Job ID = 5791230 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,138,787 reads read : 6,277,574 reads written : 6,277,574 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: 00:03:18 3138787 reads; of these: 3138787 (100.00%) were paired; of these: 305131 (9.72%) aligned concordantly 0 times 2549493 (81.23%) aligned concordantly exactly 1 time 284163 (9.05%) aligned concordantly >1 times ---- 305131 pairs aligned concordantly 0 times; of these: 108761 (35.64%) aligned discordantly 1 time ---- 196370 pairs aligned 0 times concordantly or discordantly; of these: 392740 mates make up the pairs; of these: 319071 (81.24%) aligned 0 times 44244 (11.27%) aligned exactly 1 time 29425 (7.49%) aligned >1 times 94.92% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 2327277 / 2935341 = 0.7928 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 09:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.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 09:17:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:17:41: 1000000 INFO @ Wed, 22 Apr 2020 09:17:43: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:17:43: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:17:43: #1 total tags in treatment: 583621 INFO @ Wed, 22 Apr 2020 09:17:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:17:43: #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 09:17:43: #1 tags after filtering in treatment: 513598 INFO @ Wed, 22 Apr 2020 09:17:43: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:17:43: #1 finished! INFO @ Wed, 22 Apr 2020 09:17:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:17:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:17:43: #2 number of paired peaks: 188 WARNING @ Wed, 22 Apr 2020 09:17:43: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Wed, 22 Apr 2020 09:17:43: start model_add_line... INFO @ Wed, 22 Apr 2020 09:17:43: start X-correlation... INFO @ Wed, 22 Apr 2020 09:17:43: end of X-cor INFO @ Wed, 22 Apr 2020 09:17:43: #2 finished! INFO @ Wed, 22 Apr 2020 09:17:43: #2 predicted fragment length is 190 bps INFO @ Wed, 22 Apr 2020 09:17:43: #2 alternative fragment length(s) may be 3,190,546,564 bps INFO @ Wed, 22 Apr 2020 09:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05_model.r WARNING @ Wed, 22 Apr 2020 09:17:43: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:17:43: #2 You may need to consider one of the other alternative d(s): 3,190,546,564 WARNING @ Wed, 22 Apr 2020 09:17:43: #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 09:17:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:17:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.05_summits.bed INFO @ Wed, 22 Apr 2020 09:17:45: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (41 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 @ Wed, 22 Apr 2020 09:18:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.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 09:18:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:10: 1000000 INFO @ Wed, 22 Apr 2020 09:18:12: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:18:12: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:18:12: #1 total tags in treatment: 583621 INFO @ Wed, 22 Apr 2020 09:18:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:12: #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 09:18:12: #1 tags after filtering in treatment: 513598 INFO @ Wed, 22 Apr 2020 09:18:12: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:18:12: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:12: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:12: #2 number of paired peaks: 188 WARNING @ Wed, 22 Apr 2020 09:18:12: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:12: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:12: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:12: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:12: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:12: #2 predicted fragment length is 190 bps INFO @ Wed, 22 Apr 2020 09:18:12: #2 alternative fragment length(s) may be 3,190,546,564 bps INFO @ Wed, 22 Apr 2020 09:18:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10_model.r WARNING @ Wed, 22 Apr 2020 09:18:12: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:18:12: #2 You may need to consider one of the other alternative d(s): 3,190,546,564 WARNING @ Wed, 22 Apr 2020 09:18:12: #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 09:18:12: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.10_summits.bed INFO @ Wed, 22 Apr 2020 09:18:14: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (23 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 @ Wed, 22 Apr 2020 09:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.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 09:18:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:40: 1000000 INFO @ Wed, 22 Apr 2020 09:18:42: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:18:42: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:18:42: #1 total tags in treatment: 583621 INFO @ Wed, 22 Apr 2020 09:18:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:42: #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 09:18:42: #1 tags after filtering in treatment: 513598 INFO @ Wed, 22 Apr 2020 09:18:42: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:18:42: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:42: #2 number of paired peaks: 188 WARNING @ Wed, 22 Apr 2020 09:18:42: Fewer paired peaks (188) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 188 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:42: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:42: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:42: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:42: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:42: #2 predicted fragment length is 190 bps INFO @ Wed, 22 Apr 2020 09:18:42: #2 alternative fragment length(s) may be 3,190,546,564 bps INFO @ Wed, 22 Apr 2020 09:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20_model.r WARNING @ Wed, 22 Apr 2020 09:18:42: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:18:42: #2 You may need to consider one of the other alternative d(s): 3,190,546,564 WARNING @ Wed, 22 Apr 2020 09:18:42: #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 09:18:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:44: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255996/SRX7255996.20_summits.bed INFO @ Wed, 22 Apr 2020 09:18:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (10 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。