Job ID = 14520508 SRX = SRX10705877 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1492039 spots for SRR14352030/SRR14352030.sra Written 1492039 spots for SRR14352030/SRR14352030.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: 00:00:14 1492039 reads; of these: 1492039 (100.00%) were unpaired; of these: 702291 (47.07%) aligned 0 times 711732 (47.70%) aligned exactly 1 time 78016 (5.23%) aligned >1 times 52.93% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 149545 / 789748 = 0.1894 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 19:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.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 19:16:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:23: #1 tag size is determined as 83 bps INFO @ Sat, 15 Jan 2022 19:16:23: #1 tag size = 83 INFO @ Sat, 15 Jan 2022 19:16:23: #1 total tags in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:16:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:23: #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 19:16:23: #1 tags after filtering in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:16:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:16:23: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:23: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:16:23: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:23: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:23: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:23: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:23: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:23: #2 predicted fragment length is 327 bps INFO @ Sat, 15 Jan 2022 19:16:23: #2 alternative fragment length(s) may be 2,23,56,71,327,348,353 bps INFO @ Sat, 15 Jan 2022 19:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05_model.r INFO @ Sat, 15 Jan 2022 19:16:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.05_summits.bed INFO @ Sat, 15 Jan 2022 19:16:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1130 records, 4 fields): 3 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 19:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.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 19:16:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:16:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:16:52: #1 tag size is determined as 83 bps INFO @ Sat, 15 Jan 2022 19:16:52: #1 tag size = 83 INFO @ Sat, 15 Jan 2022 19:16:52: #1 total tags in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:16:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:52: #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 19:16:52: #1 tags after filtering in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:16:52: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:52: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:16:52: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:52: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:52: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:52: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:52: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:52: #2 predicted fragment length is 327 bps INFO @ Sat, 15 Jan 2022 19:16:52: #2 alternative fragment length(s) may be 2,23,56,71,327,348,353 bps INFO @ Sat, 15 Jan 2022 19:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10_model.r INFO @ Sat, 15 Jan 2022 19:16:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.10_summits.bed INFO @ Sat, 15 Jan 2022 19:16:56: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (783 records, 4 fields): 29 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 INFO @ Sat, 15 Jan 2022 19:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.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 19:17:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:17:18: #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 @ Sat, 15 Jan 2022 19:17:23: #1 tag size is determined as 83 bps INFO @ Sat, 15 Jan 2022 19:17:23: #1 tag size = 83 INFO @ Sat, 15 Jan 2022 19:17:23: #1 total tags in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:17:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:17:23: #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 19:17:23: #1 tags after filtering in treatment: 640203 INFO @ Sat, 15 Jan 2022 19:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:17:23: #1 finished! INFO @ Sat, 15 Jan 2022 19:17:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:17:23: #2 number of paired peaks: 195 WARNING @ Sat, 15 Jan 2022 19:17:23: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Sat, 15 Jan 2022 19:17:23: start model_add_line... INFO @ Sat, 15 Jan 2022 19:17:23: start X-correlation... INFO @ Sat, 15 Jan 2022 19:17:23: end of X-cor INFO @ Sat, 15 Jan 2022 19:17:23: #2 finished! INFO @ Sat, 15 Jan 2022 19:17:23: #2 predicted fragment length is 327 bps INFO @ Sat, 15 Jan 2022 19:17:23: #2 alternative fragment length(s) may be 2,23,56,71,327,348,353 bps INFO @ Sat, 15 Jan 2022 19:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20_model.r INFO @ Sat, 15 Jan 2022 19:17:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:17:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:17:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:17:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10705877/SRX10705877.20_summits.bed INFO @ Sat, 15 Jan 2022 19:17:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (385 records, 4 fields): 11 millis CompletedMACS2peakCalling