Job ID = 7108732 SRX = SRX7960948 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12555380 spots for SRR11359453/SRR11359453.sra Written 12555380 spots for SRR11359453/SRR11359453.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: 00:03:09 12555380 reads; of these: 12555380 (100.00%) were unpaired; of these: 8064409 (64.23%) aligned 0 times 2796814 (22.28%) aligned exactly 1 time 1694157 (13.49%) aligned >1 times 35.77% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2689103 / 4490971 = 0.5988 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 @ Wed, 22 Jul 2020 13:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:45:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:45:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:45:10: 1000000 INFO @ Wed, 22 Jul 2020 13:45:15: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:45:15: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:45:15: #1 total tags in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:45:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:45:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:45:15: #1 tags after filtering in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:45:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:45:15: #1 finished! INFO @ Wed, 22 Jul 2020 13:45:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:45:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:45:16: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 13:45:16: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 13:45:16: start model_add_line... INFO @ Wed, 22 Jul 2020 13:45:16: start X-correlation... INFO @ Wed, 22 Jul 2020 13:45:16: end of X-cor INFO @ Wed, 22 Jul 2020 13:45:16: #2 finished! INFO @ Wed, 22 Jul 2020 13:45:16: #2 predicted fragment length is 244 bps INFO @ Wed, 22 Jul 2020 13:45:16: #2 alternative fragment length(s) may be 0,12,36,144,195,244,267,288 bps INFO @ Wed, 22 Jul 2020 13:45:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05_model.r WARNING @ Wed, 22 Jul 2020 13:45:16: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:45:16: #2 You may need to consider one of the other alternative d(s): 0,12,36,144,195,244,267,288 WARNING @ Wed, 22 Jul 2020 13:45:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:45:16: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:45:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:45:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.05_summits.bed INFO @ Wed, 22 Jul 2020 13:45:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (270 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 @ Wed, 22 Jul 2020 13:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:45:33: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:45:33: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:45:41: 1000000 INFO @ Wed, 22 Jul 2020 13:45:48: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:45:48: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:45:48: #1 total tags in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:45:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:45:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:45:48: #1 tags after filtering in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:45:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:45:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:45:48: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 13:45:48: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 13:45:48: start model_add_line... INFO @ Wed, 22 Jul 2020 13:45:48: start X-correlation... INFO @ Wed, 22 Jul 2020 13:45:48: end of X-cor INFO @ Wed, 22 Jul 2020 13:45:48: #2 finished! INFO @ Wed, 22 Jul 2020 13:45:48: #2 predicted fragment length is 244 bps INFO @ Wed, 22 Jul 2020 13:45:48: #2 alternative fragment length(s) may be 0,12,36,144,195,244,267,288 bps INFO @ Wed, 22 Jul 2020 13:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10_model.r WARNING @ Wed, 22 Jul 2020 13:45:48: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:45:48: #2 You may need to consider one of the other alternative d(s): 0,12,36,144,195,244,267,288 WARNING @ Wed, 22 Jul 2020 13:45:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:45:48: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:45:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.10_summits.bed INFO @ Wed, 22 Jul 2020 13:45:55: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 16 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 @ Wed, 22 Jul 2020 13:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.bam'] # control file = None # effective genome size = 1.21e+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 @ Wed, 22 Jul 2020 13:46:03: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:46:03: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:46:11: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:46:18: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:46:18: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:46:18: #1 total tags in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:46:18: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:46:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:46:18: #1 tags after filtering in treatment: 1801868 INFO @ Wed, 22 Jul 2020 13:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:46:18: #1 finished! INFO @ Wed, 22 Jul 2020 13:46:18: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:46:18: #2 number of paired peaks: 241 WARNING @ Wed, 22 Jul 2020 13:46:18: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Wed, 22 Jul 2020 13:46:18: start model_add_line... INFO @ Wed, 22 Jul 2020 13:46:18: start X-correlation... INFO @ Wed, 22 Jul 2020 13:46:18: end of X-cor INFO @ Wed, 22 Jul 2020 13:46:18: #2 finished! INFO @ Wed, 22 Jul 2020 13:46:18: #2 predicted fragment length is 244 bps INFO @ Wed, 22 Jul 2020 13:46:18: #2 alternative fragment length(s) may be 0,12,36,144,195,244,267,288 bps INFO @ Wed, 22 Jul 2020 13:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20_model.r WARNING @ Wed, 22 Jul 2020 13:46:18: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:46:18: #2 You may need to consider one of the other alternative d(s): 0,12,36,144,195,244,267,288 WARNING @ Wed, 22 Jul 2020 13:46:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 13:46:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:46:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960948/SRX7960948.20_summits.bed INFO @ Wed, 22 Jul 2020 13:46:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (34 records, 4 fields): 20 millis CompletedMACS2peakCalling