Job ID = 14521956 SRX = SRX10459799 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1025950 spots for SRR14085598/SRR14085598.sra Written 1025950 spots for SRR14085598/SRR14085598.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: 00:01:03 1025950 reads; of these: 1025950 (100.00%) were paired; of these: 214919 (20.95%) aligned concordantly 0 times 724011 (70.57%) aligned concordantly exactly 1 time 87020 (8.48%) aligned concordantly >1 times ---- 214919 pairs aligned concordantly 0 times; of these: 17063 (7.94%) aligned discordantly 1 time ---- 197856 pairs aligned 0 times concordantly or discordantly; of these: 395712 mates make up the pairs; of these: 335655 (84.82%) aligned 0 times 47176 (11.92%) aligned exactly 1 time 12881 (3.26%) aligned >1 times 83.64% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 11669 / 823926 = 0.0142 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 21:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.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 21:55:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:42: 1000000 INFO @ Sat, 15 Jan 2022 21:55:50: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:55:50: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:55:50: #1 total tags in treatment: 799474 INFO @ Sat, 15 Jan 2022 21:55:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:55:50: #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 21:55:50: #1 tags after filtering in treatment: 728969 INFO @ Sat, 15 Jan 2022 21:55:50: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:55:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:55:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:55:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:55:50: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:55:50: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:55:50: start model_add_line... INFO @ Sat, 15 Jan 2022 21:55:50: start X-correlation... INFO @ Sat, 15 Jan 2022 21:55:50: end of X-cor INFO @ Sat, 15 Jan 2022 21:55:50: #2 finished! INFO @ Sat, 15 Jan 2022 21:55:50: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 21:55:50: #2 alternative fragment length(s) may be 4,263 bps INFO @ Sat, 15 Jan 2022 21:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05_model.r INFO @ Sat, 15 Jan 2022 21:55:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:55:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:55:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:55:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:55:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.05_summits.bed INFO @ Sat, 15 Jan 2022 21:55:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 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 21:56:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.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 21:56:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:12: 1000000 INFO @ Sat, 15 Jan 2022 21:56:19: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:56:19: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:56:19: #1 total tags in treatment: 799474 INFO @ Sat, 15 Jan 2022 21:56:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:19: #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 21:56:19: #1 tags after filtering in treatment: 728969 INFO @ Sat, 15 Jan 2022 21:56:19: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:56:19: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:20: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:56:20: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:20: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:20: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:20: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:20: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:20: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 21:56:20: #2 alternative fragment length(s) may be 4,263 bps INFO @ Sat, 15 Jan 2022 21:56:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10_model.r INFO @ Sat, 15 Jan 2022 21:56:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.10_summits.bed INFO @ Sat, 15 Jan 2022 21:56:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 2 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 21:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.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 21:56:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:31: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:56:40: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:56:46: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:56:46: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:56:46: #1 total tags in treatment: 799474 INFO @ Sat, 15 Jan 2022 21:56:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:46: #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 21:56:46: #1 tags after filtering in treatment: 728969 INFO @ Sat, 15 Jan 2022 21:56:46: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 21:56:46: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:46: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:56:46: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:46: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:46: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:46: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:46: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:46: #2 predicted fragment length is 263 bps INFO @ Sat, 15 Jan 2022 21:56:46: #2 alternative fragment length(s) may be 4,263 bps INFO @ Sat, 15 Jan 2022 21:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20_model.r INFO @ Sat, 15 Jan 2022 21:56:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459799/SRX10459799.20_summits.bed INFO @ Sat, 15 Jan 2022 21:56:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis CompletedMACS2peakCalling