Job ID = 14520437 SRX = SRX11781142 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:05:51 prefetch.2.10.7: 1) Downloading 'SRR15481085'... 2022-01-15T10:05:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:06:15 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:06:16 prefetch.2.10.7: 'SRR15481085' is valid 2022-01-15T10:06:16 prefetch.2.10.7: 1) 'SRR15481085' was downloaded successfully 2022-01-15T10:06:16 prefetch.2.10.7: 'SRR15481085' has 0 unresolved dependencies Read 7149222 spots for SRR15481085/SRR15481085.sra Written 7149222 spots for SRR15481085/SRR15481085.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: 00:03:54 7149222 reads; of these: 7149222 (100.00%) were paired; of these: 4590709 (64.21%) aligned concordantly 0 times 1895213 (26.51%) aligned concordantly exactly 1 time 663300 (9.28%) aligned concordantly >1 times ---- 4590709 pairs aligned concordantly 0 times; of these: 36594 (0.80%) aligned discordantly 1 time ---- 4554115 pairs aligned 0 times concordantly or discordantly; of these: 9108230 mates make up the pairs; of these: 5053979 (55.49%) aligned 0 times 3011137 (33.06%) aligned exactly 1 time 1043114 (11.45%) aligned >1 times 64.65% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 198829 / 2594056 = 0.0766 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 19:13:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.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 19:13:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:13: 1000000 INFO @ Sat, 15 Jan 2022 19:13:19: 2000000 INFO @ Sat, 15 Jan 2022 19:13:24: 3000000 INFO @ Sat, 15 Jan 2022 19:13:29: 4000000 INFO @ Sat, 15 Jan 2022 19:13:35: 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 19:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.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 19:13:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:41: 6000000 INFO @ Sat, 15 Jan 2022 19:13:44: 1000000 INFO @ Sat, 15 Jan 2022 19:13:47: 7000000 INFO @ Sat, 15 Jan 2022 19:13:50: 2000000 INFO @ Sat, 15 Jan 2022 19:13:53: 8000000 INFO @ Sat, 15 Jan 2022 19:13:56: 3000000 INFO @ Sat, 15 Jan 2022 19:13:58: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:58: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:58: #1 total tags in treatment: 2360945 INFO @ Sat, 15 Jan 2022 19:13:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:58: #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 19:13:58: #1 tags after filtering in treatment: 1761455 INFO @ Sat, 15 Jan 2022 19:13:58: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:13:58: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:58: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:13:58: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:58: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:58: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:58: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:58: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:58: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Jan 2022 19:13:58: #2 alternative fragment length(s) may be 2,221,253,256 bps INFO @ Sat, 15 Jan 2022 19:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05_model.r INFO @ Sat, 15 Jan 2022 19:13:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:02: 4000000 INFO @ Sat, 15 Jan 2022 19:14:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.05_summits.bed INFO @ Sat, 15 Jan 2022 19:14:04: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 19:14:07: 5000000 INFO @ Sat, 15 Jan 2022 19:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.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 19:14:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:13: 6000000 INFO @ Sat, 15 Jan 2022 19:14:14: 1000000 INFO @ Sat, 15 Jan 2022 19:14:19: 7000000 INFO @ Sat, 15 Jan 2022 19:14:20: 2000000 INFO @ Sat, 15 Jan 2022 19:14:25: 8000000 INFO @ Sat, 15 Jan 2022 19:14:26: 3000000 INFO @ Sat, 15 Jan 2022 19:14:30: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:30: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:30: #1 total tags in treatment: 2360945 INFO @ Sat, 15 Jan 2022 19:14:30: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:30: #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 19:14:30: #1 tags after filtering in treatment: 1761455 INFO @ Sat, 15 Jan 2022 19:14:30: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:14:30: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:31: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:14:31: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:31: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:31: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:31: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:31: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:31: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Jan 2022 19:14:31: #2 alternative fragment length(s) may be 2,221,253,256 bps INFO @ Sat, 15 Jan 2022 19:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10_model.r INFO @ Sat, 15 Jan 2022 19:14:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:14:36: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.10_summits.bed INFO @ Sat, 15 Jan 2022 19:14:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (137 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:14:37: 5000000 INFO @ Sat, 15 Jan 2022 19:14:43: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:14:48: 7000000 INFO @ Sat, 15 Jan 2022 19:14:54: 8000000 INFO @ Sat, 15 Jan 2022 19:14:59: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:59: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:59: #1 total tags in treatment: 2360945 INFO @ Sat, 15 Jan 2022 19:14:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:59: #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 19:14:59: #1 tags after filtering in treatment: 1761455 INFO @ Sat, 15 Jan 2022 19:14:59: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:14:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:59: #2 number of paired peaks: 146 WARNING @ Sat, 15 Jan 2022 19:14:59: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:59: #2 predicted fragment length is 221 bps INFO @ Sat, 15 Jan 2022 19:14:59: #2 alternative fragment length(s) may be 2,221,253,256 bps INFO @ Sat, 15 Jan 2022 19:14:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20_model.r INFO @ Sat, 15 Jan 2022 19:14:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781142/SRX11781142.20_summits.bed INFO @ Sat, 15 Jan 2022 19:15:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 1 millis CompletedMACS2peakCalling