Job ID = 5791664 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 32,486,043 reads read : 64,972,086 reads written : 64,972,086 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:06:06 32486043 reads; of these: 32486043 (100.00%) were paired; of these: 27282245 (83.98%) aligned concordantly 0 times 4342045 (13.37%) aligned concordantly exactly 1 time 861753 (2.65%) aligned concordantly >1 times ---- 27282245 pairs aligned concordantly 0 times; of these: 2662 (0.01%) aligned discordantly 1 time ---- 27279583 pairs aligned 0 times concordantly or discordantly; of these: 54559166 mates make up the pairs; of these: 54460255 (99.82%) aligned 0 times 58680 (0.11%) aligned exactly 1 time 40231 (0.07%) aligned >1 times 16.18% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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_sort_core] merging from 8 files... [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] 987810 / 5205106 = 0.1898 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 Apr 2020 10:44:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.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 Apr 2020 10:44:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:44:12: 1000000 INFO @ Wed, 22 Apr 2020 10:44:17: 2000000 INFO @ Wed, 22 Apr 2020 10:44:21: 3000000 INFO @ Wed, 22 Apr 2020 10:44:26: 4000000 INFO @ Wed, 22 Apr 2020 10:44:31: 5000000 INFO @ Wed, 22 Apr 2020 10:44:35: 6000000 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 Apr 2020 10:44:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.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 Apr 2020 10:44:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:44:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:44:40: 7000000 INFO @ Wed, 22 Apr 2020 10:44:43: 1000000 INFO @ Wed, 22 Apr 2020 10:44:45: 8000000 INFO @ Wed, 22 Apr 2020 10:44:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:44:47: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:44:47: #1 total tags in treatment: 4216201 INFO @ Wed, 22 Apr 2020 10:44:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:44:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:44:47: #1 tags after filtering in treatment: 2284015 INFO @ Wed, 22 Apr 2020 10:44:47: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:44:47: #1 finished! INFO @ Wed, 22 Apr 2020 10:44:47: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:44:48: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 10:44:48: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 10:44:48: start model_add_line... INFO @ Wed, 22 Apr 2020 10:44:48: start X-correlation... INFO @ Wed, 22 Apr 2020 10:44:48: end of X-cor INFO @ Wed, 22 Apr 2020 10:44:48: #2 finished! INFO @ Wed, 22 Apr 2020 10:44:48: #2 predicted fragment length is 222 bps INFO @ Wed, 22 Apr 2020 10:44:48: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 22 Apr 2020 10:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05_model.r INFO @ Wed, 22 Apr 2020 10:44:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:44:48: 2000000 INFO @ Wed, 22 Apr 2020 10:44:53: 3000000 INFO @ Wed, 22 Apr 2020 10:44:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05_peaks.xls INFO @ Wed, 22 Apr 2020 10:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.05_summits.bed INFO @ Wed, 22 Apr 2020 10:44:55: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (868 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:44:58: 4000000 INFO @ Wed, 22 Apr 2020 10:45:02: 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 @ Wed, 22 Apr 2020 10:45:07: 6000000 INFO @ Wed, 22 Apr 2020 10:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.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 Apr 2020 10:45:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:45:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:45:12: 7000000 INFO @ Wed, 22 Apr 2020 10:45:13: 1000000 INFO @ Wed, 22 Apr 2020 10:45:17: 8000000 INFO @ Wed, 22 Apr 2020 10:45:18: 2000000 INFO @ Wed, 22 Apr 2020 10:45:20: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:20: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:20: #1 total tags in treatment: 4216201 INFO @ Wed, 22 Apr 2020 10:45:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:45:20: #1 tags after filtering in treatment: 2284015 INFO @ Wed, 22 Apr 2020 10:45:20: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:45:20: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:20: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 10:45:20: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 10:45:20: start model_add_line... INFO @ Wed, 22 Apr 2020 10:45:20: start X-correlation... INFO @ Wed, 22 Apr 2020 10:45:20: end of X-cor INFO @ Wed, 22 Apr 2020 10:45:20: #2 finished! INFO @ Wed, 22 Apr 2020 10:45:20: #2 predicted fragment length is 222 bps INFO @ Wed, 22 Apr 2020 10:45:20: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 22 Apr 2020 10:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10_model.r INFO @ Wed, 22 Apr 2020 10:45:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:45:23: 3000000 INFO @ Wed, 22 Apr 2020 10:45:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10_peaks.xls INFO @ Wed, 22 Apr 2020 10:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.10_summits.bed INFO @ Wed, 22 Apr 2020 10:45:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:28: 4000000 INFO @ Wed, 22 Apr 2020 10:45:33: 5000000 INFO @ Wed, 22 Apr 2020 10:45:38: 6000000 INFO @ Wed, 22 Apr 2020 10:45:43: 7000000 INFO @ Wed, 22 Apr 2020 10:45:48: 8000000 INFO @ Wed, 22 Apr 2020 10:45:50: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:50: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:50: #1 total tags in treatment: 4216201 INFO @ Wed, 22 Apr 2020 10:45:50: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:45:50: #1 tags after filtering in treatment: 2284015 INFO @ Wed, 22 Apr 2020 10:45:50: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 10:45:50: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:50: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 10:45:50: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 10:45:50: start model_add_line... INFO @ Wed, 22 Apr 2020 10:45:50: start X-correlation... INFO @ Wed, 22 Apr 2020 10:45:50: end of X-cor INFO @ Wed, 22 Apr 2020 10:45:50: #2 finished! INFO @ Wed, 22 Apr 2020 10:45:50: #2 predicted fragment length is 222 bps INFO @ Wed, 22 Apr 2020 10:45:50: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 22 Apr 2020 10:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20_model.r INFO @ Wed, 22 Apr 2020 10:45:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:45:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:45:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20_peaks.xls INFO @ Wed, 22 Apr 2020 10:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7409627/SRX7409627.20_summits.bed INFO @ Wed, 22 Apr 2020 10:45:58: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。