Job ID = 6366689 SRX = SRX222642 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:23 prefetch.2.10.7: 1) Downloading 'SRR660149'... 2020-06-15T23:00:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:48 prefetch.2.10.7: 'SRR660149' is valid 2020-06-15T23:00:48 prefetch.2.10.7: 1) 'SRR660149' was downloaded successfully Read 5641350 spots for SRR660149/SRR660149.sra Written 5641350 spots for SRR660149/SRR660149.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: 00:00:46 5641350 reads; of these: 5641350 (100.00%) were unpaired; of these: 718122 (12.73%) aligned 0 times 4210540 (74.64%) aligned exactly 1 time 712688 (12.63%) aligned >1 times 87.27% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 1824905 / 4923228 = 0.3707 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 08:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.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 08:03:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:09: 1000000 INFO @ Tue, 16 Jun 2020 08:03:14: 2000000 INFO @ Tue, 16 Jun 2020 08:03:19: 3000000 INFO @ Tue, 16 Jun 2020 08:03:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:19: #1 total tags in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:03:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:19: #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 08:03:19: #1 tags after filtering in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:19: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:03:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:19: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:03:19: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05_model.r INFO @ Tue, 16 Jun 2020 08:03:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2433 records, 4 fields): 3 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 08:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.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 08:03:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:39: 1000000 INFO @ Tue, 16 Jun 2020 08:03:44: 2000000 INFO @ Tue, 16 Jun 2020 08:03:48: 3000000 INFO @ Tue, 16 Jun 2020 08:03:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:03:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:03:49: #1 total tags in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:03:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:49: #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 08:03:49: #1 tags after filtering in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:49: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:03:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:49: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:03:49: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:03:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10_model.r INFO @ Tue, 16 Jun 2020 08:03:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.10_summits.bed INFO @ Tue, 16 Jun 2020 08:04:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1518 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 08:04:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.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 08:04:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:09: 1000000 INFO @ Tue, 16 Jun 2020 08:04:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:18: 3000000 INFO @ Tue, 16 Jun 2020 08:04:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:04:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:04:18: #1 total tags in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:04:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:18: #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 08:04:19: #1 tags after filtering in treatment: 3098323 INFO @ Tue, 16 Jun 2020 08:04:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:19: #2 number of paired peaks: 1212 INFO @ Tue, 16 Jun 2020 08:04:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:19: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 08:04:19: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 08:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20_model.r INFO @ Tue, 16 Jun 2020 08:04:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX222642/SRX222642.20_summits.bed INFO @ Tue, 16 Jun 2020 08:04:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (894 records, 4 fields): 2 millis CompletedMACS2peakCalling