Job ID = 6366121 SRX = SRX065637 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:44 prefetch.2.10.7: 1) Downloading 'SRR217343'... 2020-06-15T22:27:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:09 prefetch.2.10.7: 'SRR217343' is valid 2020-06-15T22:28:09 prefetch.2.10.7: 1) 'SRR217343' was downloaded successfully Read 5719110 spots for SRR217343/SRR217343.sra Written 5719110 spots for SRR217343/SRR217343.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: 00:00:38 5719110 reads; of these: 5719110 (100.00%) were unpaired; of these: 2372500 (41.48%) aligned 0 times 2876927 (50.30%) aligned exactly 1 time 469683 (8.21%) aligned >1 times 58.52% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 356503 / 3346610 = 0.1065 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 07:30:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.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 07:30:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:30:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:30:18: 1000000 INFO @ Tue, 16 Jun 2020 07:30:25: 2000000 INFO @ Tue, 16 Jun 2020 07:30:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:30:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:30:32: #1 total tags in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:30:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:30:32: #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 07:30:32: #1 tags after filtering in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:30:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:30:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:30:32: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 07:30:32: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 07:30:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:30:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:30:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:30:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:30:32: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 07:30:32: #2 alternative fragment length(s) may be 4,94,581 bps INFO @ Tue, 16 Jun 2020 07:30:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05_model.r INFO @ Tue, 16 Jun 2020 07:30:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:30:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:30:39: #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 07:30:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.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 07:30:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:30:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.05_summits.bed INFO @ Tue, 16 Jun 2020 07:30:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (673 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:30:48: 1000000 INFO @ Tue, 16 Jun 2020 07:30:55: 2000000 INFO @ Tue, 16 Jun 2020 07:31:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:01: #1 total tags in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:31:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:01: #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 07:31:01: #1 tags after filtering in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:01: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 07:31:01: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:01: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 07:31:01: #2 alternative fragment length(s) may be 4,94,581 bps INFO @ Tue, 16 Jun 2020 07:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10_model.r INFO @ Tue, 16 Jun 2020 07:31:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:31:08: #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 07:31:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.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 07:31:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.10_summits.bed INFO @ Tue, 16 Jun 2020 07:31:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:31:17: 1000000 INFO @ Tue, 16 Jun 2020 07:31:22: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:31:28: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:31:28: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:31:28: #1 total tags in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:31:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:31:28: #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 07:31:28: #1 tags after filtering in treatment: 2990107 INFO @ Tue, 16 Jun 2020 07:31:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:31:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:31:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:31:28: #2 number of paired peaks: 693 WARNING @ Tue, 16 Jun 2020 07:31:28: Fewer paired peaks (693) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 693 pairs to build model! INFO @ Tue, 16 Jun 2020 07:31:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:31:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:31:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:31:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:31:28: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 07:31:28: #2 alternative fragment length(s) may be 4,94,581 bps INFO @ Tue, 16 Jun 2020 07:31:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20_model.r INFO @ Tue, 16 Jun 2020 07:31:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:31:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:31:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065637/SRX065637.20_summits.bed INFO @ Tue, 16 Jun 2020 07:31:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 1 millis CompletedMACS2peakCalling