Job ID = 10224102 SRX = SRX8952656 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2932632 spots for SRR12458230/SRR12458230.sra Written 2932632 spots for SRR12458230/SRR12458230.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: 00:00:56 2932632 reads; of these: 2932632 (100.00%) were paired; of these: 2242437 (76.46%) aligned concordantly 0 times 617115 (21.04%) aligned concordantly exactly 1 time 73080 (2.49%) aligned concordantly >1 times ---- 2242437 pairs aligned concordantly 0 times; of these: 197306 (8.80%) aligned discordantly 1 time ---- 2045131 pairs aligned 0 times concordantly or discordantly; of these: 4090262 mates make up the pairs; of these: 3177319 (77.68%) aligned 0 times 808535 (19.77%) aligned exactly 1 time 104408 (2.55%) aligned >1 times 45.83% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 143093 / 875376 = 0.1635 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 09:27:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.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 09:27:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:25: 1000000 INFO @ Fri, 16 Oct 2020 09:27:30: 2000000 INFO @ Fri, 16 Oct 2020 09:27:32: #1 tag size is determined as 46 bps INFO @ Fri, 16 Oct 2020 09:27:32: #1 tag size = 46 INFO @ Fri, 16 Oct 2020 09:27:32: #1 total tags in treatment: 646891 INFO @ Fri, 16 Oct 2020 09:27:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:32: #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 09:27:32: #1 tags after filtering in treatment: 619439 INFO @ Fri, 16 Oct 2020 09:27:32: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 16 Oct 2020 09:27:32: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:32: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 09:27:32: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:32: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:32: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:32: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:32: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:32: #2 predicted fragment length is 320 bps INFO @ Fri, 16 Oct 2020 09:27:32: #2 alternative fragment length(s) may be 38,60,63,133,167,250,266,293,320,453,490,585,589 bps INFO @ Fri, 16 Oct 2020 09:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05_model.r INFO @ Fri, 16 Oct 2020 09:27:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.05_summits.bed INFO @ Fri, 16 Oct 2020 09:27:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 1 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 09:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.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 09:27:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:54: 1000000 INFO @ Fri, 16 Oct 2020 09:28:00: 2000000 INFO @ Fri, 16 Oct 2020 09:28:02: #1 tag size is determined as 46 bps INFO @ Fri, 16 Oct 2020 09:28:02: #1 tag size = 46 INFO @ Fri, 16 Oct 2020 09:28:02: #1 total tags in treatment: 646891 INFO @ Fri, 16 Oct 2020 09:28:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:02: #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 09:28:02: #1 tags after filtering in treatment: 619439 INFO @ Fri, 16 Oct 2020 09:28:02: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 16 Oct 2020 09:28:02: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:02: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 09:28:02: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:02: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:02: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:02: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:02: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:02: #2 predicted fragment length is 320 bps INFO @ Fri, 16 Oct 2020 09:28:02: #2 alternative fragment length(s) may be 38,60,63,133,167,250,266,293,320,453,490,585,589 bps INFO @ Fri, 16 Oct 2020 09:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10_model.r INFO @ Fri, 16 Oct 2020 09:28:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.10_summits.bed INFO @ Fri, 16 Oct 2020 09:28:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (62 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 09:28:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.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 09:28:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:28:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:28:25: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:28:30: 2000000 INFO @ Fri, 16 Oct 2020 09:28:32: #1 tag size is determined as 46 bps INFO @ Fri, 16 Oct 2020 09:28:32: #1 tag size = 46 INFO @ Fri, 16 Oct 2020 09:28:32: #1 total tags in treatment: 646891 INFO @ Fri, 16 Oct 2020 09:28:32: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:28:32: #1 tags after filtering in treatment: 619439 INFO @ Fri, 16 Oct 2020 09:28:32: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 16 Oct 2020 09:28:32: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:32: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:32: #2 number of paired peaks: 194 WARNING @ Fri, 16 Oct 2020 09:28:32: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:32: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:32: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:32: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:32: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:32: #2 predicted fragment length is 320 bps INFO @ Fri, 16 Oct 2020 09:28:32: #2 alternative fragment length(s) may be 38,60,63,133,167,250,266,293,320,453,490,585,589 bps INFO @ Fri, 16 Oct 2020 09:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20_model.r INFO @ Fri, 16 Oct 2020 09:28:32: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952656/SRX8952656.20_summits.bed INFO @ Fri, 16 Oct 2020 09:28:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling