Job ID = 10223974 SRX = SRX7496421 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7520777 spots for SRR10823032/SRR10823032.sra Written 7520777 spots for SRR10823032/SRR10823032.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: 00:01:38 7520777 reads; of these: 7520777 (100.00%) were paired; of these: 5518308 (73.37%) aligned concordantly 0 times 1919958 (25.53%) aligned concordantly exactly 1 time 82511 (1.10%) aligned concordantly >1 times ---- 5518308 pairs aligned concordantly 0 times; of these: 26080 (0.47%) aligned discordantly 1 time ---- 5492228 pairs aligned 0 times concordantly or discordantly; of these: 10984456 mates make up the pairs; of these: 9306546 (84.72%) aligned 0 times 1592690 (14.50%) aligned exactly 1 time 85220 (0.78%) aligned >1 times 38.13% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 560012 / 2028230 = 0.2761 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 09:03:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.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 09:03:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:03:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:03:38: 1000000 INFO @ Fri, 16 Oct 2020 09:03:44: 2000000 INFO @ Fri, 16 Oct 2020 09:03:49: 3000000 INFO @ Fri, 16 Oct 2020 09:03:54: 4000000 INFO @ Fri, 16 Oct 2020 09:03:57: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:03:57: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:03:57: #1 total tags in treatment: 1445167 INFO @ Fri, 16 Oct 2020 09:03:57: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:03:57: #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 09:03:57: #1 tags after filtering in treatment: 899055 INFO @ Fri, 16 Oct 2020 09:03:57: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 09:03:57: #1 finished! INFO @ Fri, 16 Oct 2020 09:03:57: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:03:57: #2 number of paired peaks: 241 WARNING @ Fri, 16 Oct 2020 09:03:57: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 16 Oct 2020 09:03:57: start model_add_line... INFO @ Fri, 16 Oct 2020 09:03:57: start X-correlation... INFO @ Fri, 16 Oct 2020 09:03:57: end of X-cor INFO @ Fri, 16 Oct 2020 09:03:57: #2 finished! INFO @ Fri, 16 Oct 2020 09:03:57: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 09:03:57: #2 alternative fragment length(s) may be 0,156,160,179 bps INFO @ Fri, 16 Oct 2020 09:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05_model.r INFO @ Fri, 16 Oct 2020 09:03:57: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:04:01: #3 Call peaks for each chromosome... 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 09:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.05_summits.bed INFO @ Fri, 16 Oct 2020 09:04:02: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (511 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.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 09:04:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:04:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:04:07: 1000000 INFO @ Fri, 16 Oct 2020 09:04:12: 2000000 INFO @ Fri, 16 Oct 2020 09:04:17: 3000000 INFO @ Fri, 16 Oct 2020 09:04:22: 4000000 INFO @ Fri, 16 Oct 2020 09:04:24: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:04:24: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:04:24: #1 total tags in treatment: 1445167 INFO @ Fri, 16 Oct 2020 09:04:24: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:04:24: #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 09:04:24: #1 tags after filtering in treatment: 899055 INFO @ Fri, 16 Oct 2020 09:04:24: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 09:04:24: #1 finished! INFO @ Fri, 16 Oct 2020 09:04:24: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:04:25: #2 number of paired peaks: 241 WARNING @ Fri, 16 Oct 2020 09:04:25: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 16 Oct 2020 09:04:25: start model_add_line... INFO @ Fri, 16 Oct 2020 09:04:25: start X-correlation... INFO @ Fri, 16 Oct 2020 09:04:25: end of X-cor INFO @ Fri, 16 Oct 2020 09:04:25: #2 finished! INFO @ Fri, 16 Oct 2020 09:04:25: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 09:04:25: #2 alternative fragment length(s) may be 0,156,160,179 bps INFO @ Fri, 16 Oct 2020 09:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10_model.r INFO @ Fri, 16 Oct 2020 09:04:25: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:04:28: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.10_summits.bed INFO @ Fri, 16 Oct 2020 09:04:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (238 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 09:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.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 09:04:32: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:04:32: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:04:39: 1000000 INFO @ Fri, 16 Oct 2020 09:04:45: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:04:51: 3000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:04:57: 4000000 INFO @ Fri, 16 Oct 2020 09:05:01: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 09:05:01: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 09:05:01: #1 total tags in treatment: 1445167 INFO @ Fri, 16 Oct 2020 09:05:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:05:01: #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 09:05:01: #1 tags after filtering in treatment: 899055 INFO @ Fri, 16 Oct 2020 09:05:01: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 09:05:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:05:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:05:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:05:01: #2 number of paired peaks: 241 WARNING @ Fri, 16 Oct 2020 09:05:01: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 16 Oct 2020 09:05:01: start model_add_line... INFO @ Fri, 16 Oct 2020 09:05:01: start X-correlation... INFO @ Fri, 16 Oct 2020 09:05:01: end of X-cor INFO @ Fri, 16 Oct 2020 09:05:01: #2 finished! INFO @ Fri, 16 Oct 2020 09:05:01: #2 predicted fragment length is 179 bps INFO @ Fri, 16 Oct 2020 09:05:01: #2 alternative fragment length(s) may be 0,156,160,179 bps INFO @ Fri, 16 Oct 2020 09:05:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20_model.r INFO @ Fri, 16 Oct 2020 09:05:01: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:05:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:05:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:05:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:05:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:05:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496421/SRX7496421.20_summits.bed INFO @ Fri, 16 Oct 2020 09:05:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling