Job ID = 10224096 SRX = SRX8952651 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5076145 spots for SRR12458235/SRR12458235.sra Written 5076145 spots for SRR12458235/SRR12458235.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 5076145 reads; of these: 5076145 (100.00%) were paired; of these: 4053538 (79.85%) aligned concordantly 0 times 909922 (17.93%) aligned concordantly exactly 1 time 112685 (2.22%) aligned concordantly >1 times ---- 4053538 pairs aligned concordantly 0 times; of these: 56188 (1.39%) aligned discordantly 1 time ---- 3997350 pairs aligned 0 times concordantly or discordantly; of these: 7994700 mates make up the pairs; of these: 7652577 (95.72%) aligned 0 times 258402 (3.23%) aligned exactly 1 time 83721 (1.05%) aligned >1 times 24.62% 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 279567 / 1075702 = 0.2599 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 @ Fri, 16 Oct 2020 09:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.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 @ Fri, 16 Oct 2020 09:25:38: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:25:38: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:25:43: 1000000 INFO @ Fri, 16 Oct 2020 09:25:48: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:25:48: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:25:48: #1 total tags in treatment: 762181 INFO @ Fri, 16 Oct 2020 09:25:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:25:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:25:48: #1 tags after filtering in treatment: 657017 INFO @ Fri, 16 Oct 2020 09:25:48: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:25:48: #1 finished! INFO @ Fri, 16 Oct 2020 09:25:48: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:25:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:25:48: #2 number of paired peaks: 191 WARNING @ Fri, 16 Oct 2020 09:25:48: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 16 Oct 2020 09:25:48: start model_add_line... INFO @ Fri, 16 Oct 2020 09:25:48: start X-correlation... INFO @ Fri, 16 Oct 2020 09:25:48: end of X-cor INFO @ Fri, 16 Oct 2020 09:25:48: #2 finished! INFO @ Fri, 16 Oct 2020 09:25:48: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 09:25:48: #2 alternative fragment length(s) may be 1,206,227,264,284,534,575 bps INFO @ Fri, 16 Oct 2020 09:25:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05_model.r INFO @ Fri, 16 Oct 2020 09:25:48: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:25:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:25:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.05_summits.bed INFO @ Fri, 16 Oct 2020 09:25:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 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 @ Fri, 16 Oct 2020 09:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.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 @ Fri, 16 Oct 2020 09:26:08: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:08: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:12: 1000000 INFO @ Fri, 16 Oct 2020 09:26:16: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:26:16: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:26:16: #1 total tags in treatment: 762181 INFO @ Fri, 16 Oct 2020 09:26:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:26:16: #1 tags after filtering in treatment: 657017 INFO @ Fri, 16 Oct 2020 09:26:16: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:26:16: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:16: #2 number of paired peaks: 191 WARNING @ Fri, 16 Oct 2020 09:26:16: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:16: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:16: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:16: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:16: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:16: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 09:26:16: #2 alternative fragment length(s) may be 1,206,227,264,284,534,575 bps INFO @ Fri, 16 Oct 2020 09:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10_model.r INFO @ Fri, 16 Oct 2020 09:26:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:26:18: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.10_summits.bed INFO @ Fri, 16 Oct 2020 09:26:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 1 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 @ Fri, 16 Oct 2020 09:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.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 @ Fri, 16 Oct 2020 09:26:38: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:38: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:42: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:26:46: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:26:46: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:26:46: #1 total tags in treatment: 762181 INFO @ Fri, 16 Oct 2020 09:26:46: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:26:46: #1 tags after filtering in treatment: 657017 INFO @ Fri, 16 Oct 2020 09:26:46: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:26:46: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:46: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:46: #2 number of paired peaks: 191 WARNING @ Fri, 16 Oct 2020 09:26:46: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:46: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:46: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:46: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:46: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:46: #2 predicted fragment length is 227 bps INFO @ Fri, 16 Oct 2020 09:26:46: #2 alternative fragment length(s) may be 1,206,227,264,284,534,575 bps INFO @ Fri, 16 Oct 2020 09:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20_model.r INFO @ Fri, 16 Oct 2020 09:26:46: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:26:48: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952651/SRX8952651.20_summits.bed INFO @ Fri, 16 Oct 2020 09:26:49: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling