Job ID = 10223955 SRX = SRX7496404 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3463068 spots for SRR10823015/SRR10823015.sra Written 3463068 spots for SRR10823015/SRR10823015.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: 00:00:43 3463068 reads; of these: 3463068 (100.00%) were paired; of these: 2715135 (78.40%) aligned concordantly 0 times 564467 (16.30%) aligned concordantly exactly 1 time 183466 (5.30%) aligned concordantly >1 times ---- 2715135 pairs aligned concordantly 0 times; of these: 1823 (0.07%) aligned discordantly 1 time ---- 2713312 pairs aligned 0 times concordantly or discordantly; of these: 5426624 mates make up the pairs; of these: 4897529 (90.25%) aligned 0 times 444050 (8.18%) aligned exactly 1 time 85045 (1.57%) aligned >1 times 29.29% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 92433 / 749607 = 0.1233 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 08:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.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 08:58:25: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:58:25: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:58:29: 1000000 INFO @ Fri, 16 Oct 2020 08:58:32: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:58:32: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:58:32: #1 total tags in treatment: 655515 INFO @ Fri, 16 Oct 2020 08:58:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:58:32: #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 08:58:32: #1 tags after filtering in treatment: 456104 INFO @ Fri, 16 Oct 2020 08:58:32: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 16 Oct 2020 08:58:32: #1 finished! INFO @ Fri, 16 Oct 2020 08:58:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:58:32: #2 number of paired peaks: 105 WARNING @ Fri, 16 Oct 2020 08:58:32: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Fri, 16 Oct 2020 08:58:32: start model_add_line... INFO @ Fri, 16 Oct 2020 08:58:32: start X-correlation... INFO @ Fri, 16 Oct 2020 08:58:32: end of X-cor INFO @ Fri, 16 Oct 2020 08:58:32: #2 finished! INFO @ Fri, 16 Oct 2020 08:58:32: #2 predicted fragment length is 255 bps INFO @ Fri, 16 Oct 2020 08:58:32: #2 alternative fragment length(s) may be 34,224,255,278,579 bps INFO @ Fri, 16 Oct 2020 08:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05_model.r INFO @ Fri, 16 Oct 2020 08:58:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:58:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05_peaks.xls INFO @ Fri, 16 Oct 2020 08:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.05_summits.bed INFO @ Fri, 16 Oct 2020 08:58:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.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 08:58:55: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:58:55: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:58:59: 1000000 INFO @ Fri, 16 Oct 2020 08:59:02: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:59:02: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:59:02: #1 total tags in treatment: 655515 INFO @ Fri, 16 Oct 2020 08:59:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:59:02: #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 08:59:02: #1 tags after filtering in treatment: 456104 INFO @ Fri, 16 Oct 2020 08:59:02: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 16 Oct 2020 08:59:02: #1 finished! INFO @ Fri, 16 Oct 2020 08:59:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:59:02: #2 number of paired peaks: 105 WARNING @ Fri, 16 Oct 2020 08:59:02: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Fri, 16 Oct 2020 08:59:02: start model_add_line... INFO @ Fri, 16 Oct 2020 08:59:02: start X-correlation... INFO @ Fri, 16 Oct 2020 08:59:02: end of X-cor INFO @ Fri, 16 Oct 2020 08:59:02: #2 finished! INFO @ Fri, 16 Oct 2020 08:59:02: #2 predicted fragment length is 255 bps INFO @ Fri, 16 Oct 2020 08:59:02: #2 alternative fragment length(s) may be 34,224,255,278,579 bps INFO @ Fri, 16 Oct 2020 08:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10_model.r INFO @ Fri, 16 Oct 2020 08:59:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:59:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10_peaks.xls INFO @ Fri, 16 Oct 2020 08:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.10_summits.bed INFO @ Fri, 16 Oct 2020 08:59:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (235 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.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 08:59:25: #1 read tag files... INFO @ Fri, 16 Oct 2020 08:59:25: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 08:59:29: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 08:59:33: #1 tag size is determined as 37 bps INFO @ Fri, 16 Oct 2020 08:59:33: #1 tag size = 37 INFO @ Fri, 16 Oct 2020 08:59:33: #1 total tags in treatment: 655515 INFO @ Fri, 16 Oct 2020 08:59:33: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 08:59:33: #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 08:59:33: #1 tags after filtering in treatment: 456104 INFO @ Fri, 16 Oct 2020 08:59:33: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 16 Oct 2020 08:59:33: #1 finished! INFO @ Fri, 16 Oct 2020 08:59:33: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 08:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 08:59:33: #2 number of paired peaks: 105 WARNING @ Fri, 16 Oct 2020 08:59:33: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Fri, 16 Oct 2020 08:59:33: start model_add_line... INFO @ Fri, 16 Oct 2020 08:59:33: start X-correlation... INFO @ Fri, 16 Oct 2020 08:59:33: end of X-cor INFO @ Fri, 16 Oct 2020 08:59:33: #2 finished! INFO @ Fri, 16 Oct 2020 08:59:33: #2 predicted fragment length is 255 bps INFO @ Fri, 16 Oct 2020 08:59:33: #2 alternative fragment length(s) may be 34,224,255,278,579 bps INFO @ Fri, 16 Oct 2020 08:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20_model.r INFO @ Fri, 16 Oct 2020 08:59:33: #3 Call peaks... INFO @ Fri, 16 Oct 2020 08:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 08:59:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 08:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20_peaks.xls INFO @ Fri, 16 Oct 2020 08:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 08:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496404/SRX7496404.20_summits.bed INFO @ Fri, 16 Oct 2020 08:59:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling