Job ID = 6368465 SRX = SRX5020695 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:51 prefetch.2.10.7: 1) Downloading 'SRR8201318'... 2020-06-16T00:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:19:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:19:49 prefetch.2.10.7: 'SRR8201318' is valid 2020-06-16T00:19:49 prefetch.2.10.7: 1) 'SRR8201318' was downloaded successfully Read 3720668 spots for SRR8201318/SRR8201318.sra Written 3720668 spots for SRR8201318/SRR8201318.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: 00:00:53 3720668 reads; of these: 3720668 (100.00%) were unpaired; of these: 318318 (8.56%) aligned 0 times 2878618 (77.37%) aligned exactly 1 time 523732 (14.08%) aligned >1 times 91.44% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 267877 / 3402350 = 0.0787 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 09:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.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 09:22:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:20: 1000000 INFO @ Tue, 16 Jun 2020 09:22:26: 2000000 INFO @ Tue, 16 Jun 2020 09:22:31: 3000000 INFO @ Tue, 16 Jun 2020 09:22:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:22:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:22:32: #1 total tags in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:22:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:32: #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 09:22:32: #1 tags after filtering in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:22:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:32: #2 number of paired peaks: 1048 INFO @ Tue, 16 Jun 2020 09:22:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:32: #2 predicted fragment length is 264 bps INFO @ Tue, 16 Jun 2020 09:22:32: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 16 Jun 2020 09:22:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05_model.r INFO @ Tue, 16 Jun 2020 09:22:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:40: #3 Call peaks for each chromosome... 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 09:22:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.05_summits.bed INFO @ Tue, 16 Jun 2020 09:22:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2187 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.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 09:22:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:51: 1000000 INFO @ Tue, 16 Jun 2020 09:22:56: 2000000 INFO @ Tue, 16 Jun 2020 09:23:02: 3000000 INFO @ Tue, 16 Jun 2020 09:23:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:23:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:23:03: #1 total tags in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:23:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:03: #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 09:23:03: #1 tags after filtering in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:03: #2 number of paired peaks: 1048 INFO @ Tue, 16 Jun 2020 09:23:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:03: #2 predicted fragment length is 264 bps INFO @ Tue, 16 Jun 2020 09:23:03: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 16 Jun 2020 09:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10_model.r INFO @ Tue, 16 Jun 2020 09:23:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:10: #3 Call peaks for each chromosome... 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 09:23:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1339 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.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 09:23:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:21: 1000000 INFO @ Tue, 16 Jun 2020 09:23:26: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:32: 3000000 INFO @ Tue, 16 Jun 2020 09:23:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:23:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:23:33: #1 total tags in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:23:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:33: #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 09:23:33: #1 tags after filtering in treatment: 3134473 INFO @ Tue, 16 Jun 2020 09:23:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:33: #2 number of paired peaks: 1048 INFO @ Tue, 16 Jun 2020 09:23:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:33: #2 predicted fragment length is 264 bps INFO @ Tue, 16 Jun 2020 09:23:33: #2 alternative fragment length(s) may be 264 bps INFO @ Tue, 16 Jun 2020 09:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20_model.r INFO @ Tue, 16 Jun 2020 09:23:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:23:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020695/SRX5020695.20_summits.bed INFO @ Tue, 16 Jun 2020 09:23:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling