Job ID = 10224107 SRX = SRX8952660 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5506509 spots for SRR12458226/SRR12458226.sra Written 5506509 spots for SRR12458226/SRR12458226.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: 00:11:36 5506509 reads; of these: 5506509 (100.00%) were paired; of these: 4180070 (75.91%) aligned concordantly 0 times 803393 (14.59%) aligned concordantly exactly 1 time 523046 (9.50%) aligned concordantly >1 times ---- 4180070 pairs aligned concordantly 0 times; of these: 3762 (0.09%) aligned discordantly 1 time ---- 4176308 pairs aligned 0 times concordantly or discordantly; of these: 8352616 mates make up the pairs; of these: 3768754 (45.12%) aligned 0 times 1206646 (14.45%) aligned exactly 1 time 3377216 (40.43%) aligned >1 times 65.78% overall alignment rate Time searching: 00:11:36 Overall time: 00:11:36 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] 549484 / 1325344 = 0.4146 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 09:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.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 09:39:47: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:39:47: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:39:51: 1000000 INFO @ Fri, 16 Oct 2020 09:39:55: 2000000 INFO @ Fri, 16 Oct 2020 09:39:59: 3000000 INFO @ Fri, 16 Oct 2020 09:40:02: 4000000 INFO @ Fri, 16 Oct 2020 09:40:06: 5000000 INFO @ Fri, 16 Oct 2020 09:40:10: 6000000 INFO @ Fri, 16 Oct 2020 09:40:11: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:40:11: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:40:11: #1 total tags in treatment: 776962 INFO @ Fri, 16 Oct 2020 09:40:11: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:40:11: #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 09:40:11: #1 tags after filtering in treatment: 617709 INFO @ Fri, 16 Oct 2020 09:40:11: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:40:11: #1 finished! INFO @ Fri, 16 Oct 2020 09:40:11: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:40:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:40:11: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:40:11: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:40:11: start model_add_line... INFO @ Fri, 16 Oct 2020 09:40:11: start X-correlation... INFO @ Fri, 16 Oct 2020 09:40:11: end of X-cor INFO @ Fri, 16 Oct 2020 09:40:11: #2 finished! INFO @ Fri, 16 Oct 2020 09:40:11: #2 predicted fragment length is 216 bps INFO @ Fri, 16 Oct 2020 09:40:11: #2 alternative fragment length(s) may be 3,216,229 bps INFO @ Fri, 16 Oct 2020 09:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05_model.r INFO @ Fri, 16 Oct 2020 09:40:11: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:40:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:40:13: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:40:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:40:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:40:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.05_summits.bed INFO @ Fri, 16 Oct 2020 09:40:14: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (183 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 09:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.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 09:40:17: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:40:17: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:40:21: 1000000 INFO @ Fri, 16 Oct 2020 09:40:26: 2000000 INFO @ Fri, 16 Oct 2020 09:40:31: 3000000 INFO @ Fri, 16 Oct 2020 09:40:35: 4000000 INFO @ Fri, 16 Oct 2020 09:40:39: 5000000 INFO @ Fri, 16 Oct 2020 09:40:43: 6000000 INFO @ Fri, 16 Oct 2020 09:40:44: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:40:44: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:40:44: #1 total tags in treatment: 776962 INFO @ Fri, 16 Oct 2020 09:40:44: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:40:44: #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 09:40:44: #1 tags after filtering in treatment: 617709 INFO @ Fri, 16 Oct 2020 09:40:44: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:40:44: #1 finished! INFO @ Fri, 16 Oct 2020 09:40:44: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:40:44: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:40:44: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:40:44: start model_add_line... INFO @ Fri, 16 Oct 2020 09:40:44: start X-correlation... INFO @ Fri, 16 Oct 2020 09:40:44: end of X-cor INFO @ Fri, 16 Oct 2020 09:40:44: #2 finished! INFO @ Fri, 16 Oct 2020 09:40:44: #2 predicted fragment length is 216 bps INFO @ Fri, 16 Oct 2020 09:40:44: #2 alternative fragment length(s) may be 3,216,229 bps INFO @ Fri, 16 Oct 2020 09:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10_model.r INFO @ Fri, 16 Oct 2020 09:40:44: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:40:44: #3 Pre-compute pvalue-qvalue table... 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 09:40:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.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 09:40:47: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:40:47: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:40:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:40:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:40:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.10_summits.bed INFO @ Fri, 16 Oct 2020 09:40:47: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:40:51: 1000000 INFO @ Fri, 16 Oct 2020 09:40:56: 2000000 INFO @ Fri, 16 Oct 2020 09:41:01: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:41:05: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:41:10: 5000000 INFO @ Fri, 16 Oct 2020 09:41:15: 6000000 INFO @ Fri, 16 Oct 2020 09:41:16: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:41:16: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:41:16: #1 total tags in treatment: 776962 INFO @ Fri, 16 Oct 2020 09:41:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:41:16: #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 09:41:16: #1 tags after filtering in treatment: 617709 INFO @ Fri, 16 Oct 2020 09:41:16: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:41:16: #1 finished! INFO @ Fri, 16 Oct 2020 09:41:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:41:16: #2 number of paired peaks: 229 WARNING @ Fri, 16 Oct 2020 09:41:16: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 16 Oct 2020 09:41:16: start model_add_line... INFO @ Fri, 16 Oct 2020 09:41:16: start X-correlation... INFO @ Fri, 16 Oct 2020 09:41:16: end of X-cor INFO @ Fri, 16 Oct 2020 09:41:16: #2 finished! INFO @ Fri, 16 Oct 2020 09:41:16: #2 predicted fragment length is 216 bps INFO @ Fri, 16 Oct 2020 09:41:16: #2 alternative fragment length(s) may be 3,216,229 bps INFO @ Fri, 16 Oct 2020 09:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20_model.r INFO @ Fri, 16 Oct 2020 09:41:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:41:18: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952660/SRX8952660.20_summits.bed INFO @ Fri, 16 Oct 2020 09:41:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 1 millis CompletedMACS2peakCalling