Job ID = 14520465 SRX = SRX11781155 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:09:51 prefetch.2.10.7: 1) Downloading 'SRR15481098'... 2022-01-15T10:09:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:10:06 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:10:07 prefetch.2.10.7: 'SRR15481098' is valid 2022-01-15T10:10:07 prefetch.2.10.7: 1) 'SRR15481098' was downloaded successfully 2022-01-15T10:10:07 prefetch.2.10.7: 'SRR15481098' has 0 unresolved dependencies Read 7364209 spots for SRR15481098/SRR15481098.sra Written 7364209 spots for SRR15481098/SRR15481098.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: 00:04:42 7364209 reads; of these: 7364209 (100.00%) were paired; of these: 4682775 (63.59%) aligned concordantly 0 times 2364668 (32.11%) aligned concordantly exactly 1 time 316766 (4.30%) aligned concordantly >1 times ---- 4682775 pairs aligned concordantly 0 times; of these: 70499 (1.51%) aligned discordantly 1 time ---- 4612276 pairs aligned 0 times concordantly or discordantly; of these: 9224552 mates make up the pairs; of these: 5088254 (55.16%) aligned 0 times 3597198 (39.00%) aligned exactly 1 time 539100 (5.84%) aligned >1 times 65.45% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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] 420381 / 2750859 = 0.1528 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 19:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.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 19:18:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:18:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:18:23: 1000000 INFO @ Sat, 15 Jan 2022 19:18:27: 2000000 INFO @ Sat, 15 Jan 2022 19:18:31: 3000000 INFO @ Sat, 15 Jan 2022 19:18:35: 4000000 INFO @ Sat, 15 Jan 2022 19:18:39: 5000000 INFO @ Sat, 15 Jan 2022 19:18:43: 6000000 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 19:18:47: 7000000 INFO @ Sat, 15 Jan 2022 19:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.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 19:18:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:18:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:18:51: 8000000 INFO @ Sat, 15 Jan 2022 19:18:53: 1000000 INFO @ Sat, 15 Jan 2022 19:18:55: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:18:55: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:18:55: #1 total tags in treatment: 2267119 INFO @ Sat, 15 Jan 2022 19:18:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:18:55: #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 19:18:55: #1 tags after filtering in treatment: 1608763 INFO @ Sat, 15 Jan 2022 19:18:55: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:18:55: #1 finished! INFO @ Sat, 15 Jan 2022 19:18:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:18:55: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:18:55: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:18:55: start model_add_line... INFO @ Sat, 15 Jan 2022 19:18:55: start X-correlation... INFO @ Sat, 15 Jan 2022 19:18:55: end of X-cor INFO @ Sat, 15 Jan 2022 19:18:55: #2 finished! INFO @ Sat, 15 Jan 2022 19:18:55: #2 predicted fragment length is 241 bps INFO @ Sat, 15 Jan 2022 19:18:55: #2 alternative fragment length(s) may be 0,209,241,266,327,503,598 bps INFO @ Sat, 15 Jan 2022 19:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05_model.r INFO @ Sat, 15 Jan 2022 19:18:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:18:58: 2000000 INFO @ Sat, 15 Jan 2022 19:19:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.05_summits.bed INFO @ Sat, 15 Jan 2022 19:19:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:19:02: 3000000 INFO @ Sat, 15 Jan 2022 19:19:06: 4000000 INFO @ Sat, 15 Jan 2022 19:19:11: 5000000 INFO @ Sat, 15 Jan 2022 19:19:15: 6000000 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 19:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.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 19:19:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:20: 7000000 INFO @ Sat, 15 Jan 2022 19:19:23: 1000000 INFO @ Sat, 15 Jan 2022 19:19:25: 8000000 INFO @ Sat, 15 Jan 2022 19:19:27: 2000000 INFO @ Sat, 15 Jan 2022 19:19:29: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:19:29: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:19:29: #1 total tags in treatment: 2267119 INFO @ Sat, 15 Jan 2022 19:19:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:19:29: #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 19:19:29: #1 tags after filtering in treatment: 1608763 INFO @ Sat, 15 Jan 2022 19:19:29: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:19:29: #1 finished! INFO @ Sat, 15 Jan 2022 19:19:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:19:29: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:19:29: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:19:29: start model_add_line... INFO @ Sat, 15 Jan 2022 19:19:29: start X-correlation... INFO @ Sat, 15 Jan 2022 19:19:29: end of X-cor INFO @ Sat, 15 Jan 2022 19:19:29: #2 finished! INFO @ Sat, 15 Jan 2022 19:19:29: #2 predicted fragment length is 241 bps INFO @ Sat, 15 Jan 2022 19:19:29: #2 alternative fragment length(s) may be 0,209,241,266,327,503,598 bps INFO @ Sat, 15 Jan 2022 19:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10_model.r INFO @ Sat, 15 Jan 2022 19:19:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:19:31: 3000000 INFO @ Sat, 15 Jan 2022 19:19:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.10_summits.bed INFO @ Sat, 15 Jan 2022 19:19:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:19:35: 4000000 INFO @ Sat, 15 Jan 2022 19:19:40: 5000000 INFO @ Sat, 15 Jan 2022 19:19:44: 6000000 INFO @ Sat, 15 Jan 2022 19:19:48: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:19:52: 8000000 INFO @ Sat, 15 Jan 2022 19:19:56: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:19:56: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:19:56: #1 total tags in treatment: 2267119 INFO @ Sat, 15 Jan 2022 19:19:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:19:56: #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 19:19:56: #1 tags after filtering in treatment: 1608763 INFO @ Sat, 15 Jan 2022 19:19:56: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 15 Jan 2022 19:19:56: #1 finished! INFO @ Sat, 15 Jan 2022 19:19:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:19:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:19:56: #2 number of paired peaks: 174 WARNING @ Sat, 15 Jan 2022 19:19:56: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sat, 15 Jan 2022 19:19:56: start model_add_line... INFO @ Sat, 15 Jan 2022 19:19:56: start X-correlation... INFO @ Sat, 15 Jan 2022 19:19:56: end of X-cor INFO @ Sat, 15 Jan 2022 19:19:56: #2 finished! INFO @ Sat, 15 Jan 2022 19:19:56: #2 predicted fragment length is 241 bps INFO @ Sat, 15 Jan 2022 19:19:56: #2 alternative fragment length(s) may be 0,209,241,266,327,503,598 bps INFO @ Sat, 15 Jan 2022 19:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20_model.r INFO @ Sat, 15 Jan 2022 19:19:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781155/SRX11781155.20_summits.bed INFO @ Sat, 15 Jan 2022 19:20:02: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。