Job ID = 10223937 SRX = SRX7496388 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7094288 spots for SRR10822999/SRR10822999.sra Written 7094288 spots for SRR10822999/SRR10822999.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:21 7094288 reads; of these: 7094288 (100.00%) were paired; of these: 4606146 (64.93%) aligned concordantly 0 times 1604390 (22.62%) aligned concordantly exactly 1 time 883752 (12.46%) aligned concordantly >1 times ---- 4606146 pairs aligned concordantly 0 times; of these: 8900 (0.19%) aligned discordantly 1 time ---- 4597246 pairs aligned 0 times concordantly or discordantly; of these: 9194492 mates make up the pairs; of these: 7242916 (78.77%) aligned 0 times 1458253 (15.86%) aligned exactly 1 time 493323 (5.37%) aligned >1 times 48.95% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 551591 / 2496668 = 0.2209 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 08:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 08:56:46: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:56:46: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:56:50: 1000000 INFO @ Fri, 16 Oct 2020 08:56:55: 2000000 INFO @ Fri, 16 Oct 2020 08:57:00: 3000000 INFO @ Fri, 16 Oct 2020 08:57:04: 4000000 INFO @ Fri, 16 Oct 2020 08:57:08: 5000000 INFO @ Fri, 16 Oct 2020 08:57:12: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:57:12: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:57:12: #1 total tags in treatment: 1936654 INFO @ Fri, 16 Oct 2020 08:57:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:57:12: #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 08:57:12: #1 tags after filtering in treatment: 1063120 INFO @ Fri, 16 Oct 2020 08:57:12: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 16 Oct 2020 08:57:12: #1 finished! INFO @ Fri, 16 Oct 2020 08:57:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:57:12: #2 number of paired peaks: 148 WARNING @ Fri, 16 Oct 2020 08:57:12: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 16 Oct 2020 08:57:12: start model_add_line... INFO @ Fri, 16 Oct 2020 08:57:12: start X-correlation... INFO @ Fri, 16 Oct 2020 08:57:12: end of X-cor INFO @ Fri, 16 Oct 2020 08:57:12: #2 finished! INFO @ Fri, 16 Oct 2020 08:57:12: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 08:57:12: #2 alternative fragment length(s) may be 242,268 bps INFO @ Fri, 16 Oct 2020 08:57:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_model.r INFO @ Fri, 16 Oct 2020 08:57:12: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:57:12: #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 08:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 08:57:15: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:57:15: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:57:16: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:57:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:57:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:57:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_summits.bed INFO @ Fri, 16 Oct 2020 08:57:17: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:57:20: 1000000 INFO @ Fri, 16 Oct 2020 08:57:23: 2000000 INFO @ Fri, 16 Oct 2020 08:57:27: 3000000 INFO @ Fri, 16 Oct 2020 08:57:31: 4000000 INFO @ Fri, 16 Oct 2020 08:57:35: 5000000 INFO @ Fri, 16 Oct 2020 08:57:39: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:57:39: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:57:39: #1 total tags in treatment: 1936654 INFO @ Fri, 16 Oct 2020 08:57:39: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:57:39: #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 08:57:39: #1 tags after filtering in treatment: 1063120 INFO @ Fri, 16 Oct 2020 08:57:39: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 16 Oct 2020 08:57:39: #1 finished! INFO @ Fri, 16 Oct 2020 08:57:39: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:57:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:57:39: #2 number of paired peaks: 148 WARNING @ Fri, 16 Oct 2020 08:57:39: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 16 Oct 2020 08:57:39: start model_add_line... INFO @ Fri, 16 Oct 2020 08:57:39: start X-correlation... INFO @ Fri, 16 Oct 2020 08:57:39: end of X-cor INFO @ Fri, 16 Oct 2020 08:57:39: #2 finished! INFO @ Fri, 16 Oct 2020 08:57:39: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 08:57:39: #2 alternative fragment length(s) may be 242,268 bps INFO @ Fri, 16 Oct 2020 08:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_model.r INFO @ Fri, 16 Oct 2020 08:57:39: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:57:43: #3 Call peaks for each chromosome... 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 08:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_summits.bed INFO @ Fri, 16 Oct 2020 08:57:44: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 08:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 08:57:45: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:57:45: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:57:50: 1000000 INFO @ Fri, 16 Oct 2020 08:57:54: 2000000 INFO @ Fri, 16 Oct 2020 08:57:58: 3000000 INFO @ Fri, 16 Oct 2020 08:58:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 08:58:06: 5000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:58:10: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:10: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:10: #1 total tags in treatment: 1936654 INFO @ Fri, 16 Oct 2020 08:58:10: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:10: #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 08:58:10: #1 tags after filtering in treatment: 1063120 INFO @ Fri, 16 Oct 2020 08:58:10: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 16 Oct 2020 08:58:10: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:10: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:10: #2 number of paired peaks: 148 WARNING @ Fri, 16 Oct 2020 08:58:10: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:10: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:10: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:10: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:10: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:10: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 08:58:10: #2 alternative fragment length(s) may be 242,268 bps INFO @ Fri, 16 Oct 2020 08:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_model.r INFO @ Fri, 16 Oct 2020 08:58:10: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_summits.bed INFO @ Fri, 16 Oct 2020 08:58:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 1 millis CompletedMACS2peakCalling