Job ID = 10224038 SRX = SRX8926523 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3360811 spots for SRR12430728/SRR12430728.sra Written 3360811 spots for SRR12430728/SRR12430728.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: 00:00:50 3360811 reads; of these: 3360811 (100.00%) were paired; of these: 2011827 (59.86%) aligned concordantly 0 times 1125414 (33.49%) aligned concordantly exactly 1 time 223570 (6.65%) aligned concordantly >1 times ---- 2011827 pairs aligned concordantly 0 times; of these: 497 (0.02%) aligned discordantly 1 time ---- 2011330 pairs aligned 0 times concordantly or discordantly; of these: 4022660 mates make up the pairs; of these: 4006449 (99.60%) aligned 0 times 11533 (0.29%) aligned exactly 1 time 4678 (0.12%) aligned >1 times 40.39% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 482348 / 1349367 = 0.3575 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 09:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.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 09:12:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:12:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:12:27: 1000000 INFO @ Fri, 16 Oct 2020 09:12:30: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:12:30: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:12:30: #1 total tags in treatment: 866703 INFO @ Fri, 16 Oct 2020 09:12:30: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:12:30: #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 09:12:30: #1 tags after filtering in treatment: 773405 INFO @ Fri, 16 Oct 2020 09:12:30: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:12:30: #1 finished! INFO @ Fri, 16 Oct 2020 09:12:30: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:12:30: #2 number of paired peaks: 142 WARNING @ Fri, 16 Oct 2020 09:12:30: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 16 Oct 2020 09:12:30: start model_add_line... INFO @ Fri, 16 Oct 2020 09:12:30: start X-correlation... INFO @ Fri, 16 Oct 2020 09:12:30: end of X-cor INFO @ Fri, 16 Oct 2020 09:12:30: #2 finished! INFO @ Fri, 16 Oct 2020 09:12:30: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 09:12:30: #2 alternative fragment length(s) may be 158,589 bps INFO @ Fri, 16 Oct 2020 09:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05_model.r INFO @ Fri, 16 Oct 2020 09:12:30: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:12:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.05_summits.bed INFO @ Fri, 16 Oct 2020 09:12:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (435 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 @ Fri, 16 Oct 2020 09:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.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 09:12:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:12:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:12:58: 1000000 INFO @ Fri, 16 Oct 2020 09:13:02: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:13:02: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:13:02: #1 total tags in treatment: 866703 INFO @ Fri, 16 Oct 2020 09:13:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:13:02: #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 09:13:02: #1 tags after filtering in treatment: 773405 INFO @ Fri, 16 Oct 2020 09:13:02: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:13:02: #1 finished! INFO @ Fri, 16 Oct 2020 09:13:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:13:02: #2 number of paired peaks: 142 WARNING @ Fri, 16 Oct 2020 09:13:02: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 16 Oct 2020 09:13:02: start model_add_line... INFO @ Fri, 16 Oct 2020 09:13:02: start X-correlation... INFO @ Fri, 16 Oct 2020 09:13:02: end of X-cor INFO @ Fri, 16 Oct 2020 09:13:02: #2 finished! INFO @ Fri, 16 Oct 2020 09:13:02: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 09:13:02: #2 alternative fragment length(s) may be 158,589 bps INFO @ Fri, 16 Oct 2020 09:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10_model.r INFO @ Fri, 16 Oct 2020 09:13:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:13:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.10_summits.bed INFO @ Fri, 16 Oct 2020 09:13:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 3 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 09:13:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.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 09:13:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:13:22: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:13:27: 1000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:13:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:13:32: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:13:32: #1 total tags in treatment: 866703 INFO @ Fri, 16 Oct 2020 09:13:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:13:32: #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 09:13:32: #1 tags after filtering in treatment: 773405 INFO @ Fri, 16 Oct 2020 09:13:32: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:13:32: #1 finished! INFO @ Fri, 16 Oct 2020 09:13:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:13:32: #2 number of paired peaks: 142 WARNING @ Fri, 16 Oct 2020 09:13:32: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Fri, 16 Oct 2020 09:13:32: start model_add_line... INFO @ Fri, 16 Oct 2020 09:13:32: start X-correlation... INFO @ Fri, 16 Oct 2020 09:13:32: end of X-cor INFO @ Fri, 16 Oct 2020 09:13:32: #2 finished! INFO @ Fri, 16 Oct 2020 09:13:32: #2 predicted fragment length is 158 bps INFO @ Fri, 16 Oct 2020 09:13:32: #2 alternative fragment length(s) may be 158,589 bps INFO @ Fri, 16 Oct 2020 09:13:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20_model.r INFO @ Fri, 16 Oct 2020 09:13:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:13:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:13:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:13:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:13:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:13:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926523/SRX8926523.20_summits.bed INFO @ Fri, 16 Oct 2020 09:13:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling