Job ID = 14520494 SRX = SRX11781167 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:13:39 prefetch.2.10.7: 1) Downloading 'SRR15481110'... 2022-01-15T10:13:39 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:13:53 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:13:56 prefetch.2.10.7: 'SRR15481110' is valid 2022-01-15T10:13:56 prefetch.2.10.7: 1) 'SRR15481110' was downloaded successfully 2022-01-15T10:13:56 prefetch.2.10.7: 'SRR15481110' has 0 unresolved dependencies Read 6711910 spots for SRR15481110/SRR15481110.sra Written 6711910 spots for SRR15481110/SRR15481110.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: 00:00:01 Multiseed full-index search: 00:05:06 6711910 reads; of these: 6711910 (100.00%) were paired; of these: 4165951 (62.07%) aligned concordantly 0 times 2188452 (32.61%) aligned concordantly exactly 1 time 357507 (5.33%) aligned concordantly >1 times ---- 4165951 pairs aligned concordantly 0 times; of these: 34466 (0.83%) aligned discordantly 1 time ---- 4131485 pairs aligned 0 times concordantly or discordantly; of these: 8262970 mates make up the pairs; of these: 4611582 (55.81%) aligned 0 times 3132053 (37.90%) aligned exactly 1 time 519335 (6.29%) aligned >1 times 65.65% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 356768 / 2579672 = 0.1383 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 19:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.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 19:25:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:34: 1000000 INFO @ Sat, 15 Jan 2022 19:25:42: 2000000 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 19:25:54: 3000000 INFO @ Sat, 15 Jan 2022 19:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.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 19:25:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:09: 4000000 INFO @ Sat, 15 Jan 2022 19:26:10: 1000000 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 19:26:21: 5000000 INFO @ Sat, 15 Jan 2022 19:26:22: 2000000 INFO @ Sat, 15 Jan 2022 19:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.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 19:26:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:32: 6000000 INFO @ Sat, 15 Jan 2022 19:26:34: 3000000 INFO @ Sat, 15 Jan 2022 19:26:37: 1000000 INFO @ Sat, 15 Jan 2022 19:26:43: 7000000 INFO @ Sat, 15 Jan 2022 19:26:45: 4000000 INFO @ Sat, 15 Jan 2022 19:26:49: 2000000 INFO @ Sat, 15 Jan 2022 19:26:53: 8000000 INFO @ Sat, 15 Jan 2022 19:26:54: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:54: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:54: #1 total tags in treatment: 2191624 INFO @ Sat, 15 Jan 2022 19:26:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:54: #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 19:26:54: #1 tags after filtering in treatment: 1604210 INFO @ Sat, 15 Jan 2022 19:26:54: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 19:26:54: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:54: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:26:54: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:54: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:54: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:54: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:54: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:54: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 19:26:54: #2 alternative fragment length(s) may be 0,214,240,242,246,251,270,583 bps INFO @ Sat, 15 Jan 2022 19:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05_model.r INFO @ Sat, 15 Jan 2022 19:26:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:55: 5000000 INFO @ Sat, 15 Jan 2022 19:26:59: 3000000 INFO @ Sat, 15 Jan 2022 19:27:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.05_summits.bed INFO @ Sat, 15 Jan 2022 19:27:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (24 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:27:06: 6000000 INFO @ Sat, 15 Jan 2022 19:27:10: 4000000 INFO @ Sat, 15 Jan 2022 19:27:16: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:27:22: 5000000 INFO @ Sat, 15 Jan 2022 19:27:27: 8000000 INFO @ Sat, 15 Jan 2022 19:27:28: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:27:28: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:27:28: #1 total tags in treatment: 2191624 INFO @ Sat, 15 Jan 2022 19:27:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:27:28: #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 19:27:28: #1 tags after filtering in treatment: 1604210 INFO @ Sat, 15 Jan 2022 19:27:28: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 19:27:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:27:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:27:28: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:27:28: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:27:28: start model_add_line... INFO @ Sat, 15 Jan 2022 19:27:28: start X-correlation... INFO @ Sat, 15 Jan 2022 19:27:28: end of X-cor INFO @ Sat, 15 Jan 2022 19:27:28: #2 finished! INFO @ Sat, 15 Jan 2022 19:27:28: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 19:27:28: #2 alternative fragment length(s) may be 0,214,240,242,246,251,270,583 bps INFO @ Sat, 15 Jan 2022 19:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10_model.r INFO @ Sat, 15 Jan 2022 19:27:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:43: 6000000 INFO @ Sat, 15 Jan 2022 19:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.10_summits.bed INFO @ Sat, 15 Jan 2022 19:27:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:27:52: 7000000 INFO @ Sat, 15 Jan 2022 19:28:00: 8000000 INFO @ Sat, 15 Jan 2022 19:28:00: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:28:00: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:28:00: #1 total tags in treatment: 2191624 INFO @ Sat, 15 Jan 2022 19:28:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:28:00: #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 19:28:00: #1 tags after filtering in treatment: 1604210 INFO @ Sat, 15 Jan 2022 19:28:00: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 19:28:00: #1 finished! INFO @ Sat, 15 Jan 2022 19:28:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:28:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:28:00: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:28:00: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:28:00: start model_add_line... INFO @ Sat, 15 Jan 2022 19:28:00: start X-correlation... INFO @ Sat, 15 Jan 2022 19:28:01: end of X-cor INFO @ Sat, 15 Jan 2022 19:28:01: #2 finished! INFO @ Sat, 15 Jan 2022 19:28:01: #2 predicted fragment length is 251 bps INFO @ Sat, 15 Jan 2022 19:28:01: #2 alternative fragment length(s) may be 0,214,240,242,246,251,270,583 bps INFO @ Sat, 15 Jan 2022 19:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20_model.r INFO @ Sat, 15 Jan 2022 19:28:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:28:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781167/SRX11781167.20_summits.bed INFO @ Sat, 15 Jan 2022 19:28:08: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 580 millis CompletedMACS2peakCalling