Job ID = 14520588 SRX = SRX10705896 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 390465 spots for SRR14352049/SRR14352049.sra Written 390465 spots for SRR14352049/SRR14352049.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: 00:00:04 390465 reads; of these: 390465 (100.00%) were unpaired; of these: 70009 (17.93%) aligned 0 times 280699 (71.89%) aligned exactly 1 time 39757 (10.18%) aligned >1 times 82.07% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 18135 / 320456 = 0.0566 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.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 @ Sat, 15 Jan 2022 19:25:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:25: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:25:25: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:25:25: #1 total tags in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:25:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:25:25: #1 tags after filtering in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:25:25: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:25: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:25:25: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:25: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:25: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:25: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:25: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:25: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:25:25: #2 alternative fragment length(s) may be 133,168 bps INFO @ Sat, 15 Jan 2022 19:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05_model.r WARNING @ Sat, 15 Jan 2022 19:25:25: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:25:25: #2 You may need to consider one of the other alternative d(s): 133,168 WARNING @ Sat, 15 Jan 2022 19:25:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:25:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:25:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:25:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:25:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.05_summits.bed INFO @ Sat, 15 Jan 2022 19:25:26: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 19 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.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 @ Sat, 15 Jan 2022 19:25:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:55: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:25:55: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:25:55: #1 total tags in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:25:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:25:55: #1 tags after filtering in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:25:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:25:55: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:55: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:25:55: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:55: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:55: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:55: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:55: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:55: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:25:55: #2 alternative fragment length(s) may be 133,168 bps INFO @ Sat, 15 Jan 2022 19:25:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10_model.r WARNING @ Sat, 15 Jan 2022 19:25:55: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:25:55: #2 You may need to consider one of the other alternative d(s): 133,168 WARNING @ Sat, 15 Jan 2022 19:25:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:25:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.10_summits.bed INFO @ Sat, 15 Jan 2022 19:25:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:26:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.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 @ Sat, 15 Jan 2022 19:26:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:23: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:26:25: #1 tag size is determined as 82 bps INFO @ Sat, 15 Jan 2022 19:26:25: #1 tag size = 82 INFO @ Sat, 15 Jan 2022 19:26:25: #1 total tags in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:26:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:26:25: #1 tags after filtering in treatment: 302321 INFO @ Sat, 15 Jan 2022 19:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:26:25: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:25: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 19:26:25: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:25: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:25: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:25: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:25: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:25: #2 predicted fragment length is 133 bps INFO @ Sat, 15 Jan 2022 19:26:25: #2 alternative fragment length(s) may be 133,168 bps INFO @ Sat, 15 Jan 2022 19:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20_model.r WARNING @ Sat, 15 Jan 2022 19:26:25: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:26:25: #2 You may need to consider one of the other alternative d(s): 133,168 WARNING @ Sat, 15 Jan 2022 19:26:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 19:26:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705896/SRX10705896.20_summits.bed INFO @ Sat, 15 Jan 2022 19:26:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 1 millis CompletedMACS2peakCalling