Job ID = 10224094 SRX = SRX8952649 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12515750 spots for SRR12458237/SRR12458237.sra Written 12515750 spots for SRR12458237/SRR12458237.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: 00:01:31 12515750 reads; of these: 12515750 (100.00%) were paired; of these: 12283337 (98.14%) aligned concordantly 0 times 198454 (1.59%) aligned concordantly exactly 1 time 33959 (0.27%) aligned concordantly >1 times ---- 12283337 pairs aligned concordantly 0 times; of these: 490368 (3.99%) aligned discordantly 1 time ---- 11792969 pairs aligned 0 times concordantly or discordantly; of these: 23585938 mates make up the pairs; of these: 22034554 (93.42%) aligned 0 times 1353168 (5.74%) aligned exactly 1 time 198216 (0.84%) aligned >1 times 11.97% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 380667 / 679977 = 0.5598 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 09:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.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 09:26:16: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:16: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:21: 1000000 INFO @ Fri, 16 Oct 2020 09:26:27: 2000000 INFO @ Fri, 16 Oct 2020 09:26:28: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:26:28: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:26:28: #1 total tags in treatment: 205546 INFO @ Fri, 16 Oct 2020 09:26:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:28: #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 09:26:28: #1 tags after filtering in treatment: 191911 INFO @ Fri, 16 Oct 2020 09:26:28: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:26:28: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:28: #2 number of paired peaks: 306 WARNING @ Fri, 16 Oct 2020 09:26:28: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:28: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:28: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:28: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:28: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:28: #2 predicted fragment length is 301 bps INFO @ Fri, 16 Oct 2020 09:26:28: #2 alternative fragment length(s) may be 301 bps INFO @ Fri, 16 Oct 2020 09:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05_model.r INFO @ Fri, 16 Oct 2020 09:26:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:26:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.05_summits.bed INFO @ Fri, 16 Oct 2020 09:26:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (244 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 09:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.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 09:26:46: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:26:46: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:26:51: 1000000 INFO @ Fri, 16 Oct 2020 09:26:56: 2000000 INFO @ Fri, 16 Oct 2020 09:26:58: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:26:58: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:26:58: #1 total tags in treatment: 205546 INFO @ Fri, 16 Oct 2020 09:26:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:26:58: #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 09:26:58: #1 tags after filtering in treatment: 191911 INFO @ Fri, 16 Oct 2020 09:26:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:26:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:26:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:26:58: #2 number of paired peaks: 306 WARNING @ Fri, 16 Oct 2020 09:26:58: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 16 Oct 2020 09:26:58: start model_add_line... INFO @ Fri, 16 Oct 2020 09:26:58: start X-correlation... INFO @ Fri, 16 Oct 2020 09:26:58: end of X-cor INFO @ Fri, 16 Oct 2020 09:26:58: #2 finished! INFO @ Fri, 16 Oct 2020 09:26:58: #2 predicted fragment length is 301 bps INFO @ Fri, 16 Oct 2020 09:26:58: #2 alternative fragment length(s) may be 301 bps INFO @ Fri, 16 Oct 2020 09:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10_model.r INFO @ Fri, 16 Oct 2020 09:26:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:26:59: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.10_summits.bed INFO @ Fri, 16 Oct 2020 09:26:59: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 1 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 09:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.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 09:27:16: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:16: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:21: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:27:27: 2000000 INFO @ Fri, 16 Oct 2020 09:27:28: #1 tag size is determined as 45 bps INFO @ Fri, 16 Oct 2020 09:27:28: #1 tag size = 45 INFO @ Fri, 16 Oct 2020 09:27:28: #1 total tags in treatment: 205546 INFO @ Fri, 16 Oct 2020 09:27:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:27:28: #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 09:27:28: #1 tags after filtering in treatment: 191911 INFO @ Fri, 16 Oct 2020 09:27:28: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:27:28: #1 finished! INFO @ Fri, 16 Oct 2020 09:27:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:27:28: #2 number of paired peaks: 306 WARNING @ Fri, 16 Oct 2020 09:27:28: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Fri, 16 Oct 2020 09:27:28: start model_add_line... INFO @ Fri, 16 Oct 2020 09:27:28: start X-correlation... INFO @ Fri, 16 Oct 2020 09:27:28: end of X-cor INFO @ Fri, 16 Oct 2020 09:27:28: #2 finished! INFO @ Fri, 16 Oct 2020 09:27:28: #2 predicted fragment length is 301 bps INFO @ Fri, 16 Oct 2020 09:27:28: #2 alternative fragment length(s) may be 301 bps INFO @ Fri, 16 Oct 2020 09:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20_model.r INFO @ Fri, 16 Oct 2020 09:27:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:27:29: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952649/SRX8952649.20_summits.bed INFO @ Fri, 16 Oct 2020 09:27:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 1 millis CompletedMACS2peakCalling