Job ID = 6367021 SRX = SRX2710282 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:31 prefetch.2.10.7: 1) Downloading 'SRR5418736'... 2020-06-15T23:20:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:34 prefetch.2.10.7: 1) 'SRR5418736' was downloaded successfully Read 34013526 spots for SRR5418736/SRR5418736.sra Written 34013526 spots for SRR5418736/SRR5418736.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: 00:04:48 34013526 reads; of these: 34013526 (100.00%) were unpaired; of these: 20495293 (60.26%) aligned 0 times 9373477 (27.56%) aligned exactly 1 time 4144756 (12.19%) aligned >1 times 39.74% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9075413 / 13518233 = 0.6713 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 08:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.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 08:33:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:06: 1000000 INFO @ Tue, 16 Jun 2020 08:33:12: 2000000 INFO @ Tue, 16 Jun 2020 08:33:18: 3000000 INFO @ Tue, 16 Jun 2020 08:33:24: 4000000 INFO @ Tue, 16 Jun 2020 08:33:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:26: #1 total tags in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:33:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:26: #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 08:33:27: #1 tags after filtering in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:27: #2 number of paired peaks: 4016 INFO @ Tue, 16 Jun 2020 08:33:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:27: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:33:27: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05_model.r INFO @ Tue, 16 Jun 2020 08:33:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:27: #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 08:33:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.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 08:33:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:35: 1000000 INFO @ Tue, 16 Jun 2020 08:33:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:40: 2000000 INFO @ Tue, 16 Jun 2020 08:33:45: 3000000 INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6206 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:50: 4000000 INFO @ Tue, 16 Jun 2020 08:33:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:33:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:33:53: #1 total tags in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:33:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:53: #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 08:33:53: #1 tags after filtering in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:53: #2 number of paired peaks: 4016 INFO @ Tue, 16 Jun 2020 08:33:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:53: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:33:53: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10_model.r INFO @ Tue, 16 Jun 2020 08:33:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:53: #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 08:34:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.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 08:34:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:05: 1000000 INFO @ Tue, 16 Jun 2020 08:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:10: 2000000 INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.10_summits.bed INFO @ Tue, 16 Jun 2020 08:34:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5147 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:34:15: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:34:21: 4000000 INFO @ Tue, 16 Jun 2020 08:34:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:34:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:34:23: #1 total tags in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:34:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:34:23: #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 08:34:23: #1 tags after filtering in treatment: 4442820 INFO @ Tue, 16 Jun 2020 08:34:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:34:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:34:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:34:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:34:23: #2 number of paired peaks: 4016 INFO @ Tue, 16 Jun 2020 08:34:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:34:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:34:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:34:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:34:23: #2 predicted fragment length is 175 bps INFO @ Tue, 16 Jun 2020 08:34:23: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 16 Jun 2020 08:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20_model.r INFO @ Tue, 16 Jun 2020 08:34:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:34:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710282/SRX2710282.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4258 records, 4 fields): 5 millis CompletedMACS2peakCalling