Job ID = 14521291 SRX = SRX10468533 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3116352 spots for SRR14094844/SRR14094844.sra Written 3116352 spots for SRR14094844/SRR14094844.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: 00:01:42 3116352 reads; of these: 3116352 (100.00%) were paired; of these: 1064379 (34.15%) aligned concordantly 0 times 1733271 (55.62%) aligned concordantly exactly 1 time 318702 (10.23%) aligned concordantly >1 times ---- 1064379 pairs aligned concordantly 0 times; of these: 13428 (1.26%) aligned discordantly 1 time ---- 1050951 pairs aligned 0 times concordantly or discordantly; of these: 2101902 mates make up the pairs; of these: 2038913 (97.00%) aligned 0 times 46067 (2.19%) aligned exactly 1 time 16922 (0.81%) aligned >1 times 67.29% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 63393 / 2053686 = 0.0309 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 20:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.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 20:49:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:52: 1000000 INFO @ Sat, 15 Jan 2022 20:49:57: 2000000 INFO @ Sat, 15 Jan 2022 20:50:02: 3000000 INFO @ Sat, 15 Jan 2022 20:50:07: 4000000 INFO @ Sat, 15 Jan 2022 20:50:07: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:50:07: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:50:07: #1 total tags in treatment: 1988617 INFO @ Sat, 15 Jan 2022 20:50:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:07: #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 20:50:07: #1 tags after filtering in treatment: 1508652 INFO @ Sat, 15 Jan 2022 20:50:07: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:50:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:07: #2 number of paired peaks: 593 WARNING @ Sat, 15 Jan 2022 20:50:07: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:07: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:07: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:07: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:07: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:07: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:50:07: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 15 Jan 2022 20:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05_model.r INFO @ Sat, 15 Jan 2022 20:50:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.05_summits.bed INFO @ Sat, 15 Jan 2022 20:50:13: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (839 records, 4 fields): 20 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 20:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.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 20:50:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:23: 1000000 INFO @ Sat, 15 Jan 2022 20:50:27: 2000000 INFO @ Sat, 15 Jan 2022 20:50:32: 3000000 INFO @ Sat, 15 Jan 2022 20:50:37: 4000000 INFO @ Sat, 15 Jan 2022 20:50:37: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:50:37: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:50:37: #1 total tags in treatment: 1988617 INFO @ Sat, 15 Jan 2022 20:50:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:37: #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 20:50:37: #1 tags after filtering in treatment: 1508652 INFO @ Sat, 15 Jan 2022 20:50:37: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:50:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:37: #2 number of paired peaks: 593 WARNING @ Sat, 15 Jan 2022 20:50:37: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:38: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:38: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:38: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:38: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:50:38: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 15 Jan 2022 20:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10_model.r INFO @ Sat, 15 Jan 2022 20:50:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.10_summits.bed INFO @ Sat, 15 Jan 2022 20:50:43: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 176 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 20:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.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 20:50:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:50:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:50:52: 1000000 INFO @ Sat, 15 Jan 2022 20:50:57: 2000000 INFO @ Sat, 15 Jan 2022 20:51:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:51:07: 4000000 INFO @ Sat, 15 Jan 2022 20:51:07: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:51:07: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:51:07: #1 total tags in treatment: 1988617 INFO @ Sat, 15 Jan 2022 20:51:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:51:07: #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 20:51:07: #1 tags after filtering in treatment: 1508652 INFO @ Sat, 15 Jan 2022 20:51:07: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 15 Jan 2022 20:51:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:51:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:51:07: #2 number of paired peaks: 593 WARNING @ Sat, 15 Jan 2022 20:51:07: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 15 Jan 2022 20:51:07: start model_add_line... INFO @ Sat, 15 Jan 2022 20:51:07: start X-correlation... INFO @ Sat, 15 Jan 2022 20:51:07: end of X-cor INFO @ Sat, 15 Jan 2022 20:51:07: #2 finished! INFO @ Sat, 15 Jan 2022 20:51:07: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 20:51:07: #2 alternative fragment length(s) may be 4,74 bps INFO @ Sat, 15 Jan 2022 20:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20_model.r INFO @ Sat, 15 Jan 2022 20:51:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:51:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:51:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468533/SRX10468533.20_summits.bed INFO @ Sat, 15 Jan 2022 20:51:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (259 records, 4 fields): 2 millis CompletedMACS2peakCalling