Job ID = 14519792 SRX = ERX4107466 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6853917 spots for ERR4140175/ERR4140175.sra Written 6853917 spots for ERR4140175/ERR4140175.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: 00:00:50 6853917 reads; of these: 6853917 (100.00%) were unpaired; of these: 1195557 (17.44%) aligned 0 times 4847474 (70.73%) aligned exactly 1 time 810886 (11.83%) aligned >1 times 82.56% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 4455052 / 5658360 = 0.7873 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 17:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.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 17:48:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:48:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:48:20: 1000000 INFO @ Sat, 15 Jan 2022 17:48:21: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:48:21: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:48:21: #1 total tags in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:48:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:48:21: #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 17:48:21: #1 tags after filtering in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:48:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:48:21: #1 finished! INFO @ Sat, 15 Jan 2022 17:48:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:48:21: #2 number of paired peaks: 277 WARNING @ Sat, 15 Jan 2022 17:48:21: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 15 Jan 2022 17:48:21: start model_add_line... INFO @ Sat, 15 Jan 2022 17:48:21: start X-correlation... INFO @ Sat, 15 Jan 2022 17:48:21: end of X-cor INFO @ Sat, 15 Jan 2022 17:48:21: #2 finished! INFO @ Sat, 15 Jan 2022 17:48:21: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 17:48:21: #2 alternative fragment length(s) may be 1,11,41,73,94,106,120,128,147,165,200,220,244,263,314,341,402,430,461,487,516,565 bps INFO @ Sat, 15 Jan 2022 17:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05_model.r INFO @ Sat, 15 Jan 2022 17:48:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:48:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:48:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:48:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.05_summits.bed INFO @ Sat, 15 Jan 2022 17:48:26: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (181 records, 4 fields): 2 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 17:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.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 17:48:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:48:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:48:51: 1000000 INFO @ Sat, 15 Jan 2022 17:48:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:48:52: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:48:52: #1 total tags in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:48:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:48:52: #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 17:48:52: #1 tags after filtering in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:48:52: #1 finished! INFO @ Sat, 15 Jan 2022 17:48:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:48:52: #2 number of paired peaks: 277 WARNING @ Sat, 15 Jan 2022 17:48:52: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 15 Jan 2022 17:48:52: start model_add_line... INFO @ Sat, 15 Jan 2022 17:48:52: start X-correlation... INFO @ Sat, 15 Jan 2022 17:48:52: end of X-cor INFO @ Sat, 15 Jan 2022 17:48:52: #2 finished! INFO @ Sat, 15 Jan 2022 17:48:52: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 17:48:52: #2 alternative fragment length(s) may be 1,11,41,73,94,106,120,128,147,165,200,220,244,263,314,341,402,430,461,487,516,565 bps INFO @ Sat, 15 Jan 2022 17:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10_model.r INFO @ Sat, 15 Jan 2022 17:48:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:48:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.10_summits.bed INFO @ Sat, 15 Jan 2022 17:48:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 1 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 17:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.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 17:49:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:49:15: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:49:20: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:49:22: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 17:49:22: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 17:49:22: #1 total tags in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:49:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:49:22: #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 17:49:22: #1 tags after filtering in treatment: 1203308 INFO @ Sat, 15 Jan 2022 17:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:49:22: #1 finished! INFO @ Sat, 15 Jan 2022 17:49:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:49:22: #2 number of paired peaks: 277 WARNING @ Sat, 15 Jan 2022 17:49:22: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 15 Jan 2022 17:49:22: start model_add_line... INFO @ Sat, 15 Jan 2022 17:49:22: start X-correlation... INFO @ Sat, 15 Jan 2022 17:49:22: end of X-cor INFO @ Sat, 15 Jan 2022 17:49:22: #2 finished! INFO @ Sat, 15 Jan 2022 17:49:22: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 17:49:22: #2 alternative fragment length(s) may be 1,11,41,73,94,106,120,128,147,165,200,220,244,263,314,341,402,430,461,487,516,565 bps INFO @ Sat, 15 Jan 2022 17:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20_model.r INFO @ Sat, 15 Jan 2022 17:49:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:49:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4107466/ERX4107466.20_summits.bed INFO @ Sat, 15 Jan 2022 17:49:26: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (36 records, 4 fields): 53 millis CompletedMACS2peakCalling