Job ID = 14520521 SRX = SRX11781170 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:16:56 prefetch.2.10.7: 1) Downloading 'SRR15481113'... 2022-01-15T10:16:56 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:17:12 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:17:12 prefetch.2.10.7: 'SRR15481113' is valid 2022-01-15T10:17:12 prefetch.2.10.7: 1) 'SRR15481113' was downloaded successfully 2022-01-15T10:17:12 prefetch.2.10.7: 'SRR15481113' has 0 unresolved dependencies Read 7282702 spots for SRR15481113/SRR15481113.sra Written 7282702 spots for SRR15481113/SRR15481113.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: 00:07:12 7282702 reads; of these: 7282702 (100.00%) were paired; of these: 5114425 (70.23%) aligned concordantly 0 times 1582080 (21.72%) aligned concordantly exactly 1 time 586197 (8.05%) aligned concordantly >1 times ---- 5114425 pairs aligned concordantly 0 times; of these: 39616 (0.77%) aligned discordantly 1 time ---- 5074809 pairs aligned 0 times concordantly or discordantly; of these: 10149618 mates make up the pairs; of these: 6577810 (64.81%) aligned 0 times 2684193 (26.45%) aligned exactly 1 time 887615 (8.75%) aligned >1 times 54.84% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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] 219415 / 2207011 = 0.0994 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 19:28:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.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 19:28:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:28:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:28:19: 1000000 INFO @ Sat, 15 Jan 2022 19:28:26: 2000000 INFO @ Sat, 15 Jan 2022 19:28:32: 3000000 INFO @ Sat, 15 Jan 2022 19:28:39: 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 19:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.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 19:28:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:28:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:28:45: 5000000 INFO @ Sat, 15 Jan 2022 19:28:49: 1000000 INFO @ Sat, 15 Jan 2022 19:28:52: 6000000 INFO @ Sat, 15 Jan 2022 19:28:56: 2000000 INFO @ Sat, 15 Jan 2022 19:28:59: 7000000 INFO @ Sat, 15 Jan 2022 19:29:02: 3000000 INFO @ Sat, 15 Jan 2022 19:29:03: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:03: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:03: #1 total tags in treatment: 1951478 INFO @ Sat, 15 Jan 2022 19:29:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:03: #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 19:29:03: #1 tags after filtering in treatment: 1396390 INFO @ Sat, 15 Jan 2022 19:29:03: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:29:03: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:03: #2 number of paired peaks: 207 WARNING @ Sat, 15 Jan 2022 19:29:03: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:03: #2 predicted fragment length is 237 bps INFO @ Sat, 15 Jan 2022 19:29:03: #2 alternative fragment length(s) may be 0,187,207,233,237,263 bps INFO @ Sat, 15 Jan 2022 19:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05_model.r INFO @ Sat, 15 Jan 2022 19:29:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:29:09: 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 19:29:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:29:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.05_summits.bed INFO @ Sat, 15 Jan 2022 19:29:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (338 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.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 19:29:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:29:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:29:16: 5000000 INFO @ Sat, 15 Jan 2022 19:29:19: 1000000 INFO @ Sat, 15 Jan 2022 19:29:23: 6000000 INFO @ Sat, 15 Jan 2022 19:29:25: 2000000 INFO @ Sat, 15 Jan 2022 19:29:30: 7000000 INFO @ Sat, 15 Jan 2022 19:29:31: 3000000 INFO @ Sat, 15 Jan 2022 19:29:34: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:34: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:34: #1 total tags in treatment: 1951478 INFO @ Sat, 15 Jan 2022 19:29:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:34: #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 19:29:34: #1 tags after filtering in treatment: 1396390 INFO @ Sat, 15 Jan 2022 19:29:34: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:29:34: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:34: #2 number of paired peaks: 207 WARNING @ Sat, 15 Jan 2022 19:29:34: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:34: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:34: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:34: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:34: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:34: #2 predicted fragment length is 237 bps INFO @ Sat, 15 Jan 2022 19:29:34: #2 alternative fragment length(s) may be 0,187,207,233,237,263 bps INFO @ Sat, 15 Jan 2022 19:29:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10_model.r INFO @ Sat, 15 Jan 2022 19:29:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:29:36: 4000000 INFO @ Sat, 15 Jan 2022 19:29:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.10_summits.bed INFO @ Sat, 15 Jan 2022 19:29:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:29:43: 5000000 INFO @ Sat, 15 Jan 2022 19:29:49: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:29:55: 7000000 INFO @ Sat, 15 Jan 2022 19:29:59: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:59: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:59: #1 total tags in treatment: 1951478 INFO @ Sat, 15 Jan 2022 19:29:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:59: #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 19:29:59: #1 tags after filtering in treatment: 1396390 INFO @ Sat, 15 Jan 2022 19:29:59: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 19:29:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:59: #2 number of paired peaks: 207 WARNING @ Sat, 15 Jan 2022 19:29:59: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:59: #2 predicted fragment length is 237 bps INFO @ Sat, 15 Jan 2022 19:29:59: #2 alternative fragment length(s) may be 0,187,207,233,237,263 bps INFO @ Sat, 15 Jan 2022 19:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20_model.r INFO @ Sat, 15 Jan 2022 19:30:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:30:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:30:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:30:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:30:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781170/SRX11781170.20_summits.bed INFO @ Sat, 15 Jan 2022 19:30:08: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (67 records, 4 fields): 3 millis CompletedMACS2peakCalling