Job ID = 5791216 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,887,619 reads read : 3,775,238 reads written : 1,887,619 reads 0-length : 1,887,619 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: 00:00:12 1887619 reads; of these: 1887619 (100.00%) were unpaired; of these: 96816 (5.13%) aligned 0 times 1579912 (83.70%) aligned exactly 1 time 210891 (11.17%) aligned >1 times 94.87% overall alignment rate Time searching: 00:00:12 Overall time: 00:00:12 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_rmdupse_core] 268728 / 1790803 = 0.1501 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 09:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.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 09:01:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:01:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:01:19: 1000000 INFO @ Wed, 22 Apr 2020 09:01:21: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:01:21: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:01:21: #1 total tags in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:01:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:01:21: #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 09:01:21: #1 tags after filtering in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:01:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:01:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:01:22: #2 number of paired peaks: 142 WARNING @ Wed, 22 Apr 2020 09:01:22: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 22 Apr 2020 09:01:22: start model_add_line... INFO @ Wed, 22 Apr 2020 09:01:22: start X-correlation... INFO @ Wed, 22 Apr 2020 09:01:22: end of X-cor INFO @ Wed, 22 Apr 2020 09:01:22: #2 finished! INFO @ Wed, 22 Apr 2020 09:01:22: #2 predicted fragment length is 226 bps INFO @ Wed, 22 Apr 2020 09:01:22: #2 alternative fragment length(s) may be 226,238 bps INFO @ Wed, 22 Apr 2020 09:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05_model.r INFO @ Wed, 22 Apr 2020 09:01:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:01:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.05_summits.bed INFO @ Wed, 22 Apr 2020 09:01:27: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1128 records, 4 fields): 3 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 09:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.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 09:01:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:01:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:01:49: 1000000 INFO @ Wed, 22 Apr 2020 09:01:51: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:01:51: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:01:51: #1 total tags in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:01:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:01:51: #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 09:01:52: #1 tags after filtering in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:01:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:01:52: #1 finished! INFO @ Wed, 22 Apr 2020 09:01:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:01:52: #2 number of paired peaks: 142 WARNING @ Wed, 22 Apr 2020 09:01:52: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 22 Apr 2020 09:01:52: start model_add_line... INFO @ Wed, 22 Apr 2020 09:01:52: start X-correlation... INFO @ Wed, 22 Apr 2020 09:01:52: end of X-cor INFO @ Wed, 22 Apr 2020 09:01:52: #2 finished! INFO @ Wed, 22 Apr 2020 09:01:52: #2 predicted fragment length is 226 bps INFO @ Wed, 22 Apr 2020 09:01:52: #2 alternative fragment length(s) may be 226,238 bps INFO @ Wed, 22 Apr 2020 09:01:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10_model.r INFO @ Wed, 22 Apr 2020 09:01:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:01:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.10_summits.bed INFO @ Wed, 22 Apr 2020 09:01:57: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (776 records, 4 fields): 3 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 09:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.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 09:02:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:02:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:02:19: 1000000 INFO @ Wed, 22 Apr 2020 09:02:21: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:02:21: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:02:21: #1 total tags in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:02:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:02:21: #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 09:02:22: #1 tags after filtering in treatment: 1522075 INFO @ Wed, 22 Apr 2020 09:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:02:22: #1 finished! INFO @ Wed, 22 Apr 2020 09:02:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:02:22: #2 number of paired peaks: 142 WARNING @ Wed, 22 Apr 2020 09:02:22: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 22 Apr 2020 09:02:22: start model_add_line... INFO @ Wed, 22 Apr 2020 09:02:22: start X-correlation... INFO @ Wed, 22 Apr 2020 09:02:22: end of X-cor INFO @ Wed, 22 Apr 2020 09:02:22: #2 finished! INFO @ Wed, 22 Apr 2020 09:02:22: #2 predicted fragment length is 226 bps INFO @ Wed, 22 Apr 2020 09:02:22: #2 alternative fragment length(s) may be 226,238 bps INFO @ Wed, 22 Apr 2020 09:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20_model.r INFO @ Wed, 22 Apr 2020 09:02:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:02:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6879621/SRX6879621.20_summits.bed INFO @ Wed, 22 Apr 2020 09:02:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (475 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。