Job ID = 14521341 SRX = SRX8952637 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6154468 spots for SRR12458249/SRR12458249.sra Written 6154468 spots for SRR12458249/SRR12458249.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: 00:02:58 6154468 reads; of these: 6154468 (100.00%) were paired; of these: 4499100 (73.10%) aligned concordantly 0 times 1434985 (23.32%) aligned concordantly exactly 1 time 220383 (3.58%) aligned concordantly >1 times ---- 4499100 pairs aligned concordantly 0 times; of these: 458218 (10.18%) aligned discordantly 1 time ---- 4040882 pairs aligned 0 times concordantly or discordantly; of these: 8081764 mates make up the pairs; of these: 6400527 (79.20%) aligned 0 times 1270355 (15.72%) aligned exactly 1 time 410882 (5.08%) aligned >1 times 48.00% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 631806 / 2081018 = 0.3036 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 20:56:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.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 20:56:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:56:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:56:48: 1000000 INFO @ Sat, 15 Jan 2022 20:56:52: 2000000 INFO @ Sat, 15 Jan 2022 20:56:57: 3000000 INFO @ Sat, 15 Jan 2022 20:57:02: 4000000 INFO @ Sat, 15 Jan 2022 20:57:05: #1 tag size is determined as 46 bps INFO @ Sat, 15 Jan 2022 20:57:05: #1 tag size = 46 INFO @ Sat, 15 Jan 2022 20:57:05: #1 total tags in treatment: 1262745 INFO @ Sat, 15 Jan 2022 20:57:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:05: #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 20:57:05: #1 tags after filtering in treatment: 997962 INFO @ Sat, 15 Jan 2022 20:57:05: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 20:57:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:05: #2 number of paired peaks: 315 WARNING @ Sat, 15 Jan 2022 20:57:05: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:05: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 20:57:05: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 15 Jan 2022 20:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05_model.r INFO @ Sat, 15 Jan 2022 20:57:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.05_summits.bed INFO @ Sat, 15 Jan 2022 20:57:10: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (941 records, 4 fields): 5 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 20:57:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.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 20:57:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:18: 1000000 INFO @ Sat, 15 Jan 2022 20:57:22: 2000000 INFO @ Sat, 15 Jan 2022 20:57:27: 3000000 INFO @ Sat, 15 Jan 2022 20:57:32: 4000000 INFO @ Sat, 15 Jan 2022 20:57:35: #1 tag size is determined as 46 bps INFO @ Sat, 15 Jan 2022 20:57:35: #1 tag size = 46 INFO @ Sat, 15 Jan 2022 20:57:35: #1 total tags in treatment: 1262745 INFO @ Sat, 15 Jan 2022 20:57:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:57:35: #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 20:57:35: #1 tags after filtering in treatment: 997962 INFO @ Sat, 15 Jan 2022 20:57:35: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 20:57:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:57:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:57:35: #2 number of paired peaks: 315 WARNING @ Sat, 15 Jan 2022 20:57:35: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sat, 15 Jan 2022 20:57:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:57:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:57:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:57:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:57:35: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 20:57:35: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 15 Jan 2022 20:57:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10_model.r INFO @ Sat, 15 Jan 2022 20:57:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:57:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:57:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:57:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:57:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:57:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.10_summits.bed INFO @ Sat, 15 Jan 2022 20:57:40: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (704 records, 4 fields): 4 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 20:57:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.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 20:57:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:57:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:57:50: 1000000 INFO @ Sat, 15 Jan 2022 20:57:56: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:58:02: 3000000 INFO @ Sat, 15 Jan 2022 20:58:08: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:58:13: #1 tag size is determined as 46 bps INFO @ Sat, 15 Jan 2022 20:58:13: #1 tag size = 46 INFO @ Sat, 15 Jan 2022 20:58:13: #1 total tags in treatment: 1262745 INFO @ Sat, 15 Jan 2022 20:58:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:13: #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 20:58:13: #1 tags after filtering in treatment: 997962 INFO @ Sat, 15 Jan 2022 20:58:13: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 20:58:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:13: #2 number of paired peaks: 315 WARNING @ Sat, 15 Jan 2022 20:58:13: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:13: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 20:58:13: #2 alternative fragment length(s) may be 269 bps INFO @ Sat, 15 Jan 2022 20:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20_model.r INFO @ Sat, 15 Jan 2022 20:58:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952637/SRX8952637.20_summits.bed INFO @ Sat, 15 Jan 2022 20:58:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 4 millis CompletedMACS2peakCalling