Job ID = 10224048 SRX = SRX8952605 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14871327 spots for SRR12458281/SRR12458281.sra Written 14871327 spots for SRR12458281/SRR12458281.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: 00:02:24 14871327 reads; of these: 14871327 (100.00%) were paired; of these: 14097076 (94.79%) aligned concordantly 0 times 678533 (4.56%) aligned concordantly exactly 1 time 95718 (0.64%) aligned concordantly >1 times ---- 14097076 pairs aligned concordantly 0 times; of these: 502206 (3.56%) aligned discordantly 1 time ---- 13594870 pairs aligned 0 times concordantly or discordantly; of these: 27189740 mates make up the pairs; of these: 24711540 (90.89%) aligned 0 times 2124224 (7.81%) aligned exactly 1 time 353976 (1.30%) aligned >1 times 16.92% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 588836 / 1254026 = 0.4696 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 09:18:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.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 09:18:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:18:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:18:45: 1000000 INFO @ Fri, 16 Oct 2020 09:18:51: 2000000 INFO @ Fri, 16 Oct 2020 09:18:56: 3000000 INFO @ Fri, 16 Oct 2020 09:19:01: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:19:01: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:19:01: #1 total tags in treatment: 561156 INFO @ Fri, 16 Oct 2020 09:19:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:01: #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 09:19:01: #1 tags after filtering in treatment: 446692 INFO @ Fri, 16 Oct 2020 09:19:01: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:19:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:01: #2 number of paired peaks: 165 WARNING @ Fri, 16 Oct 2020 09:19:01: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:01: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:01: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:01: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:01: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:01: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 09:19:01: #2 alternative fragment length(s) may be 4,243,268 bps INFO @ Fri, 16 Oct 2020 09:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05_model.r INFO @ Fri, 16 Oct 2020 09:19:01: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:19:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.05_summits.bed INFO @ Fri, 16 Oct 2020 09:19:03: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (126 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 09:19:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.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 09:19:09: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:09: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:15: 1000000 INFO @ Fri, 16 Oct 2020 09:19:20: 2000000 INFO @ Fri, 16 Oct 2020 09:19:25: 3000000 INFO @ Fri, 16 Oct 2020 09:19:29: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:19:29: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:19:29: #1 total tags in treatment: 561156 INFO @ Fri, 16 Oct 2020 09:19:29: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:19:29: #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 09:19:29: #1 tags after filtering in treatment: 446692 INFO @ Fri, 16 Oct 2020 09:19:29: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:19:29: #1 finished! INFO @ Fri, 16 Oct 2020 09:19:29: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:19:29: #2 number of paired peaks: 165 WARNING @ Fri, 16 Oct 2020 09:19:29: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 16 Oct 2020 09:19:29: start model_add_line... INFO @ Fri, 16 Oct 2020 09:19:29: start X-correlation... INFO @ Fri, 16 Oct 2020 09:19:29: end of X-cor INFO @ Fri, 16 Oct 2020 09:19:29: #2 finished! INFO @ Fri, 16 Oct 2020 09:19:29: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 09:19:29: #2 alternative fragment length(s) may be 4,243,268 bps INFO @ Fri, 16 Oct 2020 09:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10_model.r INFO @ Fri, 16 Oct 2020 09:19:29: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:19:31: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.10_summits.bed INFO @ Fri, 16 Oct 2020 09:19:31: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (71 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 09:19:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.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 09:19:39: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:19:39: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:19:45: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:19:51: 2000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:19:56: 3000000 INFO @ Fri, 16 Oct 2020 09:20:01: #1 tag size is determined as 44 bps INFO @ Fri, 16 Oct 2020 09:20:01: #1 tag size = 44 INFO @ Fri, 16 Oct 2020 09:20:01: #1 total tags in treatment: 561156 INFO @ Fri, 16 Oct 2020 09:20:01: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:20:01: #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 09:20:01: #1 tags after filtering in treatment: 446692 INFO @ Fri, 16 Oct 2020 09:20:01: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 16 Oct 2020 09:20:01: #1 finished! INFO @ Fri, 16 Oct 2020 09:20:01: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:20:01: #2 number of paired peaks: 165 WARNING @ Fri, 16 Oct 2020 09:20:01: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 16 Oct 2020 09:20:01: start model_add_line... INFO @ Fri, 16 Oct 2020 09:20:01: start X-correlation... INFO @ Fri, 16 Oct 2020 09:20:01: end of X-cor INFO @ Fri, 16 Oct 2020 09:20:01: #2 finished! INFO @ Fri, 16 Oct 2020 09:20:01: #2 predicted fragment length is 268 bps INFO @ Fri, 16 Oct 2020 09:20:01: #2 alternative fragment length(s) may be 4,243,268 bps INFO @ Fri, 16 Oct 2020 09:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20_model.r INFO @ Fri, 16 Oct 2020 09:20:01: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:20:03: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952605/SRX8952605.20_summits.bed INFO @ Fri, 16 Oct 2020 09:20:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 1 millis CompletedMACS2peakCalling