Job ID = 10224086 SRX = SRX8952642 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14865848 spots for SRR12458244/SRR12458244.sra Written 14865848 spots for SRR12458244/SRR12458244.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: 00:03:57 14865848 reads; of these: 14865848 (100.00%) were paired; of these: 11420655 (76.82%) aligned concordantly 0 times 2819409 (18.97%) aligned concordantly exactly 1 time 625784 (4.21%) aligned concordantly >1 times ---- 11420655 pairs aligned concordantly 0 times; of these: 942659 (8.25%) aligned discordantly 1 time ---- 10477996 pairs aligned 0 times concordantly or discordantly; of these: 20955992 mates make up the pairs; of these: 17771686 (84.80%) aligned 0 times 2584393 (12.33%) aligned exactly 1 time 599913 (2.86%) aligned >1 times 40.23% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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_sort_core] merging from 8 files... [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] 2195554 / 4364431 = 0.5031 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 09:29:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.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 09:29:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:29:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:29:33: 1000000 INFO @ Fri, 16 Oct 2020 09:29:37: 2000000 INFO @ Fri, 16 Oct 2020 09:29:41: 3000000 INFO @ Fri, 16 Oct 2020 09:29:45: 4000000 INFO @ Fri, 16 Oct 2020 09:29:50: 5000000 INFO @ Fri, 16 Oct 2020 09:29:54: 6000000 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 09:29:59: 7000000 INFO @ Fri, 16 Oct 2020 09:29:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.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 09:29:59: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:29:59: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:02: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:30:02: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:30:02: #1 total tags in treatment: 1941637 INFO @ Fri, 16 Oct 2020 09:30:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:02: #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 09:30:02: #1 tags after filtering in treatment: 1556991 INFO @ Fri, 16 Oct 2020 09:30:02: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:30:02: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:02: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:30:02: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:02: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:02: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:02: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:02: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:02: #2 predicted fragment length is 228 bps INFO @ Fri, 16 Oct 2020 09:30:02: #2 alternative fragment length(s) may be 0,158,228,250,267,587 bps INFO @ Fri, 16 Oct 2020 09:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05_model.r INFO @ Fri, 16 Oct 2020 09:30:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:30:05: 1000000 INFO @ Fri, 16 Oct 2020 09:30:06: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.05_summits.bed INFO @ Fri, 16 Oct 2020 09:30:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:30:10: 2000000 INFO @ Fri, 16 Oct 2020 09:30:15: 3000000 INFO @ Fri, 16 Oct 2020 09:30:21: 4000000 INFO @ Fri, 16 Oct 2020 09:30:27: 5000000 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 09:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.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 09:30:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:33: 6000000 INFO @ Fri, 16 Oct 2020 09:30:34: 1000000 INFO @ Fri, 16 Oct 2020 09:30:39: 2000000 INFO @ Fri, 16 Oct 2020 09:30:39: 7000000 INFO @ Fri, 16 Oct 2020 09:30:42: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:30:42: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:30:42: #1 total tags in treatment: 1941637 INFO @ Fri, 16 Oct 2020 09:30:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:42: #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 09:30:42: #1 tags after filtering in treatment: 1556991 INFO @ Fri, 16 Oct 2020 09:30:42: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:30:42: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:42: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:30:42: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:42: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:42: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:42: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:42: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:42: #2 predicted fragment length is 228 bps INFO @ Fri, 16 Oct 2020 09:30:42: #2 alternative fragment length(s) may be 0,158,228,250,267,587 bps INFO @ Fri, 16 Oct 2020 09:30:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10_model.r INFO @ Fri, 16 Oct 2020 09:30:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:30:44: 3000000 INFO @ Fri, 16 Oct 2020 09:30:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:30:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:30:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:30:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.10_summits.bed INFO @ Fri, 16 Oct 2020 09:30:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:30:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:30:53: 5000000 INFO @ Fri, 16 Oct 2020 09:30:58: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:31:03: 7000000 INFO @ Fri, 16 Oct 2020 09:31:06: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:31:06: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:31:06: #1 total tags in treatment: 1941637 INFO @ Fri, 16 Oct 2020 09:31:06: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:06: #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 09:31:06: #1 tags after filtering in treatment: 1556991 INFO @ Fri, 16 Oct 2020 09:31:06: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:31:06: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:06: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:06: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:31:06: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:06: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:06: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:06: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:06: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:06: #2 predicted fragment length is 228 bps INFO @ Fri, 16 Oct 2020 09:31:06: #2 alternative fragment length(s) may be 0,158,228,250,267,587 bps INFO @ Fri, 16 Oct 2020 09:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20_model.r INFO @ Fri, 16 Oct 2020 09:31:06: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:31:10: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:31:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952642/SRX8952642.20_summits.bed INFO @ Fri, 16 Oct 2020 09:31:11: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (118 records, 4 fields): 1 millis CompletedMACS2peakCalling