Job ID = 10224035 SRX = SRX8926520 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4121573 spots for SRR12430731/SRR12430731.sra Written 4121573 spots for SRR12430731/SRR12430731.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: 00:01:42 4121573 reads; of these: 4121573 (100.00%) were paired; of these: 1691258 (41.03%) aligned concordantly 0 times 1736166 (42.12%) aligned concordantly exactly 1 time 694149 (16.84%) aligned concordantly >1 times ---- 1691258 pairs aligned concordantly 0 times; of these: 2299 (0.14%) aligned discordantly 1 time ---- 1688959 pairs aligned 0 times concordantly or discordantly; of these: 3377918 mates make up the pairs; of these: 3345476 (99.04%) aligned 0 times 20727 (0.61%) aligned exactly 1 time 11715 (0.35%) aligned >1 times 59.42% overall alignment rate Time searching: 00:01:42 Overall time: 00:01:42 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] 499636 / 2432364 = 0.2054 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 09:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.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 09:13:51: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:13:51: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:13:58: 1000000 INFO @ Fri, 16 Oct 2020 09:14:05: 2000000 INFO @ Fri, 16 Oct 2020 09:14:12: 3000000 INFO @ Fri, 16 Oct 2020 09:14:17: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:14:17: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:14:17: #1 total tags in treatment: 1930799 INFO @ Fri, 16 Oct 2020 09:14:17: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:14:17: #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 09:14:17: #1 tags after filtering in treatment: 1467416 INFO @ Fri, 16 Oct 2020 09:14:17: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 16 Oct 2020 09:14:17: #1 finished! INFO @ Fri, 16 Oct 2020 09:14:17: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:14:18: #2 number of paired peaks: 111 WARNING @ Fri, 16 Oct 2020 09:14:18: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 16 Oct 2020 09:14:18: start model_add_line... INFO @ Fri, 16 Oct 2020 09:14:18: start X-correlation... INFO @ Fri, 16 Oct 2020 09:14:18: end of X-cor INFO @ Fri, 16 Oct 2020 09:14:18: #2 finished! INFO @ Fri, 16 Oct 2020 09:14:18: #2 predicted fragment length is 187 bps INFO @ Fri, 16 Oct 2020 09:14:18: #2 alternative fragment length(s) may be 187 bps INFO @ Fri, 16 Oct 2020 09:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05_model.r INFO @ Fri, 16 Oct 2020 09:14:18: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:14:18: #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 09:14:21: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.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 09:14:21: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:14:21: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.05_summits.bed INFO @ Fri, 16 Oct 2020 09:14:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:14:28: 1000000 INFO @ Fri, 16 Oct 2020 09:14:35: 2000000 INFO @ Fri, 16 Oct 2020 09:14:42: 3000000 INFO @ Fri, 16 Oct 2020 09:14:48: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:14:48: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:14:48: #1 total tags in treatment: 1930799 INFO @ Fri, 16 Oct 2020 09:14:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:14:48: #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 09:14:48: #1 tags after filtering in treatment: 1467416 INFO @ Fri, 16 Oct 2020 09:14:48: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 16 Oct 2020 09:14:48: #1 finished! INFO @ Fri, 16 Oct 2020 09:14:48: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:14:48: #2 number of paired peaks: 111 WARNING @ Fri, 16 Oct 2020 09:14:48: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 16 Oct 2020 09:14:48: start model_add_line... INFO @ Fri, 16 Oct 2020 09:14:48: start X-correlation... INFO @ Fri, 16 Oct 2020 09:14:48: end of X-cor INFO @ Fri, 16 Oct 2020 09:14:48: #2 finished! INFO @ Fri, 16 Oct 2020 09:14:48: #2 predicted fragment length is 187 bps INFO @ Fri, 16 Oct 2020 09:14:48: #2 alternative fragment length(s) may be 187 bps INFO @ Fri, 16 Oct 2020 09:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10_model.r INFO @ Fri, 16 Oct 2020 09:14:48: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:14:48: #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 09:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.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 09:14:51: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:14:51: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:14:52: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.10_summits.bed INFO @ Fri, 16 Oct 2020 09:14:53: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (503 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:14:58: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:15:05: 2000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:15:12: 3000000 INFO @ Fri, 16 Oct 2020 09:15:18: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:15:18: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:15:18: #1 total tags in treatment: 1930799 INFO @ Fri, 16 Oct 2020 09:15:18: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:15:18: #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 09:15:18: #1 tags after filtering in treatment: 1467416 INFO @ Fri, 16 Oct 2020 09:15:18: #1 Redundant rate of treatment: 0.24 INFO @ Fri, 16 Oct 2020 09:15:18: #1 finished! INFO @ Fri, 16 Oct 2020 09:15:18: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:15:18: #2 number of paired peaks: 111 WARNING @ Fri, 16 Oct 2020 09:15:18: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Fri, 16 Oct 2020 09:15:18: start model_add_line... INFO @ Fri, 16 Oct 2020 09:15:18: start X-correlation... INFO @ Fri, 16 Oct 2020 09:15:18: end of X-cor INFO @ Fri, 16 Oct 2020 09:15:18: #2 finished! INFO @ Fri, 16 Oct 2020 09:15:18: #2 predicted fragment length is 187 bps INFO @ Fri, 16 Oct 2020 09:15:18: #2 alternative fragment length(s) may be 187 bps INFO @ Fri, 16 Oct 2020 09:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20_model.r INFO @ Fri, 16 Oct 2020 09:15:18: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:15:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926520/SRX8926520.20_summits.bed INFO @ Fri, 16 Oct 2020 09:15:23: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (222 records, 4 fields): 2 millis CompletedMACS2peakCalling