Job ID = 6367316 SRX = SRX331078 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:22:46 prefetch.2.10.7: 1) Downloading 'SRR947302'... 2020-06-15T23:22:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:12 prefetch.2.10.7: 'SRR947302' is valid 2020-06-15T23:23:12 prefetch.2.10.7: 1) 'SRR947302' was downloaded successfully Read 3012373 spots for SRR947302/SRR947302.sra Written 3012373 spots for SRR947302/SRR947302.sra 2020-06-15T23:23:30 prefetch.2.10.7: 1) Downloading 'SRR947303'... 2020-06-15T23:23:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:53 prefetch.2.10.7: 'SRR947303' is valid 2020-06-15T23:23:53 prefetch.2.10.7: 1) 'SRR947303' was downloaded successfully Read 1919255 spots for SRR947303/SRR947303.sra Written 1919255 spots for SRR947303/SRR947303.sra 2020-06-15T23:24:09 prefetch.2.10.7: 1) Downloading 'SRR947304'... 2020-06-15T23:24:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:24:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:24:25 prefetch.2.10.7: 'SRR947304' is valid 2020-06-15T23:24:25 prefetch.2.10.7: 1) 'SRR947304' was downloaded successfully Read 2038458 spots for SRR947304/SRR947304.sra Written 2038458 spots for SRR947304/SRR947304.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:26 6970086 reads; of these: 6970086 (100.00%) were unpaired; of these: 5722236 (82.10%) aligned 0 times 1061866 (15.23%) aligned exactly 1 time 185984 (2.67%) aligned >1 times 17.90% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 331016 / 1247850 = 0.2653 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 08:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.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 08:25:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:50: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:25:50: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:25:50: #1 total tags in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:25:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:50: #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 08:25:50: #1 tags after filtering in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:50: #2 number of paired peaks: 812 WARNING @ Tue, 16 Jun 2020 08:25:50: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:50: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:25:50: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05_model.r INFO @ Tue, 16 Jun 2020 08:25:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.05_summits.bed INFO @ Tue, 16 Jun 2020 08:25:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (522 records, 4 fields): 2 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 08:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.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 08:26:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:20: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:20: #1 total tags in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:26:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:20: #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 08:26:20: #1 tags after filtering in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #2 number of paired peaks: 812 WARNING @ Tue, 16 Jun 2020 08:26:20: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:20: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10_model.r INFO @ Tue, 16 Jun 2020 08:26:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 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 08:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.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 08:26:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:46: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:50: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:26:50: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:26:50: #1 total tags in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:26:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:50: #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 08:26:50: #1 tags after filtering in treatment: 916834 INFO @ Tue, 16 Jun 2020 08:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:50: #2 number of paired peaks: 812 WARNING @ Tue, 16 Jun 2020 08:26:50: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:50: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:50: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 08:26:50: #2 alternative fragment length(s) may be 141 bps INFO @ Tue, 16 Jun 2020 08:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20_model.r INFO @ Tue, 16 Jun 2020 08:26:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:26:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331078/SRX331078.20_summits.bed INFO @ Tue, 16 Jun 2020 08:26:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 1 millis CompletedMACS2peakCalling