Job ID = 14520983 SRX = ERX4123661 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4760529 spots for ERR4157916/ERR4157916.sra Written 4760529 spots for ERR4157916/ERR4157916.sra 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: 00:01:11 4760529 reads; of these: 4760529 (100.00%) were unpaired; of these: 1019428 (21.41%) aligned 0 times 2180133 (45.80%) aligned exactly 1 time 1560968 (32.79%) aligned >1 times 78.59% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 2933373 / 3741101 = 0.7841 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.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 @ Sat, 15 Jan 2022 20:14:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:14:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:14:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:14:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:14:54: #1 total tags in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:14:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:14:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:14:54: #1 tags after filtering in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:14:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:14:54: #1 finished! INFO @ Sat, 15 Jan 2022 20:14:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:14:54: #2 number of paired peaks: 440 WARNING @ Sat, 15 Jan 2022 20:14:54: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sat, 15 Jan 2022 20:14:54: start model_add_line... INFO @ Sat, 15 Jan 2022 20:14:54: start X-correlation... INFO @ Sat, 15 Jan 2022 20:14:54: end of X-cor INFO @ Sat, 15 Jan 2022 20:14:54: #2 finished! INFO @ Sat, 15 Jan 2022 20:14:54: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 20:14:54: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 15 Jan 2022 20:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05_model.r INFO @ Sat, 15 Jan 2022 20:14:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:14:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.05_summits.bed INFO @ Sat, 15 Jan 2022 20:14:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 4 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.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 @ Sat, 15 Jan 2022 20:15:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:15:23: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:23: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:23: #1 total tags in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:15:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:15:23: #1 tags after filtering in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:23: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:24: #2 number of paired peaks: 440 WARNING @ Sat, 15 Jan 2022 20:15:24: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:24: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:24: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:24: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:24: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:24: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 20:15:24: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 15 Jan 2022 20:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10_model.r INFO @ Sat, 15 Jan 2022 20:15:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.10_summits.bed INFO @ Sat, 15 Jan 2022 20:15:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:15:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.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 @ Sat, 15 Jan 2022 20:15:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:15:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:15:54: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:15:54: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:15:54: #1 total tags in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:15:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:15:54: #1 tags after filtering in treatment: 807728 INFO @ Sat, 15 Jan 2022 20:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:15:54: #1 finished! INFO @ Sat, 15 Jan 2022 20:15:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:15:54: #2 number of paired peaks: 440 WARNING @ Sat, 15 Jan 2022 20:15:54: Fewer paired peaks (440) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 440 pairs to build model! INFO @ Sat, 15 Jan 2022 20:15:54: start model_add_line... INFO @ Sat, 15 Jan 2022 20:15:54: start X-correlation... INFO @ Sat, 15 Jan 2022 20:15:54: end of X-cor INFO @ Sat, 15 Jan 2022 20:15:54: #2 finished! INFO @ Sat, 15 Jan 2022 20:15:54: #2 predicted fragment length is 183 bps INFO @ Sat, 15 Jan 2022 20:15:54: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 15 Jan 2022 20:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20_model.r INFO @ Sat, 15 Jan 2022 20:15:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:15:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4123661/ERX4123661.20_summits.bed INFO @ Sat, 15 Jan 2022 20:15:59: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (388 records, 4 fields): 4 millis CompletedMACS2peakCalling