Job ID = 14521011 SRX = SRX9397556 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 449426 spots for SRR12933795/SRR12933795.sra Written 449426 spots for SRR12933795/SRR12933795.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: 00:00:37 449426 reads; of these: 449426 (100.00%) were paired; of these: 104641 (23.28%) aligned concordantly 0 times 302774 (67.37%) aligned concordantly exactly 1 time 42011 (9.35%) aligned concordantly >1 times ---- 104641 pairs aligned concordantly 0 times; of these: 37316 (35.66%) aligned discordantly 1 time ---- 67325 pairs aligned 0 times concordantly or discordantly; of these: 134650 mates make up the pairs; of these: 120306 (89.35%) aligned 0 times 4864 (3.61%) aligned exactly 1 time 9480 (7.04%) aligned >1 times 86.62% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 10142 / 381902 = 0.0266 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 20:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.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 20:17:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:29: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:17:29: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:17:29: #1 total tags in treatment: 335393 INFO @ Sat, 15 Jan 2022 20:17:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:29: #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 20:17:29: #1 tags after filtering in treatment: 310154 INFO @ Sat, 15 Jan 2022 20:17:29: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:17:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:29: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 20:17:29: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:29: #2 predicted fragment length is 109 bps INFO @ Sat, 15 Jan 2022 20:17:29: #2 alternative fragment length(s) may be 9,35,85,109,131,153,190,214,242,257,298,320,426,475,528,591 bps INFO @ Sat, 15 Jan 2022 20:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05_model.r INFO @ Sat, 15 Jan 2022 20:17:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:17:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.05_summits.bed INFO @ Sat, 15 Jan 2022 20:17:30: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (9 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 20:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.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 20:17:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:17:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:17:59: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:17:59: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:17:59: #1 total tags in treatment: 335393 INFO @ Sat, 15 Jan 2022 20:17:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:17:59: #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 20:17:59: #1 tags after filtering in treatment: 310154 INFO @ Sat, 15 Jan 2022 20:17:59: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:17:59: #1 finished! INFO @ Sat, 15 Jan 2022 20:17:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:17:59: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 20:17:59: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 20:17:59: start model_add_line... INFO @ Sat, 15 Jan 2022 20:17:59: start X-correlation... INFO @ Sat, 15 Jan 2022 20:17:59: end of X-cor INFO @ Sat, 15 Jan 2022 20:17:59: #2 finished! INFO @ Sat, 15 Jan 2022 20:17:59: #2 predicted fragment length is 109 bps INFO @ Sat, 15 Jan 2022 20:17:59: #2 alternative fragment length(s) may be 9,35,85,109,131,153,190,214,242,257,298,320,426,475,528,591 bps INFO @ Sat, 15 Jan 2022 20:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10_model.r INFO @ Sat, 15 Jan 2022 20:17:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:17:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.10_summits.bed INFO @ Sat, 15 Jan 2022 20:18:00: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 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 20:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.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 20:18:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:18:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:18:28: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:18:28: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:18:28: #1 total tags in treatment: 335393 INFO @ Sat, 15 Jan 2022 20:18:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:18:28: #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 20:18:28: #1 tags after filtering in treatment: 310154 INFO @ Sat, 15 Jan 2022 20:18:28: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:18:28: #1 finished! INFO @ Sat, 15 Jan 2022 20:18:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:18:28: #2 number of paired peaks: 147 WARNING @ Sat, 15 Jan 2022 20:18:28: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 15 Jan 2022 20:18:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:18:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:18:28: end of X-cor INFO @ Sat, 15 Jan 2022 20:18:28: #2 finished! INFO @ Sat, 15 Jan 2022 20:18:28: #2 predicted fragment length is 109 bps INFO @ Sat, 15 Jan 2022 20:18:28: #2 alternative fragment length(s) may be 9,35,85,109,131,153,190,214,242,257,298,320,426,475,528,591 bps INFO @ Sat, 15 Jan 2022 20:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20_model.r INFO @ Sat, 15 Jan 2022 20:18:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:18:29: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9397556/SRX9397556.20_summits.bed INFO @ Sat, 15 Jan 2022 20:18:29: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。