Job ID = 7099221 SRX = SRX6911498 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39155315 spots for SRR10191125/SRR10191125.sra Written 39155315 spots for SRR10191125/SRR10191125.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: 00:06:18 39155315 reads; of these: 39155315 (100.00%) were paired; of these: 38055678 (97.19%) aligned concordantly 0 times 839282 (2.14%) aligned concordantly exactly 1 time 260355 (0.66%) aligned concordantly >1 times ---- 38055678 pairs aligned concordantly 0 times; of these: 36147 (0.09%) aligned discordantly 1 time ---- 38019531 pairs aligned 0 times concordantly or discordantly; of these: 76039062 mates make up the pairs; of these: 75902127 (99.82%) aligned 0 times 74750 (0.10%) aligned exactly 1 time 62185 (0.08%) aligned >1 times 3.08% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 682584 / 1135249 = 0.6013 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 @ Wed, 22 Jul 2020 12:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.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 @ Wed, 22 Jul 2020 12:13:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:13:18: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:13:24: 1000000 INFO @ Wed, 22 Jul 2020 12:13:24: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:13:24: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:13:24: #1 total tags in treatment: 429702 INFO @ Wed, 22 Jul 2020 12:13:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:13:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:13:24: #1 tags after filtering in treatment: 280903 INFO @ Wed, 22 Jul 2020 12:13:24: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 12:13:24: #1 finished! INFO @ Wed, 22 Jul 2020 12:13:24: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:13:24: #2 number of paired peaks: 400 WARNING @ Wed, 22 Jul 2020 12:13:24: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 22 Jul 2020 12:13:24: start model_add_line... INFO @ Wed, 22 Jul 2020 12:13:24: start X-correlation... INFO @ Wed, 22 Jul 2020 12:13:24: end of X-cor INFO @ Wed, 22 Jul 2020 12:13:24: #2 finished! INFO @ Wed, 22 Jul 2020 12:13:24: #2 predicted fragment length is 333 bps INFO @ Wed, 22 Jul 2020 12:13:24: #2 alternative fragment length(s) may be 17,37,71,273,281,288,309,333,380 bps INFO @ Wed, 22 Jul 2020 12:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05_model.r INFO @ Wed, 22 Jul 2020 12:13:24: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:13:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.05_summits.bed INFO @ Wed, 22 Jul 2020 12:13:26: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (278 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 @ Wed, 22 Jul 2020 12:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.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 @ Wed, 22 Jul 2020 12:13:48: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:13:48: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:13:55: 1000000 INFO @ Wed, 22 Jul 2020 12:13:55: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:13:55: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:13:55: #1 total tags in treatment: 429702 INFO @ Wed, 22 Jul 2020 12:13:55: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:13:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:13:55: #1 tags after filtering in treatment: 280903 INFO @ Wed, 22 Jul 2020 12:13:55: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 12:13:55: #1 finished! INFO @ Wed, 22 Jul 2020 12:13:55: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:13:55: #2 number of paired peaks: 400 WARNING @ Wed, 22 Jul 2020 12:13:55: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 22 Jul 2020 12:13:55: start model_add_line... INFO @ Wed, 22 Jul 2020 12:13:55: start X-correlation... INFO @ Wed, 22 Jul 2020 12:13:55: end of X-cor INFO @ Wed, 22 Jul 2020 12:13:55: #2 finished! INFO @ Wed, 22 Jul 2020 12:13:55: #2 predicted fragment length is 333 bps INFO @ Wed, 22 Jul 2020 12:13:55: #2 alternative fragment length(s) may be 17,37,71,273,281,288,309,333,380 bps INFO @ Wed, 22 Jul 2020 12:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10_model.r INFO @ Wed, 22 Jul 2020 12:13:55: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:13:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.10_summits.bed INFO @ Wed, 22 Jul 2020 12:13:57: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (239 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 @ Wed, 22 Jul 2020 12:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.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 @ Wed, 22 Jul 2020 12:14:18: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:14:18: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:14:24: 1000000 INFO @ Wed, 22 Jul 2020 12:14:24: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:14:24: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:14:24: #1 total tags in treatment: 429702 INFO @ Wed, 22 Jul 2020 12:14:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:14:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:14:24: #1 tags after filtering in treatment: 280903 INFO @ Wed, 22 Jul 2020 12:14:24: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Jul 2020 12:14:24: #1 finished! INFO @ Wed, 22 Jul 2020 12:14:24: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:14:24: #2 number of paired peaks: 400 WARNING @ Wed, 22 Jul 2020 12:14:24: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Wed, 22 Jul 2020 12:14:24: start model_add_line... INFO @ Wed, 22 Jul 2020 12:14:24: start X-correlation... INFO @ Wed, 22 Jul 2020 12:14:24: end of X-cor INFO @ Wed, 22 Jul 2020 12:14:24: #2 finished! INFO @ Wed, 22 Jul 2020 12:14:24: #2 predicted fragment length is 333 bps INFO @ Wed, 22 Jul 2020 12:14:24: #2 alternative fragment length(s) may be 17,37,71,273,281,288,309,333,380 bps INFO @ Wed, 22 Jul 2020 12:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20_model.r INFO @ Wed, 22 Jul 2020 12:14:24: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:14:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911498/SRX6911498.20_summits.bed INFO @ Wed, 22 Jul 2020 12:14:26: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling