Job ID = 7113382 SRX = SRX8462165 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:33:34 prefetch.2.10.7: 1) Downloading 'SRR11915624'... 2020-07-22T05:33:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:34:40 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:34:41 prefetch.2.10.7: 'SRR11915624' is valid 2020-07-22T05:34:41 prefetch.2.10.7: 1) 'SRR11915624' was downloaded successfully 2020-07-22T05:34:41 prefetch.2.10.7: 'SRR11915624' has 0 unresolved dependencies Read 6822886 spots for SRR11915624/SRR11915624.sra Written 6822886 spots for SRR11915624/SRR11915624.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: 00:03:41 6822886 reads; of these: 6822886 (100.00%) were paired; of these: 4057814 (59.47%) aligned concordantly 0 times 2257042 (33.08%) aligned concordantly exactly 1 time 508030 (7.45%) aligned concordantly >1 times ---- 4057814 pairs aligned concordantly 0 times; of these: 32688 (0.81%) aligned discordantly 1 time ---- 4025126 pairs aligned 0 times concordantly or discordantly; of these: 8050252 mates make up the pairs; of these: 7977364 (99.09%) aligned 0 times 48018 (0.60%) aligned exactly 1 time 24870 (0.31%) aligned >1 times 41.54% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 2336266 / 2797608 = 0.8351 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 14:40:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.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 14:40:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:40:49: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:40:54: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:40:54: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:40:54: #1 total tags in treatment: 447015 INFO @ Wed, 22 Jul 2020 14:40:54: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:40:54: #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 14:40:54: #1 tags after filtering in treatment: 342249 INFO @ Wed, 22 Jul 2020 14:40:54: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:40:54: #1 finished! INFO @ Wed, 22 Jul 2020 14:40:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:40:54: #2 number of paired peaks: 130 WARNING @ Wed, 22 Jul 2020 14:40:54: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Wed, 22 Jul 2020 14:40:54: start model_add_line... INFO @ Wed, 22 Jul 2020 14:40:54: start X-correlation... INFO @ Wed, 22 Jul 2020 14:40:54: end of X-cor INFO @ Wed, 22 Jul 2020 14:40:54: #2 finished! INFO @ Wed, 22 Jul 2020 14:40:54: #2 predicted fragment length is 259 bps INFO @ Wed, 22 Jul 2020 14:40:54: #2 alternative fragment length(s) may be 4,77,96,147,175,195,228,259,330,405,433,542 bps INFO @ Wed, 22 Jul 2020 14:40:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05_model.r INFO @ Wed, 22 Jul 2020 14:40:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:40:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:40:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.05_summits.bed INFO @ Wed, 22 Jul 2020 14:40:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 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 14:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.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 14:41:19: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:41:19: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:41:24: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:41:24: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:41:24: #1 total tags in treatment: 447015 INFO @ Wed, 22 Jul 2020 14:41:24: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:41:24: #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 14:41:24: #1 tags after filtering in treatment: 342249 INFO @ Wed, 22 Jul 2020 14:41:24: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:41:24: #1 finished! INFO @ Wed, 22 Jul 2020 14:41:24: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:41:24: #2 number of paired peaks: 130 WARNING @ Wed, 22 Jul 2020 14:41:24: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Wed, 22 Jul 2020 14:41:24: start model_add_line... INFO @ Wed, 22 Jul 2020 14:41:24: start X-correlation... INFO @ Wed, 22 Jul 2020 14:41:24: end of X-cor INFO @ Wed, 22 Jul 2020 14:41:24: #2 finished! INFO @ Wed, 22 Jul 2020 14:41:24: #2 predicted fragment length is 259 bps INFO @ Wed, 22 Jul 2020 14:41:24: #2 alternative fragment length(s) may be 4,77,96,147,175,195,228,259,330,405,433,542 bps INFO @ Wed, 22 Jul 2020 14:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10_model.r INFO @ Wed, 22 Jul 2020 14:41:24: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:41:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.10_summits.bed INFO @ Wed, 22 Jul 2020 14:41:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10 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 14:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.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 14:41:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:41:49: #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 14:41:54: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 14:41:54: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 14:41:54: #1 total tags in treatment: 447015 INFO @ Wed, 22 Jul 2020 14:41:54: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:41:54: #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 14:41:54: #1 tags after filtering in treatment: 342249 INFO @ Wed, 22 Jul 2020 14:41:54: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 22 Jul 2020 14:41:54: #1 finished! INFO @ Wed, 22 Jul 2020 14:41:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:41:54: #2 number of paired peaks: 130 WARNING @ Wed, 22 Jul 2020 14:41:54: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Wed, 22 Jul 2020 14:41:54: start model_add_line... INFO @ Wed, 22 Jul 2020 14:41:54: start X-correlation... INFO @ Wed, 22 Jul 2020 14:41:54: end of X-cor INFO @ Wed, 22 Jul 2020 14:41:54: #2 finished! INFO @ Wed, 22 Jul 2020 14:41:54: #2 predicted fragment length is 259 bps INFO @ Wed, 22 Jul 2020 14:41:54: #2 alternative fragment length(s) may be 4,77,96,147,175,195,228,259,330,405,433,542 bps INFO @ Wed, 22 Jul 2020 14:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20_model.r INFO @ Wed, 22 Jul 2020 14:41:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:41:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462165/SRX8462165.20_summits.bed INFO @ Wed, 22 Jul 2020 14:41:56: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling