Job ID = 6366594 SRX = SRX208763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:53 prefetch.2.10.7: 1) Downloading 'SRR628897'... 2020-06-15T22:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:05 prefetch.2.10.7: 'SRR628897' is valid 2020-06-15T23:01:05 prefetch.2.10.7: 1) 'SRR628897' was downloaded successfully Read 11756944 spots for SRR628897/SRR628897.sra Written 11756944 spots for SRR628897/SRR628897.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: 00:02:56 11756944 reads; of these: 11756944 (100.00%) were unpaired; of these: 1166562 (9.92%) aligned 0 times 9232841 (78.53%) aligned exactly 1 time 1357541 (11.55%) aligned >1 times 90.08% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6878709 / 10590382 = 0.6495 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 08:07:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.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 08:07:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:29: 1000000 INFO @ Tue, 16 Jun 2020 08:07:35: 2000000 INFO @ Tue, 16 Jun 2020 08:07:41: 3000000 INFO @ Tue, 16 Jun 2020 08:07:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:07:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:07:46: #1 total tags in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:07:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:46: #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 08:07:46: #1 tags after filtering in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:07:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:46: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 08:07:46: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:46: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:07:46: #2 alternative fragment length(s) may be 4,56,82,98,131,148,169,186,203 bps INFO @ Tue, 16 Jun 2020 08:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05_model.r INFO @ Tue, 16 Jun 2020 08:07:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:46: #3 Pre-compute pvalue-qvalue table... 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 08:07:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.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 08:07:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:59: 1000000 INFO @ Tue, 16 Jun 2020 08:07:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (545 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:05: 2000000 INFO @ Tue, 16 Jun 2020 08:08:12: 3000000 INFO @ Tue, 16 Jun 2020 08:08:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:16: #1 total tags in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:08:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:16: #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 08:08:16: #1 tags after filtering in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:17: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 08:08:17: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:17: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:08:17: #2 alternative fragment length(s) may be 4,56,82,98,131,148,169,186,203 bps INFO @ Tue, 16 Jun 2020 08:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10_model.r INFO @ Tue, 16 Jun 2020 08:08:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:17: #3 Pre-compute pvalue-qvalue table... 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 08:08:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.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 08:08:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:29: 1000000 INFO @ Tue, 16 Jun 2020 08:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:35: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:41: 3000000 INFO @ Tue, 16 Jun 2020 08:08:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:45: #1 total tags in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:08:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:45: #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 08:08:46: #1 tags after filtering in treatment: 3711673 INFO @ Tue, 16 Jun 2020 08:08:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:46: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 08:08:46: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:46: #2 predicted fragment length is 148 bps INFO @ Tue, 16 Jun 2020 08:08:46: #2 alternative fragment length(s) may be 4,56,82,98,131,148,169,186,203 bps INFO @ Tue, 16 Jun 2020 08:08:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20_model.r INFO @ Tue, 16 Jun 2020 08:08:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208763/SRX208763.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling