Job ID = 7108429 SRX = SRX7960944 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2340312 spots for SRR11359449/SRR11359449.sra Written 2340312 spots for SRR11359449/SRR11359449.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: 00:00:52 2340312 reads; of these: 2340312 (100.00%) were unpaired; of these: 208714 (8.92%) aligned 0 times 1399461 (59.80%) aligned exactly 1 time 732137 (31.28%) aligned >1 times 91.08% overall alignment rate Time searching: 00:00:52 Overall time: 00:00:52 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] 985629 / 2131598 = 0.4624 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 13:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.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 13:40:38: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:40:38: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:40:49: 1000000 INFO @ Wed, 22 Jul 2020 13:40:51: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:40:51: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:40:51: #1 total tags in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:40:51: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:40:51: #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 13:40:51: #1 tags after filtering in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:40:51: #1 finished! INFO @ Wed, 22 Jul 2020 13:40:51: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:40:51: #2 number of paired peaks: 627 WARNING @ Wed, 22 Jul 2020 13:40:51: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Wed, 22 Jul 2020 13:40:51: start model_add_line... INFO @ Wed, 22 Jul 2020 13:40:51: start X-correlation... INFO @ Wed, 22 Jul 2020 13:40:51: end of X-cor INFO @ Wed, 22 Jul 2020 13:40:51: #2 finished! INFO @ Wed, 22 Jul 2020 13:40:51: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 13:40:51: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Jul 2020 13:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05_model.r WARNING @ Wed, 22 Jul 2020 13:40:51: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:40:51: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Wed, 22 Jul 2020 13:40:51: #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 13:40:51: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:40:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.05_summits.bed INFO @ Wed, 22 Jul 2020 13:40:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1080 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 13:41:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.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 13:41:08: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:41:08: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:41:16: 1000000 INFO @ Wed, 22 Jul 2020 13:41:17: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:41:17: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:41:17: #1 total tags in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:41:17: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:41:17: #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 13:41:17: #1 tags after filtering in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:41:17: #1 finished! INFO @ Wed, 22 Jul 2020 13:41:17: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:41:17: #2 number of paired peaks: 627 WARNING @ Wed, 22 Jul 2020 13:41:17: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Wed, 22 Jul 2020 13:41:17: start model_add_line... INFO @ Wed, 22 Jul 2020 13:41:17: start X-correlation... INFO @ Wed, 22 Jul 2020 13:41:17: end of X-cor INFO @ Wed, 22 Jul 2020 13:41:17: #2 finished! INFO @ Wed, 22 Jul 2020 13:41:17: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 13:41:17: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Jul 2020 13:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10_model.r WARNING @ Wed, 22 Jul 2020 13:41:17: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:41:17: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Wed, 22 Jul 2020 13:41:17: #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 13:41:17: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:41:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:41:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.10_summits.bed INFO @ Wed, 22 Jul 2020 13:41:22: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (925 records, 4 fields): 5 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 13:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.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 13:41:38: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:41:38: #1 read treatment tags... 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 13:41:46: 1000000 INFO @ Wed, 22 Jul 2020 13:41:48: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:41:48: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:41:48: #1 total tags in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:41:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:41:48: #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 13:41:48: #1 tags after filtering in treatment: 1145969 INFO @ Wed, 22 Jul 2020 13:41:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:41:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:41:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:41:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:41:48: #2 number of paired peaks: 627 WARNING @ Wed, 22 Jul 2020 13:41:48: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Wed, 22 Jul 2020 13:41:48: start model_add_line... INFO @ Wed, 22 Jul 2020 13:41:48: start X-correlation... INFO @ Wed, 22 Jul 2020 13:41:48: end of X-cor INFO @ Wed, 22 Jul 2020 13:41:48: #2 finished! INFO @ Wed, 22 Jul 2020 13:41:48: #2 predicted fragment length is 215 bps INFO @ Wed, 22 Jul 2020 13:41:48: #2 alternative fragment length(s) may be 215 bps INFO @ Wed, 22 Jul 2020 13:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20_model.r WARNING @ Wed, 22 Jul 2020 13:41:48: #2 Since the d (215) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:41:48: #2 You may need to consider one of the other alternative d(s): 215 WARNING @ Wed, 22 Jul 2020 13:41:48: #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 13:41:48: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:41:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960944/SRX7960944.20_summits.bed INFO @ Wed, 22 Jul 2020 13:41:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (712 records, 4 fields): 2 millis CompletedMACS2peakCalling