Job ID = 10224108 SRX = SRX8952661 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3341764 spots for SRR12458225/SRR12458225.sra Written 3341764 spots for SRR12458225/SRR12458225.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: 00:06:10 3341764 reads; of these: 3341764 (100.00%) were paired; of these: 2669085 (79.87%) aligned concordantly 0 times 525661 (15.73%) aligned concordantly exactly 1 time 147018 (4.40%) aligned concordantly >1 times ---- 2669085 pairs aligned concordantly 0 times; of these: 3452 (0.13%) aligned discordantly 1 time ---- 2665633 pairs aligned 0 times concordantly or discordantly; of these: 5331266 mates make up the pairs; of these: 2136438 (40.07%) aligned 0 times 995347 (18.67%) aligned exactly 1 time 2199481 (41.26%) aligned >1 times 68.03% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 69849 / 672600 = 0.1038 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 09:33:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.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 09:33:55: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:33:55: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:33:59: 1000000 INFO @ Fri, 16 Oct 2020 09:34:03: 2000000 INFO @ Fri, 16 Oct 2020 09:34:07: 3000000 INFO @ Fri, 16 Oct 2020 09:34:11: 4000000 INFO @ Fri, 16 Oct 2020 09:34:12: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:34:12: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:34:12: #1 total tags in treatment: 602833 INFO @ Fri, 16 Oct 2020 09:34:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:34:12: #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 09:34:12: #1 tags after filtering in treatment: 547247 INFO @ Fri, 16 Oct 2020 09:34:12: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:34:12: #1 finished! INFO @ Fri, 16 Oct 2020 09:34:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:34:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:34:12: #2 number of paired peaks: 469 WARNING @ Fri, 16 Oct 2020 09:34:12: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Fri, 16 Oct 2020 09:34:12: start model_add_line... INFO @ Fri, 16 Oct 2020 09:34:12: start X-correlation... INFO @ Fri, 16 Oct 2020 09:34:12: end of X-cor INFO @ Fri, 16 Oct 2020 09:34:12: #2 finished! INFO @ Fri, 16 Oct 2020 09:34:12: #2 predicted fragment length is 205 bps INFO @ Fri, 16 Oct 2020 09:34:12: #2 alternative fragment length(s) may be 4,205,224 bps INFO @ Fri, 16 Oct 2020 09:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05_model.r INFO @ Fri, 16 Oct 2020 09:34:12: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:34:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:34:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:34:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:34:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.05_summits.bed INFO @ Fri, 16 Oct 2020 09:34:15: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (400 records, 4 fields): 14 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 09:34:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.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 09:34:25: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:34:25: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:34:29: 1000000 INFO @ Fri, 16 Oct 2020 09:34:33: 2000000 INFO @ Fri, 16 Oct 2020 09:34:37: 3000000 INFO @ Fri, 16 Oct 2020 09:34:40: 4000000 INFO @ Fri, 16 Oct 2020 09:34:42: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:34:42: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:34:42: #1 total tags in treatment: 602833 INFO @ Fri, 16 Oct 2020 09:34:42: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:34:42: #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 09:34:42: #1 tags after filtering in treatment: 547247 INFO @ Fri, 16 Oct 2020 09:34:42: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:34:42: #1 finished! INFO @ Fri, 16 Oct 2020 09:34:42: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:34:42: #2 number of paired peaks: 469 WARNING @ Fri, 16 Oct 2020 09:34:42: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Fri, 16 Oct 2020 09:34:42: start model_add_line... INFO @ Fri, 16 Oct 2020 09:34:42: start X-correlation... INFO @ Fri, 16 Oct 2020 09:34:42: end of X-cor INFO @ Fri, 16 Oct 2020 09:34:42: #2 finished! INFO @ Fri, 16 Oct 2020 09:34:42: #2 predicted fragment length is 205 bps INFO @ Fri, 16 Oct 2020 09:34:42: #2 alternative fragment length(s) may be 4,205,224 bps INFO @ Fri, 16 Oct 2020 09:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10_model.r INFO @ Fri, 16 Oct 2020 09:34:42: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:34:44: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:34:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:34:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:34:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.10_summits.bed INFO @ Fri, 16 Oct 2020 09:34:44: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 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 09:34:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.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 09:34:55: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:34:55: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:34:59: 1000000 INFO @ Fri, 16 Oct 2020 09:35:03: 2000000 INFO @ Fri, 16 Oct 2020 09:35:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:35:11: 4000000 INFO @ Fri, 16 Oct 2020 09:35:12: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:35:12: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:35:12: #1 total tags in treatment: 602833 INFO @ Fri, 16 Oct 2020 09:35:12: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:35:12: #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 09:35:12: #1 tags after filtering in treatment: 547247 INFO @ Fri, 16 Oct 2020 09:35:12: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 16 Oct 2020 09:35:12: #1 finished! INFO @ Fri, 16 Oct 2020 09:35:12: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:35:13: #2 number of paired peaks: 469 WARNING @ Fri, 16 Oct 2020 09:35:13: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Fri, 16 Oct 2020 09:35:13: start model_add_line... INFO @ Fri, 16 Oct 2020 09:35:13: start X-correlation... INFO @ Fri, 16 Oct 2020 09:35:13: end of X-cor INFO @ Fri, 16 Oct 2020 09:35:13: #2 finished! INFO @ Fri, 16 Oct 2020 09:35:13: #2 predicted fragment length is 205 bps INFO @ Fri, 16 Oct 2020 09:35:13: #2 alternative fragment length(s) may be 4,205,224 bps INFO @ Fri, 16 Oct 2020 09:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20_model.r INFO @ Fri, 16 Oct 2020 09:35:13: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:35:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:35:14: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952661/SRX8952661.20_summits.bed INFO @ Fri, 16 Oct 2020 09:35:15: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling