Job ID = 6366214 SRX = SRX080068 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:10 prefetch.2.10.7: 1) Downloading 'SRR298888'... 2020-06-15T22:37:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:37:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:37:30 prefetch.2.10.7: 'SRR298888' is valid 2020-06-15T22:37:30 prefetch.2.10.7: 1) 'SRR298888' was downloaded successfully Read 1799780 spots for SRR298888/SRR298888.sra Written 1799780 spots for SRR298888/SRR298888.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: 00:00:12 1799780 reads; of these: 1799780 (100.00%) were unpaired; of these: 819703 (45.54%) aligned 0 times 812323 (45.13%) aligned exactly 1 time 167754 (9.32%) aligned >1 times 54.46% overall alignment rate Time searching: 00:00:12 Overall time: 00:00:12 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] 374164 / 980077 = 0.3818 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 07:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.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 07:38:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:38:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:38:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:38:32: #1 total tags in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:38:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:38:32: #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 07:38:32: #1 tags after filtering in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:38:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:38:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:38:32: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:38:32: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:38:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:38:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:38:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:38:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:38:32: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:38:32: #2 alternative fragment length(s) may be 83,112,163,220 bps INFO @ Tue, 16 Jun 2020 07:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05_model.r INFO @ Tue, 16 Jun 2020 07:38:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:38:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.05_summits.bed INFO @ Tue, 16 Jun 2020 07:38:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (133 records, 4 fields): 1 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 07:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.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 07:38:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:38:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:39:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:39:02: #1 total tags in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:39:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:02: #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 07:39:02: #1 tags after filtering in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:02: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:39:02: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:02: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:39:02: #2 alternative fragment length(s) may be 83,112,163,220 bps INFO @ Tue, 16 Jun 2020 07:39:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10_model.r INFO @ Tue, 16 Jun 2020 07:39:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.10_summits.bed INFO @ Tue, 16 Jun 2020 07:39:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (38 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 07:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.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 07:39:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:30: #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 07:39:33: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:39:33: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:39:33: #1 total tags in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:39:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:39:33: #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 07:39:33: #1 tags after filtering in treatment: 605913 INFO @ Tue, 16 Jun 2020 07:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:39:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #2 number of paired peaks: 509 WARNING @ Tue, 16 Jun 2020 07:39:33: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Tue, 16 Jun 2020 07:39:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:39:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:39:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:39:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:39:33: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2 alternative fragment length(s) may be 83,112,163,220 bps INFO @ Tue, 16 Jun 2020 07:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20_model.r INFO @ Tue, 16 Jun 2020 07:39:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:39:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:39:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:39:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:39:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX080068/SRX080068.20_summits.bed INFO @ Tue, 16 Jun 2020 07:39:36: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (11 records, 4 fields): 2 millis CompletedMACS2peakCalling