Job ID = 6368764 SRX = SRX554716 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:16 prefetch.2.10.7: 1) Downloading 'SRR1301064'... 2020-06-16T00:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:59 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:59 prefetch.2.10.7: 'SRR1301064' is valid 2020-06-16T00:29:59 prefetch.2.10.7: 1) 'SRR1301064' was downloaded successfully Read 1972973 spots for SRR1301064/SRR1301064.sra Written 1972973 spots for SRR1301064/SRR1301064.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: 00:00:31 1972973 reads; of these: 1972973 (100.00%) were unpaired; of these: 207218 (10.50%) aligned 0 times 1504155 (76.24%) aligned exactly 1 time 261600 (13.26%) aligned >1 times 89.50% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 594245 / 1765755 = 0.3365 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 09:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.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 09:31:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:38: 1000000 INFO @ Tue, 16 Jun 2020 09:31:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:39: #1 total tags in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:31:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:39: #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 09:31:39: #1 tags after filtering in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:39: #2 number of paired peaks: 2587 INFO @ Tue, 16 Jun 2020 09:31:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:39: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 09:31:39: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 09:31:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05_model.r INFO @ Tue, 16 Jun 2020 09:31:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (984 records, 4 fields): 2 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 @ Tue, 16 Jun 2020 09:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.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 09:32:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:07: 1000000 INFO @ Tue, 16 Jun 2020 09:32:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:08: #1 total tags in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:32:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:08: #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 09:32:08: #1 tags after filtering in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:32:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:08: #2 number of paired peaks: 2587 INFO @ Tue, 16 Jun 2020 09:32:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:09: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 09:32:09: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 09:32:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10_model.r INFO @ Tue, 16 Jun 2020 09:32:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (430 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 @ Tue, 16 Jun 2020 09:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.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 09:32:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:32: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:37: 1000000 INFO @ Tue, 16 Jun 2020 09:32:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:38: #1 total tags in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:32:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:38: #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 09:32:38: #1 tags after filtering in treatment: 1171510 INFO @ Tue, 16 Jun 2020 09:32:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:38: #2 number of paired peaks: 2587 INFO @ Tue, 16 Jun 2020 09:32:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:38: #2 predicted fragment length is 164 bps INFO @ Tue, 16 Jun 2020 09:32:38: #2 alternative fragment length(s) may be 164 bps INFO @ Tue, 16 Jun 2020 09:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20_model.r INFO @ Tue, 16 Jun 2020 09:32:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554716/SRX554716.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling