Job ID = 10224097 SRX = SRX8952652 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9011264 spots for SRR12458234/SRR12458234.sra Written 9011264 spots for SRR12458234/SRR12458234.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: 00:01:02 9011264 reads; of these: 9011264 (100.00%) were paired; of these: 8437892 (93.64%) aligned concordantly 0 times 508499 (5.64%) aligned concordantly exactly 1 time 64873 (0.72%) aligned concordantly >1 times ---- 8437892 pairs aligned concordantly 0 times; of these: 49019 (0.58%) aligned discordantly 1 time ---- 8388873 pairs aligned 0 times concordantly or discordantly; of these: 16777746 mates make up the pairs; of these: 16420583 (97.87%) aligned 0 times 289528 (1.73%) aligned exactly 1 time 67635 (0.40%) aligned >1 times 8.89% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 54422 / 618079 = 0.0881 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 09:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.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 09:26:59: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:59: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:05: 1000000 INFO @ Fri, 16 Oct 2020 09:27:07: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:27:07: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:27:07: #1 total tags in treatment: 528332 INFO @ Fri, 16 Oct 2020 09:27:07: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:07: #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 09:27:07: #1 tags after filtering in treatment: 494526 INFO @ Fri, 16 Oct 2020 09:27:07: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:27:07: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:07: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:07: #2 number of paired peaks: 199 WARNING @ Fri, 16 Oct 2020 09:27:07: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:07: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:07: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:07: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:07: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:07: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 09:27:07: #2 alternative fragment length(s) may be 4,190,211,222 bps INFO @ Fri, 16 Oct 2020 09:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05_model.r INFO @ Fri, 16 Oct 2020 09:27:07: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.05_summits.bed INFO @ Fri, 16 Oct 2020 09:27:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (134 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 09:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.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 09:27:29: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:29: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:34: 1000000 INFO @ Fri, 16 Oct 2020 09:27:37: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:27:37: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:27:37: #1 total tags in treatment: 528332 INFO @ Fri, 16 Oct 2020 09:27:37: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:37: #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 09:27:37: #1 tags after filtering in treatment: 494526 INFO @ Fri, 16 Oct 2020 09:27:37: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:27:37: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:37: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:37: #2 number of paired peaks: 199 WARNING @ Fri, 16 Oct 2020 09:27:37: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:37: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:37: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:37: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:37: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:37: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 09:27:37: #2 alternative fragment length(s) may be 4,190,211,222 bps INFO @ Fri, 16 Oct 2020 09:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10_model.r INFO @ Fri, 16 Oct 2020 09:27:37: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.10_summits.bed INFO @ Fri, 16 Oct 2020 09:27:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (74 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 09:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.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 09:27:59: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:59: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:28:04: 1000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:28:07: #1 tag size is determined as 34 bps INFO @ Fri, 16 Oct 2020 09:28:07: #1 tag size = 34 INFO @ Fri, 16 Oct 2020 09:28:07: #1 total tags in treatment: 528332 INFO @ Fri, 16 Oct 2020 09:28:07: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:07: #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 09:28:07: #1 tags after filtering in treatment: 494526 INFO @ Fri, 16 Oct 2020 09:28:07: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 16 Oct 2020 09:28:07: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:07: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:07: #2 number of paired peaks: 199 WARNING @ Fri, 16 Oct 2020 09:28:07: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:07: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:07: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:07: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:07: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:07: #2 predicted fragment length is 211 bps INFO @ Fri, 16 Oct 2020 09:28:07: #2 alternative fragment length(s) may be 4,190,211,222 bps INFO @ Fri, 16 Oct 2020 09:28:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20_model.r INFO @ Fri, 16 Oct 2020 09:28:07: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952652/SRX8952652.20_summits.bed INFO @ Fri, 16 Oct 2020 09:28:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling