Job ID = 5790964 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,121,853 reads read : 4,243,706 reads written : 4,243,706 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:36 2121853 reads; of these: 2121853 (100.00%) were paired; of these: 113787 (5.36%) aligned concordantly 0 times 1591537 (75.01%) aligned concordantly exactly 1 time 416529 (19.63%) aligned concordantly >1 times ---- 113787 pairs aligned concordantly 0 times; of these: 844 (0.74%) aligned discordantly 1 time ---- 112943 pairs aligned 0 times concordantly or discordantly; of these: 225886 mates make up the pairs; of these: 210972 (93.40%) aligned 0 times 10212 (4.52%) aligned exactly 1 time 4702 (2.08%) aligned >1 times 95.03% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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] 27832 / 2006548 = 0.0139 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 Apr 2020 08:12:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.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 Apr 2020 08:12:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:51: 1000000 INFO @ Wed, 22 Apr 2020 08:12:58: 2000000 INFO @ Wed, 22 Apr 2020 08:13:05: 3000000 INFO @ Wed, 22 Apr 2020 08:13:10: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:10: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:10: #1 total tags in treatment: 1980236 INFO @ Wed, 22 Apr 2020 08:13:10: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:13:10: #1 tags after filtering in treatment: 1729608 INFO @ Wed, 22 Apr 2020 08:13:10: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:13:10: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:10: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:10: #2 number of paired peaks: 141 WARNING @ Wed, 22 Apr 2020 08:13:10: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:10: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:10: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:10: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:10: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:10: #2 predicted fragment length is 151 bps INFO @ Wed, 22 Apr 2020 08:13:10: #2 alternative fragment length(s) may be 2,106,109,118,151,186,559 bps INFO @ Wed, 22 Apr 2020 08:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05_model.r INFO @ Wed, 22 Apr 2020 08:13:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:10: #3 Pre-compute pvalue-qvalue table... 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 Apr 2020 08:13:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.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 Apr 2020 08:13:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:15: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.05_summits.bed INFO @ Wed, 22 Apr 2020 08:13:16: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (340 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:19: 1000000 INFO @ Wed, 22 Apr 2020 08:13:25: 2000000 INFO @ Wed, 22 Apr 2020 08:13:31: 3000000 INFO @ Wed, 22 Apr 2020 08:13:36: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:36: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:36: #1 total tags in treatment: 1980236 INFO @ Wed, 22 Apr 2020 08:13:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:13:36: #1 tags after filtering in treatment: 1729608 INFO @ Wed, 22 Apr 2020 08:13:36: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:13:36: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:37: #2 number of paired peaks: 141 WARNING @ Wed, 22 Apr 2020 08:13:37: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:37: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:37: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:37: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:37: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:37: #2 predicted fragment length is 151 bps INFO @ Wed, 22 Apr 2020 08:13:37: #2 alternative fragment length(s) may be 2,106,109,118,151,186,559 bps INFO @ Wed, 22 Apr 2020 08:13:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10_model.r INFO @ Wed, 22 Apr 2020 08:13:37: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:41: #3 Call peaks for each chromosome... 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 Apr 2020 08:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.10_summits.bed INFO @ Wed, 22 Apr 2020 08:13:42: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.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 Apr 2020 08:13:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:50: 1000000 INFO @ Wed, 22 Apr 2020 08:13:55: 2000000 INFO @ Wed, 22 Apr 2020 08:14:01: 3000000 INFO @ Wed, 22 Apr 2020 08:14:07: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:07: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:07: #1 total tags in treatment: 1980236 INFO @ Wed, 22 Apr 2020 08:14:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:14:07: #1 tags after filtering in treatment: 1729608 INFO @ Wed, 22 Apr 2020 08:14:07: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 08:14:07: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:07: #2 number of paired peaks: 141 WARNING @ Wed, 22 Apr 2020 08:14:07: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:07: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:07: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:07: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:07: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:07: #2 predicted fragment length is 151 bps INFO @ Wed, 22 Apr 2020 08:14:07: #2 alternative fragment length(s) may be 2,106,109,118,151,186,559 bps INFO @ Wed, 22 Apr 2020 08:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20_model.r INFO @ Wed, 22 Apr 2020 08:14:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874476/SRX5874476.20_summits.bed INFO @ Wed, 22 Apr 2020 08:14:12: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。