Job ID = 6366096 SRX = SRX059274 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:38:06 prefetch.2.10.7: 1) Downloading 'SRR190714'... 2020-06-15T22:38:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:38 prefetch.2.10.7: 'SRR190714' is valid 2020-06-15T22:39:38 prefetch.2.10.7: 1) 'SRR190714' was downloaded successfully Read 16264926 spots for SRR190714/SRR190714.sra Written 16264926 spots for SRR190714/SRR190714.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: 00:02:04 16264926 reads; of these: 16264926 (100.00%) were unpaired; of these: 10752791 (66.11%) aligned 0 times 4783477 (29.41%) aligned exactly 1 time 728658 (4.48%) aligned >1 times 33.89% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 659934 / 5512135 = 0.1197 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 07:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.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 07:44:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:35: 1000000 INFO @ Tue, 16 Jun 2020 07:44:40: 2000000 INFO @ Tue, 16 Jun 2020 07:44:47: 3000000 INFO @ Tue, 16 Jun 2020 07:44:53: 4000000 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 07:44:58: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:44:58: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:44:58: #1 total tags in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:44:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:58: #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 07:44:58: #1 tags after filtering in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:44:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:59: #2 number of paired peaks: 2961 INFO @ Tue, 16 Jun 2020 07:44:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.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 07:44:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:44:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:59: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 07:44:59: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 07:44:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05_model.r INFO @ Tue, 16 Jun 2020 07:44:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:05: 1000000 INFO @ Tue, 16 Jun 2020 07:45:11: 2000000 INFO @ Tue, 16 Jun 2020 07:45:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:16: 3000000 INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.05_summits.bed INFO @ Tue, 16 Jun 2020 07:45:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3908 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:22: 4000000 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 07:45:27: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:27: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:27: #1 total tags in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:45:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:27: #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 07:45:27: #1 tags after filtering in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:27: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:28: #2 number of paired peaks: 2961 INFO @ Tue, 16 Jun 2020 07:45:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:28: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 07:45:28: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 07:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10_model.r INFO @ Tue, 16 Jun 2020 07:45:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.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 07:45:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:34: 1000000 INFO @ Tue, 16 Jun 2020 07:45:40: 2000000 INFO @ Tue, 16 Jun 2020 07:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:45:45: 3000000 INFO @ Tue, 16 Jun 2020 07:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.10_summits.bed INFO @ Tue, 16 Jun 2020 07:45:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3114 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:45:50: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:45:54: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:45:54: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:45:54: #1 total tags in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:45:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:45:54: #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 07:45:54: #1 tags after filtering in treatment: 4852201 INFO @ Tue, 16 Jun 2020 07:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:45:54: #1 finished! INFO @ Tue, 16 Jun 2020 07:45:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:45:55: #2 number of paired peaks: 2961 INFO @ Tue, 16 Jun 2020 07:45:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:45:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:45:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:45:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:45:55: #2 predicted fragment length is 244 bps INFO @ Tue, 16 Jun 2020 07:45:55: #2 alternative fragment length(s) may be 244 bps INFO @ Tue, 16 Jun 2020 07:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20_model.r INFO @ Tue, 16 Jun 2020 07:45:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:45:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:46:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:46:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:46:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:46:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059274/SRX059274.20_summits.bed INFO @ Tue, 16 Jun 2020 07:46:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2168 records, 4 fields): 4 millis CompletedMACS2peakCalling