Job ID = 5791072 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,880,970 reads read : 5,761,940 reads written : 5,761,940 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: 00:01:05 2880970 reads; of these: 2880970 (100.00%) were paired; of these: 921055 (31.97%) aligned concordantly 0 times 1685476 (58.50%) aligned concordantly exactly 1 time 274439 (9.53%) aligned concordantly >1 times ---- 921055 pairs aligned concordantly 0 times; of these: 13662 (1.48%) aligned discordantly 1 time ---- 907393 pairs aligned 0 times concordantly or discordantly; of these: 1814786 mates make up the pairs; of these: 1165929 (64.25%) aligned 0 times 546597 (30.12%) aligned exactly 1 time 102260 (5.63%) aligned >1 times 79.76% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 664153 / 1970680 = 0.3370 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 08:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.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 08:29:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:26: 1000000 INFO @ Wed, 22 Apr 2020 08:29:30: 2000000 INFO @ Wed, 22 Apr 2020 08:29:34: 3000000 INFO @ Wed, 22 Apr 2020 08:29:35: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2020 08:29:35: #1 tag size = 39 INFO @ Wed, 22 Apr 2020 08:29:35: #1 total tags in treatment: 1299754 INFO @ Wed, 22 Apr 2020 08:29:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:29:35: #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 08:29:35: #1 tags after filtering in treatment: 1160632 INFO @ Wed, 22 Apr 2020 08:29:35: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:29:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:29:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:29:35: #2 number of paired peaks: 105 WARNING @ Wed, 22 Apr 2020 08:29:35: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 22 Apr 2020 08:29:35: start model_add_line... INFO @ Wed, 22 Apr 2020 08:29:35: start X-correlation... INFO @ Wed, 22 Apr 2020 08:29:35: end of X-cor INFO @ Wed, 22 Apr 2020 08:29:35: #2 finished! INFO @ Wed, 22 Apr 2020 08:29:35: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:29:35: #2 alternative fragment length(s) may be 2,17,33,594 bps INFO @ Wed, 22 Apr 2020 08:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05_model.r WARNING @ Wed, 22 Apr 2020 08:29:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:29:35: #2 You may need to consider one of the other alternative d(s): 2,17,33,594 WARNING @ Wed, 22 Apr 2020 08:29:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:29:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:29:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:29:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:29:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:29:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.05_summits.bed INFO @ Wed, 22 Apr 2020 08:29:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 @ Wed, 22 Apr 2020 08:29:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.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 08:29:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:29:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:29:57: 1000000 INFO @ Wed, 22 Apr 2020 08:30:01: 2000000 INFO @ Wed, 22 Apr 2020 08:30:05: 3000000 INFO @ Wed, 22 Apr 2020 08:30:06: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2020 08:30:06: #1 tag size = 39 INFO @ Wed, 22 Apr 2020 08:30:06: #1 total tags in treatment: 1299754 INFO @ Wed, 22 Apr 2020 08:30:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:30:06: #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 08:30:06: #1 tags after filtering in treatment: 1160632 INFO @ Wed, 22 Apr 2020 08:30:06: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:30:06: #1 finished! INFO @ Wed, 22 Apr 2020 08:30:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:30:06: #2 number of paired peaks: 105 WARNING @ Wed, 22 Apr 2020 08:30:06: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 22 Apr 2020 08:30:06: start model_add_line... INFO @ Wed, 22 Apr 2020 08:30:06: start X-correlation... INFO @ Wed, 22 Apr 2020 08:30:06: end of X-cor INFO @ Wed, 22 Apr 2020 08:30:06: #2 finished! INFO @ Wed, 22 Apr 2020 08:30:06: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:30:06: #2 alternative fragment length(s) may be 2,17,33,594 bps INFO @ Wed, 22 Apr 2020 08:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10_model.r WARNING @ Wed, 22 Apr 2020 08:30:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:30:06: #2 You may need to consider one of the other alternative d(s): 2,17,33,594 WARNING @ Wed, 22 Apr 2020 08:30:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:30:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:30:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.10_summits.bed INFO @ Wed, 22 Apr 2020 08:30:09: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 @ Wed, 22 Apr 2020 08:30:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.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 08:30:22: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:30:22: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:30:26: 1000000 INFO @ Wed, 22 Apr 2020 08:30:30: 2000000 INFO @ Wed, 22 Apr 2020 08:30:34: 3000000 INFO @ Wed, 22 Apr 2020 08:30:35: #1 tag size is determined as 39 bps INFO @ Wed, 22 Apr 2020 08:30:35: #1 tag size = 39 INFO @ Wed, 22 Apr 2020 08:30:35: #1 total tags in treatment: 1299754 INFO @ Wed, 22 Apr 2020 08:30:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:30:35: #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 08:30:35: #1 tags after filtering in treatment: 1160632 INFO @ Wed, 22 Apr 2020 08:30:35: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 22 Apr 2020 08:30:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:30:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:30:35: #2 number of paired peaks: 105 WARNING @ Wed, 22 Apr 2020 08:30:35: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 22 Apr 2020 08:30:35: start model_add_line... INFO @ Wed, 22 Apr 2020 08:30:35: start X-correlation... INFO @ Wed, 22 Apr 2020 08:30:35: end of X-cor INFO @ Wed, 22 Apr 2020 08:30:35: #2 finished! INFO @ Wed, 22 Apr 2020 08:30:35: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:30:35: #2 alternative fragment length(s) may be 2,17,33,594 bps INFO @ Wed, 22 Apr 2020 08:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20_model.r WARNING @ Wed, 22 Apr 2020 08:30:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:30:35: #2 You may need to consider one of the other alternative d(s): 2,17,33,594 WARNING @ Wed, 22 Apr 2020 08:30:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:30:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:30:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5883295/SRX5883295.20_summits.bed INFO @ Wed, 22 Apr 2020 08:30:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。