Job ID = 6365873 SRX = SRX005630 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:18:27 prefetch.2.10.7: 1) Downloading 'SRR017599'... 2020-06-15T22:18:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:18:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:18:53 prefetch.2.10.7: 'SRR017599' is valid 2020-06-15T22:18:53 prefetch.2.10.7: 1) 'SRR017599' was downloaded successfully Read 4436069 spots for SRR017599/SRR017599.sra Written 4436069 spots for SRR017599/SRR017599.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: 00:00:33 4436069 reads; of these: 4436069 (100.00%) were unpaired; of these: 2039331 (45.97%) aligned 0 times 1984045 (44.73%) aligned exactly 1 time 412693 (9.30%) aligned >1 times 54.03% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 140540 / 2396738 = 0.0586 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 07:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.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 07:20:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:20:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:20:48: 1000000 INFO @ Tue, 16 Jun 2020 07:20:54: 2000000 INFO @ Tue, 16 Jun 2020 07:20:55: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:20:55: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:20:55: #1 total tags in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:20:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:20:55: #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 07:20:55: #1 tags after filtering in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:20:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:20:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:20:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:20:56: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 07:20:56: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 07:20:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:20:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:20:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:20:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:20:56: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 07:20:56: #2 alternative fragment length(s) may be 60,532 bps INFO @ Tue, 16 Jun 2020 07:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05_model.r INFO @ Tue, 16 Jun 2020 07:20:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:21:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.05_summits.bed INFO @ Tue, 16 Jun 2020 07:21:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (606 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 07:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.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 07:21:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:21:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:21:18: 1000000 INFO @ Tue, 16 Jun 2020 07:21:24: 2000000 INFO @ Tue, 16 Jun 2020 07:21:26: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:21:26: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:21:26: #1 total tags in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:21:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:21:26: #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 07:21:26: #1 tags after filtering in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:21:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:21:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:21:26: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 07:21:26: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 07:21:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:21:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:21:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:21:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:21:26: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 07:21:26: #2 alternative fragment length(s) may be 60,532 bps INFO @ Tue, 16 Jun 2020 07:21:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10_model.r INFO @ Tue, 16 Jun 2020 07:21:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:21:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:21:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.10_summits.bed INFO @ Tue, 16 Jun 2020 07:21:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (161 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 07:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.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 07:21:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:21:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:21:47: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:21:53: 2000000 INFO @ Tue, 16 Jun 2020 07:21:55: #1 tag size is determined as 27 bps INFO @ Tue, 16 Jun 2020 07:21:55: #1 tag size = 27 INFO @ Tue, 16 Jun 2020 07:21:55: #1 total tags in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:21:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:21:55: #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 07:21:55: #1 tags after filtering in treatment: 2256198 INFO @ Tue, 16 Jun 2020 07:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:21:55: #1 finished! INFO @ Tue, 16 Jun 2020 07:21:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:21:55: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 07:21:55: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 07:21:55: start model_add_line... INFO @ Tue, 16 Jun 2020 07:21:55: start X-correlation... INFO @ Tue, 16 Jun 2020 07:21:55: end of X-cor INFO @ Tue, 16 Jun 2020 07:21:55: #2 finished! INFO @ Tue, 16 Jun 2020 07:21:55: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 07:21:55: #2 alternative fragment length(s) may be 60,532 bps INFO @ Tue, 16 Jun 2020 07:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20_model.r INFO @ Tue, 16 Jun 2020 07:21:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:21:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:22:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:22:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:22:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:22:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX005630/SRX005630.20_summits.bed INFO @ Tue, 16 Jun 2020 07:22:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling