Job ID = 14520435 SRX = SRX11781140 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:05:36 prefetch.2.10.7: 1) Downloading 'SRR15481083'... 2022-01-15T10:05:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:05:57 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:05:58 prefetch.2.10.7: 'SRR15481083' is valid 2022-01-15T10:05:58 prefetch.2.10.7: 1) 'SRR15481083' was downloaded successfully 2022-01-15T10:05:58 prefetch.2.10.7: 'SRR15481083' has 0 unresolved dependencies Read 8368457 spots for SRR15481083/SRR15481083.sra Written 8368457 spots for SRR15481083/SRR15481083.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: 00:07:48 8368457 reads; of these: 8368457 (100.00%) were paired; of these: 5346971 (63.89%) aligned concordantly 0 times 2108126 (25.19%) aligned concordantly exactly 1 time 913360 (10.91%) aligned concordantly >1 times ---- 5346971 pairs aligned concordantly 0 times; of these: 38587 (0.72%) aligned discordantly 1 time ---- 5308384 pairs aligned 0 times concordantly or discordantly; of these: 10616768 mates make up the pairs; of these: 6054461 (57.03%) aligned 0 times 3211615 (30.25%) aligned exactly 1 time 1350692 (12.72%) aligned >1 times 63.83% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 234119 / 3058497 = 0.0765 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 19:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.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 19:18:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:18:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:18:05: 1000000 INFO @ Sat, 15 Jan 2022 19:18:10: 2000000 INFO @ Sat, 15 Jan 2022 19:18:15: 3000000 INFO @ Sat, 15 Jan 2022 19:18:20: 4000000 INFO @ Sat, 15 Jan 2022 19:18:26: 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 19:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.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 19:18:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:18:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:18:32: 6000000 INFO @ Sat, 15 Jan 2022 19:18:36: 1000000 INFO @ Sat, 15 Jan 2022 19:18:38: 7000000 INFO @ Sat, 15 Jan 2022 19:18:42: 2000000 INFO @ Sat, 15 Jan 2022 19:18:43: 8000000 INFO @ Sat, 15 Jan 2022 19:18:48: 3000000 INFO @ Sat, 15 Jan 2022 19:18:48: 9000000 INFO @ Sat, 15 Jan 2022 19:18:53: 4000000 INFO @ Sat, 15 Jan 2022 19:18:54: 10000000 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: 2788837 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: 1995876 INFO @ Sat, 15 Jan 2022 19:18:55: #1 Redundant rate of treatment: 0.28 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: 119 WARNING @ Sat, 15 Jan 2022 19:18:55: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 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 188 bps INFO @ Sat, 15 Jan 2022 19:18:55: #2 alternative fragment length(s) may be 2,148,188,193,231 bps INFO @ Sat, 15 Jan 2022 19:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05_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... 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 19:18:59: 5000000 INFO @ Sat, 15 Jan 2022 19:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.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 19:19:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:19:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:19:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:19:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:19:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:19:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.05_summits.bed INFO @ Sat, 15 Jan 2022 19:19:05: Done! INFO @ Sat, 15 Jan 2022 19:19:05: 6000000 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (603 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:19:06: 1000000 INFO @ Sat, 15 Jan 2022 19:19:10: 7000000 INFO @ Sat, 15 Jan 2022 19:19:11: 2000000 INFO @ Sat, 15 Jan 2022 19:19:16: 8000000 INFO @ Sat, 15 Jan 2022 19:19:17: 3000000 INFO @ Sat, 15 Jan 2022 19:19:22: 9000000 INFO @ Sat, 15 Jan 2022 19:19:23: 4000000 INFO @ Sat, 15 Jan 2022 19:19:27: 10000000 INFO @ Sat, 15 Jan 2022 19:19:28: 5000000 INFO @ Sat, 15 Jan 2022 19:19:28: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:19:28: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:19:28: #1 total tags in treatment: 2788837 INFO @ Sat, 15 Jan 2022 19:19:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:19:28: #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 19:19:28: #1 tags after filtering in treatment: 1995876 INFO @ Sat, 15 Jan 2022 19:19:28: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:19:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:19:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:19:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:19:29: #2 number of paired peaks: 119 WARNING @ Sat, 15 Jan 2022 19:19:29: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 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 188 bps INFO @ Sat, 15 Jan 2022 19:19:29: #2 alternative fragment length(s) may be 2,148,188,193,231 bps INFO @ Sat, 15 Jan 2022 19:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10_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 19:19:33: 6000000 INFO @ Sat, 15 Jan 2022 19:19:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.10_summits.bed INFO @ Sat, 15 Jan 2022 19:19:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:19:39: 7000000 INFO @ Sat, 15 Jan 2022 19:19:44: 8000000 INFO @ Sat, 15 Jan 2022 19:19:50: 9000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:19:55: 10000000 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: 2788837 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: 1995876 INFO @ Sat, 15 Jan 2022 19:19:56: #1 Redundant rate of treatment: 0.28 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 19:19:57: #2 number of paired peaks: 119 WARNING @ Sat, 15 Jan 2022 19:19:57: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 15 Jan 2022 19:19:57: start model_add_line... INFO @ Sat, 15 Jan 2022 19:19:57: start X-correlation... INFO @ Sat, 15 Jan 2022 19:19:57: end of X-cor INFO @ Sat, 15 Jan 2022 19:19:57: #2 finished! INFO @ Sat, 15 Jan 2022 19:19:57: #2 predicted fragment length is 188 bps INFO @ Sat, 15 Jan 2022 19:19:57: #2 alternative fragment length(s) may be 2,148,188,193,231 bps INFO @ Sat, 15 Jan 2022 19:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20_model.r INFO @ Sat, 15 Jan 2022 19:19:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:20:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781140/SRX11781140.20_summits.bed INFO @ Sat, 15 Jan 2022 19:20:06: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (120 records, 4 fields): 11 millis CompletedMACS2peakCalling