Job ID = 6368560 SRX = SRX5020786 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:15:21 prefetch.2.10.7: 1) Downloading 'SRR8201409'... 2020-06-16T00:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:17:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:17:08 prefetch.2.10.7: 'SRR8201409' is valid 2020-06-16T00:17:08 prefetch.2.10.7: 1) 'SRR8201409' was downloaded successfully Read 7467832 spots for SRR8201409/SRR8201409.sra Written 7467832 spots for SRR8201409/SRR8201409.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:00 7467832 reads; of these: 7467832 (100.00%) were unpaired; of these: 4762887 (63.78%) aligned 0 times 2228370 (29.84%) aligned exactly 1 time 476575 (6.38%) aligned >1 times 36.22% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 797409 / 2704945 = 0.2948 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 09:19:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.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 09:19:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:02: 1000000 INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:08: #1 total tags in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:20:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:08: #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 09:20:08: #1 tags after filtering in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:20:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:08: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:20:08: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:08: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:20:08: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:08: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:20:08: #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 09:20:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (453 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 09:20:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.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 09:20:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:32: 1000000 INFO @ Tue, 16 Jun 2020 09:20:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:37: #1 total tags in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:20:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:37: #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 09:20:37: #1 tags after filtering in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:37: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:20:37: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:37: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:20:37: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:20:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:37: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:37: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:20:37: #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 09:20:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 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 09:20:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.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 09:20:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:02: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:08: #1 total tags in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:21:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:08: #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 09:21:08: #1 tags after filtering in treatment: 1907536 INFO @ Tue, 16 Jun 2020 09:21:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:08: #2 number of paired peaks: 558 WARNING @ Tue, 16 Jun 2020 09:21:08: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:08: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:21:08: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 16 Jun 2020 09:21:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:08: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:08: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 16 Jun 2020 09:21:08: #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 09:21:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020786/SRX5020786.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling