Job ID = 5791221 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,659,046 reads read : 11,318,092 reads written : 5,659,046 reads 0-length : 5,659,046 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: 00:00:38 5659046 reads; of these: 5659046 (100.00%) were unpaired; of these: 1226938 (21.68%) aligned 0 times 3704735 (65.47%) aligned exactly 1 time 727373 (12.85%) aligned >1 times 78.32% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 2694850 / 4432108 = 0.6080 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 09:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.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 09:06:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:06:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:06:26: 1000000 INFO @ Wed, 22 Apr 2020 09:06:30: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:06:30: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:06:30: #1 total tags in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:06:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:06:30: #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 09:06:30: #1 tags after filtering in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:06:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:06:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:06:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:06:30: #2 number of paired peaks: 782 WARNING @ Wed, 22 Apr 2020 09:06:30: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Wed, 22 Apr 2020 09:06:30: start model_add_line... INFO @ Wed, 22 Apr 2020 09:06:30: start X-correlation... INFO @ Wed, 22 Apr 2020 09:06:30: end of X-cor INFO @ Wed, 22 Apr 2020 09:06:30: #2 finished! INFO @ Wed, 22 Apr 2020 09:06:30: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 09:06:30: #2 alternative fragment length(s) may be 2,142,182,211,251,261 bps INFO @ Wed, 22 Apr 2020 09:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05_model.r INFO @ Wed, 22 Apr 2020 09:06:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:06:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:06:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.05_summits.bed INFO @ Wed, 22 Apr 2020 09:06:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (594 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 09:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.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 09:06:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:06:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:06:57: 1000000 INFO @ Wed, 22 Apr 2020 09:07:01: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:07:01: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:07:01: #1 total tags in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:07:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:01: #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 09:07:01: #1 tags after filtering in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:07:01: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:01: #2 number of paired peaks: 782 WARNING @ Wed, 22 Apr 2020 09:07:01: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Wed, 22 Apr 2020 09:07:01: start model_add_line... INFO @ Wed, 22 Apr 2020 09:07:01: start X-correlation... INFO @ Wed, 22 Apr 2020 09:07:01: end of X-cor INFO @ Wed, 22 Apr 2020 09:07:01: #2 finished! INFO @ Wed, 22 Apr 2020 09:07:01: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 09:07:01: #2 alternative fragment length(s) may be 2,142,182,211,251,261 bps INFO @ Wed, 22 Apr 2020 09:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10_model.r INFO @ Wed, 22 Apr 2020 09:07:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:07:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:07:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:07:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:07:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.10_summits.bed INFO @ Wed, 22 Apr 2020 09:07:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 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 09:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.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 09:07:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:07:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:07:26: 1000000 INFO @ Wed, 22 Apr 2020 09:07:31: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 09:07:31: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 09:07:31: #1 total tags in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:07:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:07:31: #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 09:07:31: #1 tags after filtering in treatment: 1737258 INFO @ Wed, 22 Apr 2020 09:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 09:07:31: #1 finished! INFO @ Wed, 22 Apr 2020 09:07:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:07:31: #2 number of paired peaks: 782 WARNING @ Wed, 22 Apr 2020 09:07:31: Fewer paired peaks (782) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 782 pairs to build model! INFO @ Wed, 22 Apr 2020 09:07:31: start model_add_line... INFO @ Wed, 22 Apr 2020 09:07:31: start X-correlation... INFO @ Wed, 22 Apr 2020 09:07:31: end of X-cor INFO @ Wed, 22 Apr 2020 09:07:31: #2 finished! INFO @ Wed, 22 Apr 2020 09:07:31: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Apr 2020 09:07:31: #2 alternative fragment length(s) may be 2,142,182,211,251,261 bps INFO @ Wed, 22 Apr 2020 09:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20_model.r INFO @ Wed, 22 Apr 2020 09:07:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:07:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:07:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:07:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:07:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:07:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7107358/SRX7107358.20_summits.bed INFO @ Wed, 22 Apr 2020 09:07:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 3 millis CompletedMACS2peakCalling