Job ID = 5791009 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,371,870 reads read : 4,743,740 reads written : 4,743,740 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: 00:00:43 2371870 reads; of these: 2371870 (100.00%) were paired; of these: 1661743 (70.06%) aligned concordantly 0 times 579925 (24.45%) aligned concordantly exactly 1 time 130202 (5.49%) aligned concordantly >1 times ---- 1661743 pairs aligned concordantly 0 times; of these: 1147 (0.07%) aligned discordantly 1 time ---- 1660596 pairs aligned 0 times concordantly or discordantly; of these: 3321192 mates make up the pairs; of these: 3306625 (99.56%) aligned 0 times 10463 (0.32%) aligned exactly 1 time 4104 (0.12%) aligned >1 times 30.29% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 24130 / 710293 = 0.0340 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 08:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.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 08:16:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:15: 1000000 INFO @ Wed, 22 Apr 2020 08:16:17: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:17: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:17: #1 total tags in treatment: 686033 INFO @ Wed, 22 Apr 2020 08:16:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:17: #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 08:16:17: #1 tags after filtering in treatment: 648719 INFO @ Wed, 22 Apr 2020 08:16:17: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 22 Apr 2020 08:16:17: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:17: #2 number of paired peaks: 341 WARNING @ Wed, 22 Apr 2020 08:16:17: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:17: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:17: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:17: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:17: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:17: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 08:16:17: #2 alternative fragment length(s) may be 4,154,177 bps INFO @ Wed, 22 Apr 2020 08:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05_model.r INFO @ Wed, 22 Apr 2020 08:16:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.05_summits.bed INFO @ Wed, 22 Apr 2020 08:16:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (132 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 Apr 2020 08:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.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 08:16:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:46: 1000000 INFO @ Wed, 22 Apr 2020 08:16:48: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:48: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:48: #1 total tags in treatment: 686033 INFO @ Wed, 22 Apr 2020 08:16:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:48: #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 08:16:48: #1 tags after filtering in treatment: 648719 INFO @ Wed, 22 Apr 2020 08:16:48: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 22 Apr 2020 08:16:48: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:48: #2 number of paired peaks: 341 WARNING @ Wed, 22 Apr 2020 08:16:48: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:48: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:48: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:48: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:48: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:48: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 08:16:48: #2 alternative fragment length(s) may be 4,154,177 bps INFO @ Wed, 22 Apr 2020 08:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10_model.r INFO @ Wed, 22 Apr 2020 08:16:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (94 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 Apr 2020 08:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.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 08:17:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:14: 1000000 INFO @ Wed, 22 Apr 2020 08:17:17: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:17: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:17: #1 total tags in treatment: 686033 INFO @ Wed, 22 Apr 2020 08:17:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:17: #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 08:17:17: #1 tags after filtering in treatment: 648719 INFO @ Wed, 22 Apr 2020 08:17:17: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 22 Apr 2020 08:17:17: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:17: #2 number of paired peaks: 341 WARNING @ Wed, 22 Apr 2020 08:17:17: Fewer paired peaks (341) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 341 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:17: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:17: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:17: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:17: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:17: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 08:17:17: #2 alternative fragment length(s) may be 4,154,177 bps INFO @ Wed, 22 Apr 2020 08:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20_model.r INFO @ Wed, 22 Apr 2020 08:17:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:17:19: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874506/SRX5874506.20_summits.bed INFO @ Wed, 22 Apr 2020 08:17:19: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (51 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。