Job ID = 14520941 SRX = SRX10574727 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-15T11:09:11 prefetch.2.10.7: 1) Downloading 'SRR14207996'... 2022-01-15T11:09:11 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T11:09:14 prefetch.2.10.7: HTTPS download succeed 2022-01-15T11:09:14 prefetch.2.10.7: 'SRR14207996' is valid 2022-01-15T11:09:14 prefetch.2.10.7: 1) 'SRR14207996' was downloaded successfully 2022-01-15T11:09:14 prefetch.2.10.7: 'SRR14207996' has 0 unresolved dependencies Read 263213 spots for SRR14207996/SRR14207996.sra Written 263213 spots for SRR14207996/SRR14207996.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: 00:00:02 263213 reads; of these: 263213 (100.00%) were unpaired; of these: 25479 (9.68%) aligned 0 times 203530 (77.33%) aligned exactly 1 time 34204 (12.99%) aligned >1 times 90.32% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 9412 / 237734 = 0.0396 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 20:09:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.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 20:09:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:09:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:09:57: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:09:57: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:09:57: #1 total tags in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:09:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:09:57: #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 20:09:57: #1 tags after filtering in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:09:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:09:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:09:57: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 20:09:57: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 20:09:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:09:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:09:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:09:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:09:57: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Jan 2022 20:09:57: #2 alternative fragment length(s) may be 150,589 bps INFO @ Sat, 15 Jan 2022 20:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05_model.r INFO @ Sat, 15 Jan 2022 20:09:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:09:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:09:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:09:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:09:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.05_summits.bed INFO @ Sat, 15 Jan 2022 20:09:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (767 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 20:10:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.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 20:10:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:27: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:10:27: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:10:27: #1 total tags in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:10:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:27: #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 20:10:27: #1 tags after filtering in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:10:27: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:27: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 20:10:27: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:27: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:27: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:27: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:27: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:27: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Jan 2022 20:10:27: #2 alternative fragment length(s) may be 150,589 bps INFO @ Sat, 15 Jan 2022 20:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10_model.r INFO @ Sat, 15 Jan 2022 20:10:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:10:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.10_summits.bed INFO @ Sat, 15 Jan 2022 20:10:27: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 3 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 20:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.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 20:10:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:10:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:10:57: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:10:57: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:10:57: #1 total tags in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:10:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:10:57: #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 20:10:57: #1 tags after filtering in treatment: 228322 INFO @ Sat, 15 Jan 2022 20:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:10:57: #1 finished! INFO @ Sat, 15 Jan 2022 20:10:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:10:57: #2 number of paired peaks: 139 WARNING @ Sat, 15 Jan 2022 20:10:57: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sat, 15 Jan 2022 20:10:57: start model_add_line... INFO @ Sat, 15 Jan 2022 20:10:57: start X-correlation... INFO @ Sat, 15 Jan 2022 20:10:57: end of X-cor INFO @ Sat, 15 Jan 2022 20:10:57: #2 finished! INFO @ Sat, 15 Jan 2022 20:10:57: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Jan 2022 20:10:57: #2 alternative fragment length(s) may be 150,589 bps INFO @ Sat, 15 Jan 2022 20:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20_model.r INFO @ Sat, 15 Jan 2022 20:10:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:10:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:10:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10574727/SRX10574727.20_summits.bed INFO @ Sat, 15 Jan 2022 20:10:58: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis CompletedMACS2peakCalling