Job ID = 6367346 SRX = SRX331106 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:29 prefetch.2.10.7: 1) Downloading 'SRR947337'... 2020-06-15T23:43:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:05 prefetch.2.10.7: 'SRR947337' is valid 2020-06-15T23:44:05 prefetch.2.10.7: 1) 'SRR947337' was downloaded successfully Read 6678742 spots for SRR947337/SRR947337.sra Written 6678742 spots for SRR947337/SRR947337.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: 00:00:51 6678742 reads; of these: 6678742 (100.00%) were unpaired; of these: 1479096 (22.15%) aligned 0 times 4432472 (66.37%) aligned exactly 1 time 767174 (11.49%) aligned >1 times 77.85% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 948362 / 5199646 = 0.1824 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 08:47:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.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 08:47:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:05: 1000000 INFO @ Tue, 16 Jun 2020 08:47:10: 2000000 INFO @ Tue, 16 Jun 2020 08:47:14: 3000000 INFO @ Tue, 16 Jun 2020 08:47:20: 4000000 INFO @ Tue, 16 Jun 2020 08:47:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:47:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:47:21: #1 total tags in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:47:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:21: #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 08:47:21: #1 tags after filtering in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:47:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:21: #2 number of paired peaks: 2061 INFO @ Tue, 16 Jun 2020 08:47:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:21: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:47:21: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05_model.r INFO @ Tue, 16 Jun 2020 08:47:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:21: #3 Pre-compute pvalue-qvalue table... 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 08:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.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 08:47:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:35: 1000000 INFO @ Tue, 16 Jun 2020 08:47:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4328 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:40: 2000000 INFO @ Tue, 16 Jun 2020 08:47:45: 3000000 INFO @ Tue, 16 Jun 2020 08:47:51: 4000000 INFO @ Tue, 16 Jun 2020 08:47:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:47:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:47:52: #1 total tags in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:47:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:52: #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 08:47:52: #1 tags after filtering in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:52: #2 number of paired peaks: 2061 INFO @ Tue, 16 Jun 2020 08:47:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:52: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:47:52: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:47:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10_model.r INFO @ Tue, 16 Jun 2020 08:47:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:52: #3 Pre-compute pvalue-qvalue table... 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 08:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.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 08:47:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:04: 1000000 INFO @ Tue, 16 Jun 2020 08:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3197 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:09: 2000000 INFO @ Tue, 16 Jun 2020 08:48:14: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:19: 4000000 INFO @ Tue, 16 Jun 2020 08:48:21: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:48:21: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:48:21: #1 total tags in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:48:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:21: #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 08:48:21: #1 tags after filtering in treatment: 4251284 INFO @ Tue, 16 Jun 2020 08:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:21: #2 number of paired peaks: 2061 INFO @ Tue, 16 Jun 2020 08:48:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:21: #2 predicted fragment length is 159 bps INFO @ Tue, 16 Jun 2020 08:48:21: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 16 Jun 2020 08:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20_model.r INFO @ Tue, 16 Jun 2020 08:48:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331106/SRX331106.20_summits.bed INFO @ Tue, 16 Jun 2020 08:48:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2232 records, 4 fields): 4 millis CompletedMACS2peakCalling