Job ID = 10224055 SRX = SRX8952612 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7403087 spots for SRR12458274/SRR12458274.sra Written 7403087 spots for SRR12458274/SRR12458274.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: 00:01:53 7403087 reads; of these: 7403087 (100.00%) were paired; of these: 5174289 (69.89%) aligned concordantly 0 times 1946519 (26.29%) aligned concordantly exactly 1 time 282279 (3.81%) aligned concordantly >1 times ---- 5174289 pairs aligned concordantly 0 times; of these: 211047 (4.08%) aligned discordantly 1 time ---- 4963242 pairs aligned 0 times concordantly or discordantly; of these: 9926484 mates make up the pairs; of these: 8801984 (88.67%) aligned 0 times 958815 (9.66%) aligned exactly 1 time 165685 (1.67%) aligned >1 times 40.55% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 472711 / 2434048 = 0.1942 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 09:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.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 09:19:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:08: 1000000 INFO @ Fri, 16 Oct 2020 09:19:13: 2000000 INFO @ Fri, 16 Oct 2020 09:19:17: 3000000 INFO @ Fri, 16 Oct 2020 09:19:22: 4000000 INFO @ Fri, 16 Oct 2020 09:19:27: 5000000 INFO @ Fri, 16 Oct 2020 09:19:27: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:19:27: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:19:27: #1 total tags in treatment: 1843246 INFO @ Fri, 16 Oct 2020 09:19:27: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:27: #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 09:19:27: #1 tags after filtering in treatment: 1526866 INFO @ Fri, 16 Oct 2020 09:19:27: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:19:27: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:27: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:27: #2 number of paired peaks: 222 WARNING @ Fri, 16 Oct 2020 09:19:27: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:27: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:27: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:27: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:27: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:27: #2 predicted fragment length is 308 bps INFO @ Fri, 16 Oct 2020 09:19:27: #2 alternative fragment length(s) may be 3,308 bps INFO @ Fri, 16 Oct 2020 09:19:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05_model.r INFO @ Fri, 16 Oct 2020 09:19:27: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:27: #3 Pre-compute pvalue-qvalue table... 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 09:19:32: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:19:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:19:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:19:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.05_summits.bed INFO @ Fri, 16 Oct 2020 09:19:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (734 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.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 09:19:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:39: 1000000 INFO @ Fri, 16 Oct 2020 09:19:43: 2000000 INFO @ Fri, 16 Oct 2020 09:19:48: 3000000 INFO @ Fri, 16 Oct 2020 09:19:53: 4000000 INFO @ Fri, 16 Oct 2020 09:19:58: 5000000 INFO @ Fri, 16 Oct 2020 09:19:58: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:19:58: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:19:58: #1 total tags in treatment: 1843246 INFO @ Fri, 16 Oct 2020 09:19:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:58: #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 09:19:58: #1 tags after filtering in treatment: 1526866 INFO @ Fri, 16 Oct 2020 09:19:58: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:19:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:58: #2 number of paired peaks: 222 WARNING @ Fri, 16 Oct 2020 09:19:58: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:58: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:58: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:58: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:58: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:58: #2 predicted fragment length is 308 bps INFO @ Fri, 16 Oct 2020 09:19:58: #2 alternative fragment length(s) may be 3,308 bps INFO @ Fri, 16 Oct 2020 09:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10_model.r INFO @ Fri, 16 Oct 2020 09:19:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:58: #3 Pre-compute pvalue-qvalue table... 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 09:20:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.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 09:20:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:20:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.10_summits.bed INFO @ Fri, 16 Oct 2020 09:20:04: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:20:08: 1000000 INFO @ Fri, 16 Oct 2020 09:20:13: 2000000 INFO @ Fri, 16 Oct 2020 09:20:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:20:23: 4000000 INFO @ Fri, 16 Oct 2020 09:20:28: 5000000 INFO @ Fri, 16 Oct 2020 09:20:28: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:20:28: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:20:28: #1 total tags in treatment: 1843246 INFO @ Fri, 16 Oct 2020 09:20:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:28: #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 09:20:28: #1 tags after filtering in treatment: 1526866 INFO @ Fri, 16 Oct 2020 09:20:28: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:20:28: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:28: #2 number of paired peaks: 222 WARNING @ Fri, 16 Oct 2020 09:20:28: Fewer paired peaks (222) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 222 pairs to build model! INFO @ Fri, 16 Oct 2020 09:20:28: start model_add_line... INFO @ Fri, 16 Oct 2020 09:20:28: start X-correlation... INFO @ Fri, 16 Oct 2020 09:20:28: end of X-cor INFO @ Fri, 16 Oct 2020 09:20:28: #2 finished! INFO @ Fri, 16 Oct 2020 09:20:28: #2 predicted fragment length is 308 bps INFO @ Fri, 16 Oct 2020 09:20:28: #2 alternative fragment length(s) may be 3,308 bps INFO @ Fri, 16 Oct 2020 09:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20_model.r INFO @ Fri, 16 Oct 2020 09:20:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:20:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:20:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952612/SRX8952612.20_summits.bed INFO @ Fri, 16 Oct 2020 09:20:34: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (277 records, 4 fields): 2 millis CompletedMACS2peakCalling