Job ID = 14520462 SRX = SRX11781152 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:09:37 prefetch.2.10.7: 1) Downloading 'SRR15481095'... 2022-01-15T10:09:37 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:09:51 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:09:51 prefetch.2.10.7: 'SRR15481095' is valid 2022-01-15T10:09:51 prefetch.2.10.7: 1) 'SRR15481095' was downloaded successfully 2022-01-15T10:09:51 prefetch.2.10.7: 'SRR15481095' has 0 unresolved dependencies Read 7013513 spots for SRR15481095/SRR15481095.sra Written 7013513 spots for SRR15481095/SRR15481095.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: 00:06:05 7013513 reads; of these: 7013513 (100.00%) were paired; of these: 4960398 (70.73%) aligned concordantly 0 times 1437533 (20.50%) aligned concordantly exactly 1 time 615582 (8.78%) aligned concordantly >1 times ---- 4960398 pairs aligned concordantly 0 times; of these: 26685 (0.54%) aligned discordantly 1 time ---- 4933713 pairs aligned 0 times concordantly or discordantly; of these: 9867426 mates make up the pairs; of these: 5919371 (59.99%) aligned 0 times 2765899 (28.03%) aligned exactly 1 time 1182156 (11.98%) aligned >1 times 57.80% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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] 142537 / 2078887 = 0.0686 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 19:19:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.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 19:19:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:33: 1000000 INFO @ Sat, 15 Jan 2022 19:19:41: 2000000 INFO @ Sat, 15 Jan 2022 19:19:48: 3000000 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 19:19:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.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 19:19:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:56: 4000000 INFO @ Sat, 15 Jan 2022 19:20:03: 1000000 INFO @ Sat, 15 Jan 2022 19:20:04: 5000000 INFO @ Sat, 15 Jan 2022 19:20:12: 2000000 INFO @ Sat, 15 Jan 2022 19:20:13: 6000000 INFO @ Sat, 15 Jan 2022 19:20:20: 3000000 INFO @ Sat, 15 Jan 2022 19:20:21: 7000000 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 19:20:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.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 19:20:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:20:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:20:28: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:28: 4000000 INFO @ Sat, 15 Jan 2022 19:20:29: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:29: #1 total tags in treatment: 1911502 INFO @ Sat, 15 Jan 2022 19:20:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:29: #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 19:20:29: #1 tags after filtering in treatment: 1409492 INFO @ Sat, 15 Jan 2022 19:20:29: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:20:29: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:29: #2 number of paired peaks: 132 WARNING @ Sat, 15 Jan 2022 19:20:29: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:29: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:29: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:29: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:29: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:29: #2 predicted fragment length is 260 bps INFO @ Sat, 15 Jan 2022 19:20:29: #2 alternative fragment length(s) may be 1,159,219,234,260 bps INFO @ Sat, 15 Jan 2022 19:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05_model.r INFO @ Sat, 15 Jan 2022 19:20:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:33: 1000000 INFO @ Sat, 15 Jan 2022 19:20:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.05_summits.bed INFO @ Sat, 15 Jan 2022 19:20:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:20:37: 5000000 INFO @ Sat, 15 Jan 2022 19:20:41: 2000000 INFO @ Sat, 15 Jan 2022 19:20:45: 6000000 INFO @ Sat, 15 Jan 2022 19:20:49: 3000000 INFO @ Sat, 15 Jan 2022 19:20:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:20:58: 4000000 INFO @ Sat, 15 Jan 2022 19:20:59: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:20:59: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:20:59: #1 total tags in treatment: 1911502 INFO @ Sat, 15 Jan 2022 19:20:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:20:59: #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 19:20:59: #1 tags after filtering in treatment: 1409492 INFO @ Sat, 15 Jan 2022 19:20:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:20:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:20:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:20:59: #2 number of paired peaks: 132 WARNING @ Sat, 15 Jan 2022 19:20:59: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Jan 2022 19:20:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:20:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:20:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:20:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:20:59: #2 predicted fragment length is 260 bps INFO @ Sat, 15 Jan 2022 19:20:59: #2 alternative fragment length(s) may be 1,159,219,234,260 bps INFO @ Sat, 15 Jan 2022 19:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10_model.r INFO @ Sat, 15 Jan 2022 19:20:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:06: 5000000 INFO @ Sat, 15 Jan 2022 19:21:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.10_summits.bed INFO @ Sat, 15 Jan 2022 19:21:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:21:14: 6000000 INFO @ Sat, 15 Jan 2022 19:21:22: 7000000 INFO @ Sat, 15 Jan 2022 19:21:28: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:21:28: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:21:28: #1 total tags in treatment: 1911502 INFO @ Sat, 15 Jan 2022 19:21:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:21:28: #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 19:21:28: #1 tags after filtering in treatment: 1409492 INFO @ Sat, 15 Jan 2022 19:21:28: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:21:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:21:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:21:28: #2 number of paired peaks: 132 WARNING @ Sat, 15 Jan 2022 19:21:28: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Sat, 15 Jan 2022 19:21:28: start model_add_line... INFO @ Sat, 15 Jan 2022 19:21:28: start X-correlation... INFO @ Sat, 15 Jan 2022 19:21:28: end of X-cor INFO @ Sat, 15 Jan 2022 19:21:28: #2 finished! INFO @ Sat, 15 Jan 2022 19:21:28: #2 predicted fragment length is 260 bps INFO @ Sat, 15 Jan 2022 19:21:28: #2 alternative fragment length(s) may be 1,159,219,234,260 bps INFO @ Sat, 15 Jan 2022 19:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20_model.r INFO @ Sat, 15 Jan 2022 19:21:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:21:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781152/SRX11781152.20_summits.bed INFO @ Sat, 15 Jan 2022 19:21:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (60 records, 4 fields): 2 millis CompletedMACS2peakCalling