Job ID = 5790999 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,809,469 reads read : 3,618,938 reads written : 3,618,938 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: 00:01:13 1809469 reads; of these: 1809469 (100.00%) were paired; of these: 229949 (12.71%) aligned concordantly 0 times 1237420 (68.39%) aligned concordantly exactly 1 time 342100 (18.91%) aligned concordantly >1 times ---- 229949 pairs aligned concordantly 0 times; of these: 616 (0.27%) aligned discordantly 1 time ---- 229333 pairs aligned 0 times concordantly or discordantly; of these: 458666 mates make up the pairs; of these: 448855 (97.86%) aligned 0 times 5985 (1.30%) aligned exactly 1 time 3826 (0.83%) aligned >1 times 87.60% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 17419 / 1577489 = 0.0110 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 08:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.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 08:13:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:33: 1000000 INFO @ Wed, 22 Apr 2020 08:13:41: 2000000 INFO @ Wed, 22 Apr 2020 08:13:48: 3000000 INFO @ Wed, 22 Apr 2020 08:13:49: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:49: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:49: #1 total tags in treatment: 1562103 INFO @ Wed, 22 Apr 2020 08:13:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:49: #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 08:13:49: #1 tags after filtering in treatment: 1393367 INFO @ Wed, 22 Apr 2020 08:13:49: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:13:49: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:49: #2 number of paired peaks: 199 WARNING @ Wed, 22 Apr 2020 08:13:49: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:49: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:49: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:49: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:49: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:49: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2020 08:13:49: #2 alternative fragment length(s) may be 3,98,123,149,176 bps INFO @ Wed, 22 Apr 2020 08:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05_model.r INFO @ Wed, 22 Apr 2020 08:13:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.05_summits.bed INFO @ Wed, 22 Apr 2020 08:13:54: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (392 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 Apr 2020 08:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.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 08:13:56: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:56: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:03: 1000000 INFO @ Wed, 22 Apr 2020 08:14:11: 2000000 INFO @ Wed, 22 Apr 2020 08:14:18: 3000000 INFO @ Wed, 22 Apr 2020 08:14:19: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:19: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:19: #1 total tags in treatment: 1562103 INFO @ Wed, 22 Apr 2020 08:14:19: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:19: #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 08:14:19: #1 tags after filtering in treatment: 1393367 INFO @ Wed, 22 Apr 2020 08:14:19: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:14:19: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:19: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:19: #2 number of paired peaks: 199 WARNING @ Wed, 22 Apr 2020 08:14:19: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:19: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:19: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:19: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:19: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:19: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2020 08:14:19: #2 alternative fragment length(s) may be 3,98,123,149,176 bps INFO @ Wed, 22 Apr 2020 08:14:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10_model.r INFO @ Wed, 22 Apr 2020 08:14:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:23: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Wed, 22 Apr 2020 08:14:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.10_summits.bed INFO @ Wed, 22 Apr 2020 08:14:24: Done! 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 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.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 08:14:26: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:26: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:33: 1000000 INFO @ Wed, 22 Apr 2020 08:14:41: 2000000 INFO @ Wed, 22 Apr 2020 08:14:48: 3000000 INFO @ Wed, 22 Apr 2020 08:14:49: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:49: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:49: #1 total tags in treatment: 1562103 INFO @ Wed, 22 Apr 2020 08:14:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:49: #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 08:14:49: #1 tags after filtering in treatment: 1393367 INFO @ Wed, 22 Apr 2020 08:14:49: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:14:49: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:49: #2 number of paired peaks: 199 WARNING @ Wed, 22 Apr 2020 08:14:49: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:49: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:49: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:49: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:49: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:49: #2 predicted fragment length is 149 bps INFO @ Wed, 22 Apr 2020 08:14:49: #2 alternative fragment length(s) may be 3,98,123,149,176 bps INFO @ Wed, 22 Apr 2020 08:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20_model.r INFO @ Wed, 22 Apr 2020 08:14:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874498/SRX5874498.20_summits.bed INFO @ Wed, 22 Apr 2020 08:14:54: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。