Job ID = 14519780 SRX = SRX9390800 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 431684 spots for SRR12926695/SRR12926695.sra Written 431684 spots for SRR12926695/SRR12926695.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: 00:00:18 431684 reads; of these: 431684 (100.00%) were paired; of these: 255069 (59.09%) aligned concordantly 0 times 129048 (29.89%) aligned concordantly exactly 1 time 47567 (11.02%) aligned concordantly >1 times ---- 255069 pairs aligned concordantly 0 times; of these: 36665 (14.37%) aligned discordantly 1 time ---- 218404 pairs aligned 0 times concordantly or discordantly; of these: 436808 mates make up the pairs; of these: 230271 (52.72%) aligned 0 times 66993 (15.34%) aligned exactly 1 time 139544 (31.95%) aligned >1 times 73.33% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 30684 / 211986 = 0.1447 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 17:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.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 17:44:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:44:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:44:27: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 17:44:27: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 17:44:27: #1 total tags in treatment: 150168 INFO @ Sat, 15 Jan 2022 17:44:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:27: #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 17:44:27: #1 tags after filtering in treatment: 130312 INFO @ Sat, 15 Jan 2022 17:44:27: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 17:44:27: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:44:27: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 17:44:27: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 17:44:27: start model_add_line... INFO @ Sat, 15 Jan 2022 17:44:27: start X-correlation... INFO @ Sat, 15 Jan 2022 17:44:27: end of X-cor INFO @ Sat, 15 Jan 2022 17:44:27: #2 finished! INFO @ Sat, 15 Jan 2022 17:44:27: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 17:44:27: #2 alternative fragment length(s) may be 158,550 bps INFO @ Sat, 15 Jan 2022 17:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05_model.r INFO @ Sat, 15 Jan 2022 17:44:27: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:44:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.05_summits.bed INFO @ Sat, 15 Jan 2022 17:44:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 17:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.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 17:44:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:44:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:44:57: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 17:44:57: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 17:44:57: #1 total tags in treatment: 150168 INFO @ Sat, 15 Jan 2022 17:44:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:44:57: #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 17:44:57: #1 tags after filtering in treatment: 130312 INFO @ Sat, 15 Jan 2022 17:44:57: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 17:44:57: #1 finished! INFO @ Sat, 15 Jan 2022 17:44:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:44:57: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 17:44:57: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 17:44:57: start model_add_line... INFO @ Sat, 15 Jan 2022 17:44:57: start X-correlation... INFO @ Sat, 15 Jan 2022 17:44:57: end of X-cor INFO @ Sat, 15 Jan 2022 17:44:57: #2 finished! INFO @ Sat, 15 Jan 2022 17:44:57: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 17:44:57: #2 alternative fragment length(s) may be 158,550 bps INFO @ Sat, 15 Jan 2022 17:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10_model.r INFO @ Sat, 15 Jan 2022 17:44:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:44:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.10_summits.bed INFO @ Sat, 15 Jan 2022 17:44:58: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 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 17:45:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.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 17:45:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:45:25: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:45:28: #1 tag size is determined as 32 bps INFO @ Sat, 15 Jan 2022 17:45:28: #1 tag size = 32 INFO @ Sat, 15 Jan 2022 17:45:28: #1 total tags in treatment: 150168 INFO @ Sat, 15 Jan 2022 17:45:28: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:45:28: #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 17:45:28: #1 tags after filtering in treatment: 130312 INFO @ Sat, 15 Jan 2022 17:45:28: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 17:45:28: #1 finished! INFO @ Sat, 15 Jan 2022 17:45:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:45:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:45:28: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 17:45:28: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 17:45:28: start model_add_line... INFO @ Sat, 15 Jan 2022 17:45:28: start X-correlation... INFO @ Sat, 15 Jan 2022 17:45:28: end of X-cor INFO @ Sat, 15 Jan 2022 17:45:28: #2 finished! INFO @ Sat, 15 Jan 2022 17:45:28: #2 predicted fragment length is 158 bps INFO @ Sat, 15 Jan 2022 17:45:28: #2 alternative fragment length(s) may be 158,550 bps INFO @ Sat, 15 Jan 2022 17:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20_model.r INFO @ Sat, 15 Jan 2022 17:45:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:45:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:45:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:45:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:45:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9390800/SRX9390800.20_summits.bed INFO @ Sat, 15 Jan 2022 17:45:29: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling