Job ID = 6368614 SRX = SRX5020839 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:48 prefetch.2.10.7: 1) Downloading 'SRR8201462'... 2020-06-16T00:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:24 prefetch.2.10.7: 'SRR8201462' is valid 2020-06-16T00:26:24 prefetch.2.10.7: 1) 'SRR8201462' was downloaded successfully Read 6722011 spots for SRR8201462/SRR8201462.sra Written 6722011 spots for SRR8201462/SRR8201462.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: 00:01:38 6722011 reads; of these: 6722011 (100.00%) were unpaired; of these: 301447 (4.48%) aligned 0 times 5375918 (79.97%) aligned exactly 1 time 1044646 (15.54%) aligned >1 times 95.52% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 326895 / 6420564 = 0.0509 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 09:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.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 09:30:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:41: 1000000 INFO @ Tue, 16 Jun 2020 09:30:48: 2000000 INFO @ Tue, 16 Jun 2020 09:30:55: 3000000 INFO @ Tue, 16 Jun 2020 09:31:02: 4000000 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 09:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.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 09:31:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:09: 5000000 INFO @ Tue, 16 Jun 2020 09:31:11: 1000000 INFO @ Tue, 16 Jun 2020 09:31:17: 6000000 INFO @ Tue, 16 Jun 2020 09:31:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:17: #1 total tags in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:31:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:17: #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 09:31:17: #1 tags after filtering in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:18: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:31:18: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:18: 2000000 INFO @ Tue, 16 Jun 2020 09:31:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:18: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:31:18: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:18: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:31:18: #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 09:31:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:24: 3000000 INFO @ Tue, 16 Jun 2020 09:31:30: 4000000 INFO @ Tue, 16 Jun 2020 09:31:30: #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 09:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.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 09:31:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:37: 5000000 INFO @ Tue, 16 Jun 2020 09:31:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:40: 1000000 INFO @ Tue, 16 Jun 2020 09:31:43: 6000000 INFO @ Tue, 16 Jun 2020 09:31:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:44: #1 total tags in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:31:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:44: #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 09:31:44: #1 tags after filtering in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:44: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:31:44: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:45: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:31:45: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:45: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:45: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:31:45: #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 09:31:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:46: 2000000 INFO @ Tue, 16 Jun 2020 09:31:53: 3000000 INFO @ Tue, 16 Jun 2020 09:31:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:59: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (301 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:05: 5000000 INFO @ Tue, 16 Jun 2020 09:32:11: 6000000 INFO @ Tue, 16 Jun 2020 09:32:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:12: #1 total tags in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:32:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:12: #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 09:32:12: #1 tags after filtering in treatment: 6093669 INFO @ Tue, 16 Jun 2020 09:32:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:12: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:32:12: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:12: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:32:12: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:12: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:12: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:32:12: #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 09:32:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020839/SRX5020839.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 1 millis CompletedMACS2peakCalling