Job ID = 14520527 SRX = SRX11781176 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:18:23 prefetch.2.10.7: 1) Downloading 'SRR15481119'... 2022-01-15T10:18:23 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:18:38 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:18:38 prefetch.2.10.7: 'SRR15481119' is valid 2022-01-15T10:18:38 prefetch.2.10.7: 1) 'SRR15481119' was downloaded successfully 2022-01-15T10:18:38 prefetch.2.10.7: 'SRR15481119' has 0 unresolved dependencies Read 7350061 spots for SRR15481119/SRR15481119.sra Written 7350061 spots for SRR15481119/SRR15481119.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: 00:06:20 7350061 reads; of these: 7350061 (100.00%) were paired; of these: 4887318 (66.49%) aligned concordantly 0 times 1443766 (19.64%) aligned concordantly exactly 1 time 1018977 (13.86%) aligned concordantly >1 times ---- 4887318 pairs aligned concordantly 0 times; of these: 34428 (0.70%) aligned discordantly 1 time ---- 4852890 pairs aligned 0 times concordantly or discordantly; of these: 9705780 mates make up the pairs; of these: 6063761 (62.48%) aligned 0 times 2189871 (22.56%) aligned exactly 1 time 1452148 (14.96%) aligned >1 times 58.75% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 216841 / 2496351 = 0.0869 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 19:28:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.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 19:28:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:28:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:28:45: 1000000 INFO @ Sat, 15 Jan 2022 19:28:50: 2000000 INFO @ Sat, 15 Jan 2022 19:28:54: 3000000 INFO @ Sat, 15 Jan 2022 19:28:58: 4000000 INFO @ Sat, 15 Jan 2022 19:29:03: 5000000 INFO @ Sat, 15 Jan 2022 19:29:07: 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 19:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.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 19:29:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:29:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:29:12: 7000000 INFO @ Sat, 15 Jan 2022 19:29:15: 1000000 INFO @ Sat, 15 Jan 2022 19:29:16: 8000000 INFO @ Sat, 15 Jan 2022 19:29:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:17: #1 total tags in treatment: 2247946 INFO @ Sat, 15 Jan 2022 19:29:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:17: #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 19:29:17: #1 tags after filtering in treatment: 1427200 INFO @ Sat, 15 Jan 2022 19:29:17: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 19:29:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:18: #2 number of paired peaks: 199 WARNING @ Sat, 15 Jan 2022 19:29:18: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:18: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:18: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:18: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:18: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:18: #2 predicted fragment length is 286 bps INFO @ Sat, 15 Jan 2022 19:29:18: #2 alternative fragment length(s) may be 1,286,310 bps INFO @ Sat, 15 Jan 2022 19:29:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05_model.r INFO @ Sat, 15 Jan 2022 19:29:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:29:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:29:20: 2000000 INFO @ Sat, 15 Jan 2022 19:29:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:29:23: 3000000 INFO @ Sat, 15 Jan 2022 19:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.05_summits.bed INFO @ Sat, 15 Jan 2022 19:29:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:29:28: 4000000 INFO @ Sat, 15 Jan 2022 19:29:32: 5000000 INFO @ Sat, 15 Jan 2022 19:29:37: 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 19:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.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 19:29:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:29:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:29:41: 7000000 INFO @ Sat, 15 Jan 2022 19:29:46: 1000000 INFO @ Sat, 15 Jan 2022 19:29:46: 8000000 INFO @ Sat, 15 Jan 2022 19:29:47: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:47: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:47: #1 total tags in treatment: 2247946 INFO @ Sat, 15 Jan 2022 19:29:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:47: #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 19:29:47: #1 tags after filtering in treatment: 1427200 INFO @ Sat, 15 Jan 2022 19:29:47: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 19:29:47: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:47: #2 number of paired peaks: 199 WARNING @ Sat, 15 Jan 2022 19:29:47: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:47: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:47: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:47: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:47: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:47: #2 predicted fragment length is 286 bps INFO @ Sat, 15 Jan 2022 19:29:47: #2 alternative fragment length(s) may be 1,286,310 bps INFO @ Sat, 15 Jan 2022 19:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10_model.r INFO @ Sat, 15 Jan 2022 19:29:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:29:50: 2000000 INFO @ Sat, 15 Jan 2022 19:29:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:29:54: 3000000 INFO @ Sat, 15 Jan 2022 19:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.10_summits.bed INFO @ Sat, 15 Jan 2022 19:29:54: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:29:58: 4000000 INFO @ Sat, 15 Jan 2022 19:30:03: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:30:07: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:30:12: 7000000 INFO @ Sat, 15 Jan 2022 19:30:16: 8000000 INFO @ Sat, 15 Jan 2022 19:30:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:30:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:30:17: #1 total tags in treatment: 2247946 INFO @ Sat, 15 Jan 2022 19:30:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:30:17: #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 19:30:17: #1 tags after filtering in treatment: 1427200 INFO @ Sat, 15 Jan 2022 19:30:17: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 15 Jan 2022 19:30:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:30:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:30:17: #2 number of paired peaks: 199 WARNING @ Sat, 15 Jan 2022 19:30:17: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Sat, 15 Jan 2022 19:30:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:30:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:30:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:30:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:30:17: #2 predicted fragment length is 286 bps INFO @ Sat, 15 Jan 2022 19:30:17: #2 alternative fragment length(s) may be 1,286,310 bps INFO @ Sat, 15 Jan 2022 19:30:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20_model.r INFO @ Sat, 15 Jan 2022 19:30:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:30:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:30:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:30:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:30:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781176/SRX11781176.20_summits.bed INFO @ Sat, 15 Jan 2022 19:30:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 1 millis CompletedMACS2peakCalling