Job ID = 6367245 SRX = SRX3104608 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:21:46 prefetch.2.10.7: 1) Downloading 'SRR5946213'... 2020-06-15T23:21:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:22:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:22:51 prefetch.2.10.7: 'SRR5946213' is valid 2020-06-15T23:22:51 prefetch.2.10.7: 1) 'SRR5946213' was downloaded successfully 2020-06-15T23:22:51 prefetch.2.10.7: 'SRR5946213' has 0 unresolved dependencies Read 21658245 spots for SRR5946213/SRR5946213.sra Written 21658245 spots for SRR5946213/SRR5946213.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: 00:02:43 21658245 reads; of these: 21658245 (100.00%) were unpaired; of these: 14699373 (67.87%) aligned 0 times 6009534 (27.75%) aligned exactly 1 time 949338 (4.38%) aligned >1 times 32.13% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 5135042 / 6958872 = 0.7379 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 08:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.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 08:28:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:12: 1000000 INFO @ Tue, 16 Jun 2020 08:28:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:16: #1 total tags in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:28:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:16: #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 08:28:16: #1 tags after filtering in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:28:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:16: #2 number of paired peaks: 614 WARNING @ Tue, 16 Jun 2020 08:28:16: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:16: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:28:16: #2 alternative fragment length(s) may be 52,476,575 bps INFO @ Tue, 16 Jun 2020 08:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05_model.r WARNING @ Tue, 16 Jun 2020 08:28:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:16: #2 You may need to consider one of the other alternative d(s): 52,476,575 WARNING @ Tue, 16 Jun 2020 08:28:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (513 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 08:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.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 08:28:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:28:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:28:42: 1000000 INFO @ Tue, 16 Jun 2020 08:28:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:46: #1 total tags in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:28:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:46: #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 08:28:46: #1 tags after filtering in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:46: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:46: #2 number of paired peaks: 614 WARNING @ Tue, 16 Jun 2020 08:28:46: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:46: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:28:46: #2 alternative fragment length(s) may be 52,476,575 bps INFO @ Tue, 16 Jun 2020 08:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:46: #2 You may need to consider one of the other alternative d(s): 52,476,575 WARNING @ Tue, 16 Jun 2020 08:28:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (291 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 08:29:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.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 08:29:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:13: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:29:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:29:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:29:17: #1 total tags in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:29:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:17: #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 08:29:17: #1 tags after filtering in treatment: 1823830 INFO @ Tue, 16 Jun 2020 08:29:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:18: #2 number of paired peaks: 614 WARNING @ Tue, 16 Jun 2020 08:29:18: Fewer paired peaks (614) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 614 pairs to build model! INFO @ Tue, 16 Jun 2020 08:29:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:18: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:29:18: #2 alternative fragment length(s) may be 52,476,575 bps INFO @ Tue, 16 Jun 2020 08:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:18: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:18: #2 You may need to consider one of the other alternative d(s): 52,476,575 WARNING @ Tue, 16 Jun 2020 08:29:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:29:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3104608/SRX3104608.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling