Job ID = 14520523 SRX = SRX11781172 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:17:53 prefetch.2.10.7: 1) Downloading 'SRR15481115'... 2022-01-15T10:17:53 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:18:07 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:18:07 prefetch.2.10.7: 'SRR15481115' is valid 2022-01-15T10:18:07 prefetch.2.10.7: 1) 'SRR15481115' was downloaded successfully 2022-01-15T10:18:07 prefetch.2.10.7: 'SRR15481115' has 0 unresolved dependencies Read 6591266 spots for SRR15481115/SRR15481115.sra Written 6591266 spots for SRR15481115/SRR15481115.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: 00:03:41 6591266 reads; of these: 6591266 (100.00%) were paired; of these: 4171805 (63.29%) aligned concordantly 0 times 1927274 (29.24%) aligned concordantly exactly 1 time 492187 (7.47%) aligned concordantly >1 times ---- 4171805 pairs aligned concordantly 0 times; of these: 27495 (0.66%) aligned discordantly 1 time ---- 4144310 pairs aligned 0 times concordantly or discordantly; of these: 8288620 mates make up the pairs; of these: 4815359 (58.10%) aligned 0 times 2761582 (33.32%) aligned exactly 1 time 711679 (8.59%) aligned >1 times 63.47% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 105331 / 2446163 = 0.0431 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 19:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.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 19:25:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:16: 1000000 INFO @ Sat, 15 Jan 2022 19:25:21: 2000000 INFO @ Sat, 15 Jan 2022 19:25:26: 3000000 INFO @ Sat, 15 Jan 2022 19:25:31: 4000000 INFO @ Sat, 15 Jan 2022 19:25:37: 5000000 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 19:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.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 19:25:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:42: 6000000 INFO @ Sat, 15 Jan 2022 19:25:46: 1000000 INFO @ Sat, 15 Jan 2022 19:25:48: 7000000 INFO @ Sat, 15 Jan 2022 19:25:52: 2000000 INFO @ Sat, 15 Jan 2022 19:25:53: 8000000 INFO @ Sat, 15 Jan 2022 19:25:54: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:25:54: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:25:54: #1 total tags in treatment: 2314747 INFO @ Sat, 15 Jan 2022 19:25:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:54: #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 19:25:54: #1 tags after filtering in treatment: 1836552 INFO @ Sat, 15 Jan 2022 19:25:54: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:25:54: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:54: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:25:54: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:54: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:54: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:54: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:54: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:54: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 19:25:54: #2 alternative fragment length(s) may be 1,209,242 bps INFO @ Sat, 15 Jan 2022 19:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05_model.r INFO @ Sat, 15 Jan 2022 19:25:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:57: 3000000 INFO @ Sat, 15 Jan 2022 19:26:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.05_summits.bed INFO @ Sat, 15 Jan 2022 19:26:02: Done! INFO @ Sat, 15 Jan 2022 19:26:02: 4000000 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (181 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:07: 5000000 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 19:26:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.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 19:26:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:12: 6000000 INFO @ Sat, 15 Jan 2022 19:26:16: 1000000 INFO @ Sat, 15 Jan 2022 19:26:17: 7000000 INFO @ Sat, 15 Jan 2022 19:26:22: 8000000 INFO @ Sat, 15 Jan 2022 19:26:22: 2000000 INFO @ Sat, 15 Jan 2022 19:26:23: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:23: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:23: #1 total tags in treatment: 2314747 INFO @ Sat, 15 Jan 2022 19:26:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:23: #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 19:26:23: #1 tags after filtering in treatment: 1836552 INFO @ Sat, 15 Jan 2022 19:26:23: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:26:23: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:23: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:26:23: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:23: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:23: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:23: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:23: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:23: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 19:26:23: #2 alternative fragment length(s) may be 1,209,242 bps INFO @ Sat, 15 Jan 2022 19:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10_model.r INFO @ Sat, 15 Jan 2022 19:26:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:28: 3000000 INFO @ Sat, 15 Jan 2022 19:26:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.10_summits.bed INFO @ Sat, 15 Jan 2022 19:26:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:33: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:26:39: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:26:44: 6000000 INFO @ Sat, 15 Jan 2022 19:26:50: 7000000 INFO @ Sat, 15 Jan 2022 19:26:56: 8000000 INFO @ Sat, 15 Jan 2022 19:26:56: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:56: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:56: #1 total tags in treatment: 2314747 INFO @ Sat, 15 Jan 2022 19:26:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:56: #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 19:26:56: #1 tags after filtering in treatment: 1836552 INFO @ Sat, 15 Jan 2022 19:26:56: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:26:56: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:56: #2 number of paired peaks: 176 WARNING @ Sat, 15 Jan 2022 19:26:56: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:56: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:56: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:56: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:56: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:56: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 19:26:56: #2 alternative fragment length(s) may be 1,209,242 bps INFO @ Sat, 15 Jan 2022 19:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20_model.r INFO @ Sat, 15 Jan 2022 19:26:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781172/SRX11781172.20_summits.bed INFO @ Sat, 15 Jan 2022 19:27:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling