Job ID = 7105060 SRX = SRX6911530 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5340513 spots for SRR10191141/SRR10191141.sra Written 5340513 spots for SRR10191141/SRR10191141.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: 00:02:41 5340513 reads; of these: 5340513 (100.00%) were paired; of these: 4231558 (79.24%) aligned concordantly 0 times 597530 (11.19%) aligned concordantly exactly 1 time 511425 (9.58%) aligned concordantly >1 times ---- 4231558 pairs aligned concordantly 0 times; of these: 141625 (3.35%) aligned discordantly 1 time ---- 4089933 pairs aligned 0 times concordantly or discordantly; of these: 8179866 mates make up the pairs; of these: 7688645 (93.99%) aligned 0 times 98722 (1.21%) aligned exactly 1 time 392499 (4.80%) aligned >1 times 28.02% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 505697 / 1250382 = 0.4044 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 @ Wed, 22 Jul 2020 12:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.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 @ Wed, 22 Jul 2020 12:39:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:39:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:39:49: 1000000 INFO @ Wed, 22 Jul 2020 12:39:54: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:39:54: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:39:54: #1 total tags in treatment: 652378 INFO @ Wed, 22 Jul 2020 12:39:54: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:39:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:39:54: #1 tags after filtering in treatment: 330993 INFO @ Wed, 22 Jul 2020 12:39:54: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Jul 2020 12:39:54: #1 finished! INFO @ Wed, 22 Jul 2020 12:39:54: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:39:54: #2 number of paired peaks: 274 WARNING @ Wed, 22 Jul 2020 12:39:54: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Wed, 22 Jul 2020 12:39:54: start model_add_line... INFO @ Wed, 22 Jul 2020 12:39:54: start X-correlation... INFO @ Wed, 22 Jul 2020 12:39:54: end of X-cor INFO @ Wed, 22 Jul 2020 12:39:54: #2 finished! INFO @ Wed, 22 Jul 2020 12:39:54: #2 predicted fragment length is 269 bps INFO @ Wed, 22 Jul 2020 12:39:54: #2 alternative fragment length(s) may be 3,208,230,267,269,297,318 bps INFO @ Wed, 22 Jul 2020 12:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05_model.r INFO @ Wed, 22 Jul 2020 12:39:54: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:39:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:39:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:39:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:39:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.05_summits.bed INFO @ Wed, 22 Jul 2020 12:39:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (173 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 @ Wed, 22 Jul 2020 12:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.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 @ Wed, 22 Jul 2020 12:40:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:40:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:40:20: 1000000 INFO @ Wed, 22 Jul 2020 12:40:26: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:40:26: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:40:26: #1 total tags in treatment: 652378 INFO @ Wed, 22 Jul 2020 12:40:26: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:40:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:40:26: #1 tags after filtering in treatment: 330993 INFO @ Wed, 22 Jul 2020 12:40:26: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Jul 2020 12:40:26: #1 finished! INFO @ Wed, 22 Jul 2020 12:40:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:40:26: #2 number of paired peaks: 274 WARNING @ Wed, 22 Jul 2020 12:40:26: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Wed, 22 Jul 2020 12:40:26: start model_add_line... INFO @ Wed, 22 Jul 2020 12:40:26: start X-correlation... INFO @ Wed, 22 Jul 2020 12:40:26: end of X-cor INFO @ Wed, 22 Jul 2020 12:40:26: #2 finished! INFO @ Wed, 22 Jul 2020 12:40:26: #2 predicted fragment length is 269 bps INFO @ Wed, 22 Jul 2020 12:40:26: #2 alternative fragment length(s) may be 3,208,230,267,269,297,318 bps INFO @ Wed, 22 Jul 2020 12:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10_model.r INFO @ Wed, 22 Jul 2020 12:40:26: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:40:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.10_summits.bed INFO @ Wed, 22 Jul 2020 12:40:28: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (52 records, 4 fields): 3 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 @ Wed, 22 Jul 2020 12:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.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 @ Wed, 22 Jul 2020 12:40:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:40:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:40:50: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:40:56: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:40:56: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:40:56: #1 total tags in treatment: 652378 INFO @ Wed, 22 Jul 2020 12:40:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:40:57: #1 tags after filtering in treatment: 330993 INFO @ Wed, 22 Jul 2020 12:40:57: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Jul 2020 12:40:57: #1 finished! INFO @ Wed, 22 Jul 2020 12:40:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:40:57: #2 number of paired peaks: 274 WARNING @ Wed, 22 Jul 2020 12:40:57: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Wed, 22 Jul 2020 12:40:57: start model_add_line... INFO @ Wed, 22 Jul 2020 12:40:57: start X-correlation... INFO @ Wed, 22 Jul 2020 12:40:57: end of X-cor INFO @ Wed, 22 Jul 2020 12:40:57: #2 finished! INFO @ Wed, 22 Jul 2020 12:40:57: #2 predicted fragment length is 269 bps INFO @ Wed, 22 Jul 2020 12:40:57: #2 alternative fragment length(s) may be 3,208,230,267,269,297,318 bps INFO @ Wed, 22 Jul 2020 12:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20_model.r INFO @ Wed, 22 Jul 2020 12:40:57: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:40:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911530/SRX6911530.20_summits.bed INFO @ Wed, 22 Jul 2020 12:40:58: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 3 millis CompletedMACS2peakCalling