Job ID = 10224103 SRX = SRX8952657 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12700397 spots for SRR12458229/SRR12458229.sra Written 12700397 spots for SRR12458229/SRR12458229.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: 00:02:43 12700397 reads; of these: 12700397 (100.00%) were paired; of these: 11030673 (86.85%) aligned concordantly 0 times 1459643 (11.49%) aligned concordantly exactly 1 time 210081 (1.65%) aligned concordantly >1 times ---- 11030673 pairs aligned concordantly 0 times; of these: 371022 (3.36%) aligned discordantly 1 time ---- 10659651 pairs aligned 0 times concordantly or discordantly; of these: 21319302 mates make up the pairs; of these: 18153153 (85.15%) aligned 0 times 2763312 (12.96%) aligned exactly 1 time 402837 (1.89%) aligned >1 times 28.53% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 506707 / 2030214 = 0.2496 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 09:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.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 09:31:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:11: 1000000 INFO @ Fri, 16 Oct 2020 09:31:17: 2000000 INFO @ Fri, 16 Oct 2020 09:31:22: 3000000 INFO @ Fri, 16 Oct 2020 09:31:28: 4000000 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 09:31:35: 5000000 INFO @ Fri, 16 Oct 2020 09:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.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 09:31:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:41: 6000000 INFO @ Fri, 16 Oct 2020 09:31:42: 1000000 INFO @ Fri, 16 Oct 2020 09:31:42: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:31:42: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:31:42: #1 total tags in treatment: 1369509 INFO @ Fri, 16 Oct 2020 09:31:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:42: #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 09:31:42: #1 tags after filtering in treatment: 1207372 INFO @ Fri, 16 Oct 2020 09:31:42: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:31:42: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:42: #2 number of paired peaks: 180 WARNING @ Fri, 16 Oct 2020 09:31:42: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:42: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:42: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:42: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:42: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:42: #2 predicted fragment length is 299 bps INFO @ Fri, 16 Oct 2020 09:31:42: #2 alternative fragment length(s) may be 21,53,79,95,140,153,171,189,220,264,299,332,349,352,358,379,412,437,452,495,510,554,582,593,596 bps INFO @ Fri, 16 Oct 2020 09:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05_model.r INFO @ Fri, 16 Oct 2020 09:31:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:31:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:47: 2000000 INFO @ Fri, 16 Oct 2020 09:31:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.05_summits.bed INFO @ Fri, 16 Oct 2020 09:31:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 88 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:31:52: 3000000 INFO @ Fri, 16 Oct 2020 09:31:58: 4000000 INFO @ Fri, 16 Oct 2020 09:32:03: 5000000 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 09:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.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 09:32:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:32:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:32:08: 6000000 INFO @ Fri, 16 Oct 2020 09:32:09: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:32:09: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:32:09: #1 total tags in treatment: 1369509 INFO @ Fri, 16 Oct 2020 09:32:09: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:09: #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 09:32:09: #1 tags after filtering in treatment: 1207372 INFO @ Fri, 16 Oct 2020 09:32:09: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:32:09: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:09: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:10: #2 number of paired peaks: 180 WARNING @ Fri, 16 Oct 2020 09:32:10: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 16 Oct 2020 09:32:10: start model_add_line... INFO @ Fri, 16 Oct 2020 09:32:10: start X-correlation... INFO @ Fri, 16 Oct 2020 09:32:10: end of X-cor INFO @ Fri, 16 Oct 2020 09:32:10: #2 finished! INFO @ Fri, 16 Oct 2020 09:32:10: #2 predicted fragment length is 299 bps INFO @ Fri, 16 Oct 2020 09:32:10: #2 alternative fragment length(s) may be 21,53,79,95,140,153,171,189,220,264,299,332,349,352,358,379,412,437,452,495,510,554,582,593,596 bps INFO @ Fri, 16 Oct 2020 09:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10_model.r INFO @ Fri, 16 Oct 2020 09:32:10: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:32:12: 1000000 INFO @ Fri, 16 Oct 2020 09:32:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.10_summits.bed INFO @ Fri, 16 Oct 2020 09:32:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:32:17: 2000000 INFO @ Fri, 16 Oct 2020 09:32:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:32:27: 4000000 INFO @ Fri, 16 Oct 2020 09:32:33: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:32:38: 6000000 INFO @ Fri, 16 Oct 2020 09:32:39: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:32:39: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:32:39: #1 total tags in treatment: 1369509 INFO @ Fri, 16 Oct 2020 09:32:39: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:32:39: #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 09:32:39: #1 tags after filtering in treatment: 1207372 INFO @ Fri, 16 Oct 2020 09:32:39: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 16 Oct 2020 09:32:39: #1 finished! INFO @ Fri, 16 Oct 2020 09:32:39: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:32:39: #2 number of paired peaks: 180 WARNING @ Fri, 16 Oct 2020 09:32:39: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Fri, 16 Oct 2020 09:32:39: start model_add_line... INFO @ Fri, 16 Oct 2020 09:32:39: start X-correlation... INFO @ Fri, 16 Oct 2020 09:32:39: end of X-cor INFO @ Fri, 16 Oct 2020 09:32:39: #2 finished! INFO @ Fri, 16 Oct 2020 09:32:39: #2 predicted fragment length is 299 bps INFO @ Fri, 16 Oct 2020 09:32:39: #2 alternative fragment length(s) may be 21,53,79,95,140,153,171,189,220,264,299,332,349,352,358,379,412,437,452,495,510,554,582,593,596 bps INFO @ Fri, 16 Oct 2020 09:32:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20_model.r INFO @ Fri, 16 Oct 2020 09:32:39: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:32:42: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:32:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:32:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:32:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952657/SRX8952657.20_summits.bed INFO @ Fri, 16 Oct 2020 09:32:43: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling