2020 07:41:14: 4000000 INFO @ Tue, 16 Jun 2020 07:41:19: 5000000 INFO @ Tue, 16 Jun 2020 07:41:22: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:41:22: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:41:22: #1 total tags in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:41:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:41:22: #1 tags after filtering in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:41:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:22: #2 looking for paired plus/minus strand peaks... 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 @ Tue, 16 Jun 2020 07:41:22: #2 number of paired peaks: 1863 INFO @ Tue, 16 Jun 2020 07:41:22: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:22: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:22: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:22: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:22: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 07:41:22: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 07:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05_model.r INFO @ Tue, 16 Jun 2020 07:41:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:41:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:29: 1000000 INFO @ Tue, 16 Jun 2020 07:41:34: 2000000 INFO @ Tue, 16 Jun 2020 07:41:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:39: 3000000 INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:44: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (12747 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:41:45: 4000000 INFO @ Tue, 16 Jun 2020 07:41:50: 5000000 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 @ Tue, 16 Jun 2020 07:41:52: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:41:52: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:41:52: #1 total tags in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:41:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:41:52: #1 tags after filtering in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:53: #2 number of paired peaks: 1863 INFO @ Tue, 16 Jun 2020 07:41:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:53: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 07:41:53: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 07:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10_model.r INFO @ Tue, 16 Jun 2020 07:41:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 07:41:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:01: 1000000 INFO @ Tue, 16 Jun 2020 07:42:07: 2000000 INFO @ Tue, 16 Jun 2020 07:42:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:12: 3000000 INFO @ Tue, 16 Jun 2020 07:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5195 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:42:17: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:22: 5000000 INFO @ Tue, 16 Jun 2020 07:42:25: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 07:42:25: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 07:42:25: #1 total tags in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:42:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:42:25: #1 tags after filtering in treatment: 5489193 INFO @ Tue, 16 Jun 2020 07:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:25: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:26: #2 number of paired peaks: 1863 INFO @ Tue, 16 Jun 2020 07:42:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:26: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 07:42:26: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 16 Jun 2020 07:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20_model.r INFO @ Tue, 16 Jun 2020 07:42:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:42:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003824/SRX003824.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1850 records, 4 fields): 4 millis CompletedMACS2peakCalling