Job ID = 10224111 SRX = SRX8952664 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4909918 spots for SRR12458222/SRR12458222.sra Written 4909918 spots for SRR12458222/SRR12458222.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: 00:01:49 4909918 reads; of these: 4909918 (100.00%) were paired; of these: 2901719 (59.10%) aligned concordantly 0 times 1611728 (32.83%) aligned concordantly exactly 1 time 396471 (8.07%) aligned concordantly >1 times ---- 2901719 pairs aligned concordantly 0 times; of these: 393315 (13.55%) aligned discordantly 1 time ---- 2508404 pairs aligned 0 times concordantly or discordantly; of these: 5016808 mates make up the pairs; of these: 3828613 (76.32%) aligned 0 times 903808 (18.02%) aligned exactly 1 time 284387 (5.67%) aligned >1 times 61.01% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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] 439859 / 2197397 = 0.2002 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 09:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.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 09:30:31: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:31: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:36: 1000000 INFO @ Fri, 16 Oct 2020 09:30:40: 2000000 INFO @ Fri, 16 Oct 2020 09:30:45: 3000000 INFO @ Fri, 16 Oct 2020 09:30:49: 4000000 INFO @ Fri, 16 Oct 2020 09:30:54: 5000000 INFO @ Fri, 16 Oct 2020 09:30:54: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:30:54: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:30:54: #1 total tags in treatment: 1650714 INFO @ Fri, 16 Oct 2020 09:30:54: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:54: #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 09:30:55: #1 tags after filtering in treatment: 1363778 INFO @ Fri, 16 Oct 2020 09:30:55: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:30:55: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:55: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:55: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:30:55: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:55: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:55: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:55: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:55: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:55: #2 predicted fragment length is 213 bps INFO @ Fri, 16 Oct 2020 09:30:55: #2 alternative fragment length(s) may be 1,178,196,213,552,580 bps INFO @ Fri, 16 Oct 2020 09:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05_model.r INFO @ Fri, 16 Oct 2020 09:30:55: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:30:58: #3 Call peaks for each chromosome... 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 09:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.05_summits.bed INFO @ Fri, 16 Oct 2020 09:31:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.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 09:31:01: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:01: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:06: 1000000 INFO @ Fri, 16 Oct 2020 09:31:11: 2000000 INFO @ Fri, 16 Oct 2020 09:31:16: 3000000 INFO @ Fri, 16 Oct 2020 09:31:21: 4000000 INFO @ Fri, 16 Oct 2020 09:31:26: 5000000 INFO @ Fri, 16 Oct 2020 09:31:26: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:31:26: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:31:26: #1 total tags in treatment: 1650714 INFO @ Fri, 16 Oct 2020 09:31:26: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:26: #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 09:31:26: #1 tags after filtering in treatment: 1363778 INFO @ Fri, 16 Oct 2020 09:31:26: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:31:26: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:26: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:26: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:31:26: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:26: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:26: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:26: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:26: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:26: #2 predicted fragment length is 213 bps INFO @ Fri, 16 Oct 2020 09:31:26: #2 alternative fragment length(s) may be 1,178,196,213,552,580 bps INFO @ Fri, 16 Oct 2020 09:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10_model.r INFO @ Fri, 16 Oct 2020 09:31:26: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:26: #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 09:31:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:31:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:31:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:31:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.10_summits.bed INFO @ Fri, 16 Oct 2020 09:31:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.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 09:31:31: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:31:31: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:31:36: 1000000 INFO @ Fri, 16 Oct 2020 09:31:41: 2000000 INFO @ Fri, 16 Oct 2020 09:31:47: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:31:52: 4000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:31:57: 5000000 INFO @ Fri, 16 Oct 2020 09:31:58: #1 tag size is determined as 40 bps INFO @ Fri, 16 Oct 2020 09:31:58: #1 tag size = 40 INFO @ Fri, 16 Oct 2020 09:31:58: #1 total tags in treatment: 1650714 INFO @ Fri, 16 Oct 2020 09:31:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:31:58: #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 09:31:58: #1 tags after filtering in treatment: 1363778 INFO @ Fri, 16 Oct 2020 09:31:58: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 16 Oct 2020 09:31:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:31:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:31:58: #2 number of paired peaks: 184 WARNING @ Fri, 16 Oct 2020 09:31:58: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Fri, 16 Oct 2020 09:31:58: start model_add_line... INFO @ Fri, 16 Oct 2020 09:31:58: start X-correlation... INFO @ Fri, 16 Oct 2020 09:31:58: end of X-cor INFO @ Fri, 16 Oct 2020 09:31:58: #2 finished! INFO @ Fri, 16 Oct 2020 09:31:58: #2 predicted fragment length is 213 bps INFO @ Fri, 16 Oct 2020 09:31:58: #2 alternative fragment length(s) may be 1,178,196,213,552,580 bps INFO @ Fri, 16 Oct 2020 09:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20_model.r INFO @ Fri, 16 Oct 2020 09:31:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:32:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952664/SRX8952664.20_summits.bed INFO @ Fri, 16 Oct 2020 09:32:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling