Job ID = 5791234 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,000,000 reads read : 8,000,000 reads written : 8,000,000 spots read : 529,629 reads read : 1,059,258 reads written : 1,059,258 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: 00:04:20 4529629 reads; of these: 4529629 (100.00%) were paired; of these: 349765 (7.72%) aligned concordantly 0 times 3701761 (81.72%) aligned concordantly exactly 1 time 478103 (10.56%) aligned concordantly >1 times ---- 349765 pairs aligned concordantly 0 times; of these: 67579 (19.32%) aligned discordantly 1 time ---- 282186 pairs aligned 0 times concordantly or discordantly; of these: 564372 mates make up the pairs; of these: 496347 (87.95%) aligned 0 times 38501 (6.82%) aligned exactly 1 time 29524 (5.23%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 1559306 / 4240965 = 0.3677 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 09:23:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.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 09:23:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:23:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:23:38: 1000000 INFO @ Wed, 22 Apr 2020 09:23:44: 2000000 INFO @ Wed, 22 Apr 2020 09:23:51: 3000000 INFO @ Wed, 22 Apr 2020 09:23:58: 4000000 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 09:24:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.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 09:24:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:24:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:24:04: 5000000 INFO @ Wed, 22 Apr 2020 09:24:07: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:24:07: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:24:07: #1 total tags in treatment: 2643907 INFO @ Wed, 22 Apr 2020 09:24:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:24:07: #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 09:24:07: #1 tags after filtering in treatment: 1183212 INFO @ Wed, 22 Apr 2020 09:24:07: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 22 Apr 2020 09:24:07: #1 finished! INFO @ Wed, 22 Apr 2020 09:24:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:24:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:24:07: #2 number of paired peaks: 191 WARNING @ Wed, 22 Apr 2020 09:24:07: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 22 Apr 2020 09:24:07: start model_add_line... INFO @ Wed, 22 Apr 2020 09:24:07: start X-correlation... INFO @ Wed, 22 Apr 2020 09:24:07: end of X-cor INFO @ Wed, 22 Apr 2020 09:24:07: #2 finished! INFO @ Wed, 22 Apr 2020 09:24:07: #2 predicted fragment length is 256 bps INFO @ Wed, 22 Apr 2020 09:24:07: #2 alternative fragment length(s) may be 1,256 bps INFO @ Wed, 22 Apr 2020 09:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05_model.r INFO @ Wed, 22 Apr 2020 09:24:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:24:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:24:08: 1000000 INFO @ Wed, 22 Apr 2020 09:24:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:24:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:24:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.05_summits.bed INFO @ Wed, 22 Apr 2020 09:24:12: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (435 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:24:15: 2000000 INFO @ Wed, 22 Apr 2020 09:24:22: 3000000 INFO @ Wed, 22 Apr 2020 09:24:29: 4000000 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 09:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.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 09:24:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:24:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:24:35: 5000000 INFO @ Wed, 22 Apr 2020 09:24:38: 1000000 INFO @ Wed, 22 Apr 2020 09:24:39: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:24:39: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:24:39: #1 total tags in treatment: 2643907 INFO @ Wed, 22 Apr 2020 09:24:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:24:39: #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 09:24:39: #1 tags after filtering in treatment: 1183212 INFO @ Wed, 22 Apr 2020 09:24:39: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 22 Apr 2020 09:24:39: #1 finished! INFO @ Wed, 22 Apr 2020 09:24:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:24:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:24:39: #2 number of paired peaks: 191 WARNING @ Wed, 22 Apr 2020 09:24:39: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 22 Apr 2020 09:24:39: start model_add_line... INFO @ Wed, 22 Apr 2020 09:24:39: start X-correlation... INFO @ Wed, 22 Apr 2020 09:24:39: end of X-cor INFO @ Wed, 22 Apr 2020 09:24:39: #2 finished! INFO @ Wed, 22 Apr 2020 09:24:39: #2 predicted fragment length is 256 bps INFO @ Wed, 22 Apr 2020 09:24:39: #2 alternative fragment length(s) may be 1,256 bps INFO @ Wed, 22 Apr 2020 09:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10_model.r INFO @ Wed, 22 Apr 2020 09:24:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:24:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.10_summits.bed INFO @ Wed, 22 Apr 2020 09:24:43: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:24:45: 2000000 INFO @ Wed, 22 Apr 2020 09:24:52: 3000000 INFO @ Wed, 22 Apr 2020 09:24:59: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:25:06: 5000000 INFO @ Wed, 22 Apr 2020 09:25:09: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:25:09: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:25:09: #1 total tags in treatment: 2643907 INFO @ Wed, 22 Apr 2020 09:25:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:25:09: #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 09:25:09: #1 tags after filtering in treatment: 1183212 INFO @ Wed, 22 Apr 2020 09:25:09: #1 Redundant rate of treatment: 0.55 INFO @ Wed, 22 Apr 2020 09:25:09: #1 finished! INFO @ Wed, 22 Apr 2020 09:25:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:25:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:25:09: #2 number of paired peaks: 191 WARNING @ Wed, 22 Apr 2020 09:25:09: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 22 Apr 2020 09:25:09: start model_add_line... INFO @ Wed, 22 Apr 2020 09:25:09: start X-correlation... INFO @ Wed, 22 Apr 2020 09:25:09: end of X-cor INFO @ Wed, 22 Apr 2020 09:25:09: #2 finished! INFO @ Wed, 22 Apr 2020 09:25:09: #2 predicted fragment length is 256 bps INFO @ Wed, 22 Apr 2020 09:25:09: #2 alternative fragment length(s) may be 1,256 bps INFO @ Wed, 22 Apr 2020 09:25:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20_model.r INFO @ Wed, 22 Apr 2020 09:25:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:25:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:25:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256000/SRX7256000.20_summits.bed INFO @ Wed, 22 Apr 2020 09:25:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 2 millis CompletedMACS2peakCalling