Job ID = 14520526 SRX = SRX11781175 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:18:09 prefetch.2.10.7: 1) Downloading 'SRR15481118'... 2022-01-15T10:18:09 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:18:21 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:18:22 prefetch.2.10.7: 'SRR15481118' is valid 2022-01-15T10:18:22 prefetch.2.10.7: 1) 'SRR15481118' was downloaded successfully 2022-01-15T10:18:22 prefetch.2.10.7: 'SRR15481118' has 0 unresolved dependencies Read 4865080 spots for SRR15481118/SRR15481118.sra Written 4865080 spots for SRR15481118/SRR15481118.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: 00:02:52 4865080 reads; of these: 4865080 (100.00%) were paired; of these: 3062003 (62.94%) aligned concordantly 0 times 1615391 (33.20%) aligned concordantly exactly 1 time 187686 (3.86%) aligned concordantly >1 times ---- 3062003 pairs aligned concordantly 0 times; of these: 41655 (1.36%) aligned discordantly 1 time ---- 3020348 pairs aligned 0 times concordantly or discordantly; of these: 6040696 mates make up the pairs; of these: 3371132 (55.81%) aligned 0 times 2352130 (38.94%) aligned exactly 1 time 317434 (5.25%) aligned >1 times 65.35% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 250363 / 1844048 = 0.1358 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 19:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.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 19:24:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:24:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:24:59: 1000000 INFO @ Sat, 15 Jan 2022 19:25:05: 2000000 INFO @ Sat, 15 Jan 2022 19:25:11: 3000000 INFO @ Sat, 15 Jan 2022 19:25:17: 4000000 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: 5000000 INFO @ Sat, 15 Jan 2022 19:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.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 19:25:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:28: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:25:28: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:25:28: #1 total tags in treatment: 1555543 INFO @ Sat, 15 Jan 2022 19:25:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:25:28: #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 19:25:28: #1 tags after filtering in treatment: 1213816 INFO @ Sat, 15 Jan 2022 19:25:28: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:25:28: #1 finished! INFO @ Sat, 15 Jan 2022 19:25:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:25:28: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 19:25:28: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 19:25:28: start model_add_line... INFO @ Sat, 15 Jan 2022 19:25:28: start X-correlation... INFO @ Sat, 15 Jan 2022 19:25:28: end of X-cor INFO @ Sat, 15 Jan 2022 19:25:28: #2 finished! INFO @ Sat, 15 Jan 2022 19:25:28: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:25:28: #2 alternative fragment length(s) may be 0,254 bps INFO @ Sat, 15 Jan 2022 19:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05_model.r INFO @ Sat, 15 Jan 2022 19:25:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:25:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:25:29: 1000000 INFO @ Sat, 15 Jan 2022 19:25:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.05_summits.bed INFO @ Sat, 15 Jan 2022 19:25:33: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:25:36: 2000000 INFO @ Sat, 15 Jan 2022 19:25:42: 3000000 INFO @ Sat, 15 Jan 2022 19:25:48: 4000000 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 19:25:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.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 19:25:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:55: 5000000 INFO @ Sat, 15 Jan 2022 19:26:00: 1000000 INFO @ Sat, 15 Jan 2022 19:26:00: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:00: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:00: #1 total tags in treatment: 1555543 INFO @ Sat, 15 Jan 2022 19:26:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:00: #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 19:26:00: #1 tags after filtering in treatment: 1213816 INFO @ Sat, 15 Jan 2022 19:26:00: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:26:00: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:00: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 19:26:00: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:00: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:00: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:00: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:00: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:00: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:26:00: #2 alternative fragment length(s) may be 0,254 bps INFO @ Sat, 15 Jan 2022 19:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10_model.r INFO @ Sat, 15 Jan 2022 19:26:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.10_summits.bed INFO @ Sat, 15 Jan 2022 19:26:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:26:06: 2000000 INFO @ Sat, 15 Jan 2022 19:26:13: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:26:19: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:26:26: 5000000 INFO @ Sat, 15 Jan 2022 19:26:31: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:26:31: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:26:31: #1 total tags in treatment: 1555543 INFO @ Sat, 15 Jan 2022 19:26:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:26:31: #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 19:26:31: #1 tags after filtering in treatment: 1213816 INFO @ Sat, 15 Jan 2022 19:26:31: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:26:31: #1 finished! INFO @ Sat, 15 Jan 2022 19:26:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:26:31: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 19:26:31: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 19:26:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:26:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:26:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:26:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:26:31: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:26:31: #2 alternative fragment length(s) may be 0,254 bps INFO @ Sat, 15 Jan 2022 19:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20_model.r INFO @ Sat, 15 Jan 2022 19:26:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781175/SRX11781175.20_summits.bed INFO @ Sat, 15 Jan 2022 19:26:37: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 15 millis CompletedMACS2peakCalling