Job ID = 5790955 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,060,526 reads read : 4,121,052 reads written : 4,121,052 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: 00:01:30 2060526 reads; of these: 2060526 (100.00%) were paired; of these: 116254 (5.64%) aligned concordantly 0 times 1395106 (67.71%) aligned concordantly exactly 1 time 549166 (26.65%) aligned concordantly >1 times ---- 116254 pairs aligned concordantly 0 times; of these: 5990 (5.15%) aligned discordantly 1 time ---- 110264 pairs aligned 0 times concordantly or discordantly; of these: 220528 mates make up the pairs; of these: 194822 (88.34%) aligned 0 times 13256 (6.01%) aligned exactly 1 time 12450 (5.65%) aligned >1 times 95.27% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 29152 / 1922596 = 0.0152 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 08:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.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 08:10:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:10:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:10:58: 1000000 INFO @ Wed, 22 Apr 2020 08:11:05: 2000000 INFO @ Wed, 22 Apr 2020 08:11:11: 3000000 INFO @ Wed, 22 Apr 2020 08:11:16: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:11:16: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:11:16: #1 total tags in treatment: 1915138 INFO @ Wed, 22 Apr 2020 08:11:16: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:11:16: #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 08:11:16: #1 tags after filtering in treatment: 1550242 INFO @ Wed, 22 Apr 2020 08:11:16: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:11:16: #1 finished! INFO @ Wed, 22 Apr 2020 08:11:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:11:16: #2 number of paired peaks: 186 WARNING @ Wed, 22 Apr 2020 08:11:16: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Wed, 22 Apr 2020 08:11:16: start model_add_line... INFO @ Wed, 22 Apr 2020 08:11:16: start X-correlation... INFO @ Wed, 22 Apr 2020 08:11:16: end of X-cor INFO @ Wed, 22 Apr 2020 08:11:16: #2 finished! INFO @ Wed, 22 Apr 2020 08:11:16: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:11:16: #2 alternative fragment length(s) may be 2,146,172 bps INFO @ Wed, 22 Apr 2020 08:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05_model.r WARNING @ Wed, 22 Apr 2020 08:11:16: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:11:16: #2 You may need to consider one of the other alternative d(s): 2,146,172 WARNING @ Wed, 22 Apr 2020 08:11:16: #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 08:11:16: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:11:16: #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 08:11:20: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:11:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:11:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:11:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.05_summits.bed INFO @ Wed, 22 Apr 2020 08:11:21: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.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 08:11:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:11:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:11:27: 1000000 INFO @ Wed, 22 Apr 2020 08:11:33: 2000000 INFO @ Wed, 22 Apr 2020 08:11:38: 3000000 INFO @ Wed, 22 Apr 2020 08:11:43: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:11:43: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:11:43: #1 total tags in treatment: 1915138 INFO @ Wed, 22 Apr 2020 08:11:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:11:43: #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 08:11:43: #1 tags after filtering in treatment: 1550242 INFO @ Wed, 22 Apr 2020 08:11:43: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:11:43: #1 finished! INFO @ Wed, 22 Apr 2020 08:11:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:11:43: #2 number of paired peaks: 186 WARNING @ Wed, 22 Apr 2020 08:11:43: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Wed, 22 Apr 2020 08:11:43: start model_add_line... INFO @ Wed, 22 Apr 2020 08:11:43: start X-correlation... INFO @ Wed, 22 Apr 2020 08:11:43: end of X-cor INFO @ Wed, 22 Apr 2020 08:11:43: #2 finished! INFO @ Wed, 22 Apr 2020 08:11:43: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:11:43: #2 alternative fragment length(s) may be 2,146,172 bps INFO @ Wed, 22 Apr 2020 08:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10_model.r WARNING @ Wed, 22 Apr 2020 08:11:43: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:11:43: #2 You may need to consider one of the other alternative d(s): 2,146,172 WARNING @ Wed, 22 Apr 2020 08:11:43: #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 08:11:43: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:11:47: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.10_summits.bed INFO @ Wed, 22 Apr 2020 08:11:49: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (192 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 08:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.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 08:11:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:11:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:11:57: 1000000 INFO @ Wed, 22 Apr 2020 08:12:03: 2000000 INFO @ Wed, 22 Apr 2020 08:12:09: 3000000 INFO @ Wed, 22 Apr 2020 08:12:13: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:12:13: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:12:13: #1 total tags in treatment: 1915138 INFO @ Wed, 22 Apr 2020 08:12:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:12:13: #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 08:12:13: #1 tags after filtering in treatment: 1550242 INFO @ Wed, 22 Apr 2020 08:12:13: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Apr 2020 08:12:13: #1 finished! INFO @ Wed, 22 Apr 2020 08:12:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:12:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:12:13: #2 number of paired peaks: 186 WARNING @ Wed, 22 Apr 2020 08:12:13: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Wed, 22 Apr 2020 08:12:13: start model_add_line... INFO @ Wed, 22 Apr 2020 08:12:14: start X-correlation... INFO @ Wed, 22 Apr 2020 08:12:14: end of X-cor INFO @ Wed, 22 Apr 2020 08:12:14: #2 finished! INFO @ Wed, 22 Apr 2020 08:12:14: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:12:14: #2 alternative fragment length(s) may be 2,146,172 bps INFO @ Wed, 22 Apr 2020 08:12:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20_model.r WARNING @ Wed, 22 Apr 2020 08:12:14: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:12:14: #2 You may need to consider one of the other alternative d(s): 2,146,172 WARNING @ Wed, 22 Apr 2020 08:12:14: #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 08:12:14: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:12:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:12:17: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:12:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:12:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:12:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874470/SRX5874470.20_summits.bed INFO @ Wed, 22 Apr 2020 08:12:19: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (78 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。