Job ID = 10224034 SRX = SRX8926519 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5239509 spots for SRR12430732/SRR12430732.sra Written 5239509 spots for SRR12430732/SRR12430732.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: 00:02:36 5239509 reads; of these: 5239509 (100.00%) were paired; of these: 1340181 (25.58%) aligned concordantly 0 times 2468724 (47.12%) aligned concordantly exactly 1 time 1430604 (27.30%) aligned concordantly >1 times ---- 1340181 pairs aligned concordantly 0 times; of these: 8601 (0.64%) aligned discordantly 1 time ---- 1331580 pairs aligned 0 times concordantly or discordantly; of these: 2663160 mates make up the pairs; of these: 2610328 (98.02%) aligned 0 times 24358 (0.91%) aligned exactly 1 time 28474 (1.07%) aligned >1 times 75.09% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 824838 / 3907446 = 0.2111 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:15:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.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 @ Fri, 16 Oct 2020 09:15:26: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:15:26: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:15:31: 1000000 INFO @ Fri, 16 Oct 2020 09:15:35: 2000000 INFO @ Fri, 16 Oct 2020 09:15:40: 3000000 INFO @ Fri, 16 Oct 2020 09:15:44: 4000000 INFO @ Fri, 16 Oct 2020 09:15:49: 5000000 INFO @ Fri, 16 Oct 2020 09:15:53: 6000000 INFO @ Fri, 16 Oct 2020 09:15:54: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:15:54: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:15:54: #1 total tags in treatment: 3074686 INFO @ Fri, 16 Oct 2020 09:15:54: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:15:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:15:54: #1 tags after filtering in treatment: 2071298 INFO @ Fri, 16 Oct 2020 09:15:54: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 16 Oct 2020 09:15:54: #1 finished! INFO @ Fri, 16 Oct 2020 09:15:54: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:15:54: #2 number of paired peaks: 144 WARNING @ Fri, 16 Oct 2020 09:15:54: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 16 Oct 2020 09:15:54: start model_add_line... INFO @ Fri, 16 Oct 2020 09:15:54: start X-correlation... INFO @ Fri, 16 Oct 2020 09:15:54: end of X-cor INFO @ Fri, 16 Oct 2020 09:15:54: #2 finished! INFO @ Fri, 16 Oct 2020 09:15:54: #2 predicted fragment length is 191 bps INFO @ Fri, 16 Oct 2020 09:15:54: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 16 Oct 2020 09:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05_model.r INFO @ Fri, 16 Oct 2020 09:15:54: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:15:54: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.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 @ Fri, 16 Oct 2020 09:15:56: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:15:56: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:16:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:16:01: 1000000 INFO @ Fri, 16 Oct 2020 09:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.05_summits.bed INFO @ Fri, 16 Oct 2020 09:16:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1389 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:16:05: 2000000 INFO @ Fri, 16 Oct 2020 09:16:10: 3000000 INFO @ Fri, 16 Oct 2020 09:16:14: 4000000 INFO @ Fri, 16 Oct 2020 09:16:19: 5000000 INFO @ Fri, 16 Oct 2020 09:16:23: 6000000 INFO @ Fri, 16 Oct 2020 09:16:24: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:16:24: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:16:24: #1 total tags in treatment: 3074686 INFO @ Fri, 16 Oct 2020 09:16:24: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:16:24: #1 tags after filtering in treatment: 2071298 INFO @ Fri, 16 Oct 2020 09:16:24: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 16 Oct 2020 09:16:24: #1 finished! INFO @ Fri, 16 Oct 2020 09:16:24: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:16:24: #2 number of paired peaks: 144 WARNING @ Fri, 16 Oct 2020 09:16:24: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 16 Oct 2020 09:16:24: start model_add_line... INFO @ Fri, 16 Oct 2020 09:16:24: start X-correlation... INFO @ Fri, 16 Oct 2020 09:16:24: end of X-cor INFO @ Fri, 16 Oct 2020 09:16:24: #2 finished! INFO @ Fri, 16 Oct 2020 09:16:24: #2 predicted fragment length is 191 bps INFO @ Fri, 16 Oct 2020 09:16:24: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 16 Oct 2020 09:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10_model.r INFO @ Fri, 16 Oct 2020 09:16:24: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:16:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.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 @ Fri, 16 Oct 2020 09:16:26: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:16:26: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:16:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:16:32: 1000000 INFO @ Fri, 16 Oct 2020 09:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.10_summits.bed INFO @ Fri, 16 Oct 2020 09:16:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (948 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:16:37: 2000000 INFO @ Fri, 16 Oct 2020 09:16:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:16:48: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:16:53: 5000000 INFO @ Fri, 16 Oct 2020 09:16:58: 6000000 INFO @ Fri, 16 Oct 2020 09:16:59: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:16:59: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:16:59: #1 total tags in treatment: 3074686 INFO @ Fri, 16 Oct 2020 09:16:59: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:16:59: #1 tags after filtering in treatment: 2071298 INFO @ Fri, 16 Oct 2020 09:16:59: #1 Redundant rate of treatment: 0.33 INFO @ Fri, 16 Oct 2020 09:16:59: #1 finished! INFO @ Fri, 16 Oct 2020 09:16:59: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:16:59: #2 number of paired peaks: 144 WARNING @ Fri, 16 Oct 2020 09:16:59: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 16 Oct 2020 09:16:59: start model_add_line... INFO @ Fri, 16 Oct 2020 09:16:59: start X-correlation... INFO @ Fri, 16 Oct 2020 09:16:59: end of X-cor INFO @ Fri, 16 Oct 2020 09:16:59: #2 finished! INFO @ Fri, 16 Oct 2020 09:16:59: #2 predicted fragment length is 191 bps INFO @ Fri, 16 Oct 2020 09:16:59: #2 alternative fragment length(s) may be 191 bps INFO @ Fri, 16 Oct 2020 09:16:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20_model.r INFO @ Fri, 16 Oct 2020 09:16:59: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:16:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:17:05: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926519/SRX8926519.20_summits.bed INFO @ Fri, 16 Oct 2020 09:17:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 3 millis CompletedMACS2peakCalling