Job ID = 5791233 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,585,865 reads read : 7,171,730 reads written : 7,171,730 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: 00:00:41 3585865 reads; of these: 3585865 (100.00%) were paired; of these: 3423997 (95.49%) aligned concordantly 0 times 129970 (3.62%) aligned concordantly exactly 1 time 31898 (0.89%) aligned concordantly >1 times ---- 3423997 pairs aligned concordantly 0 times; of these: 21636 (0.63%) aligned discordantly 1 time ---- 3402361 pairs aligned 0 times concordantly or discordantly; of these: 6804722 mates make up the pairs; of these: 6740583 (99.06%) aligned 0 times 53434 (0.79%) aligned exactly 1 time 10705 (0.16%) aligned >1 times 6.01% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 101173 / 182972 = 0.5529 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 09:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.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 09:13:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:56: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:13:56: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:13:56: #1 total tags in treatment: 69630 INFO @ Wed, 22 Apr 2020 09:13:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:13:56: #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 09:13:56: #1 tags after filtering in treatment: 55853 INFO @ Wed, 22 Apr 2020 09:13:56: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:13:56: #1 finished! INFO @ Wed, 22 Apr 2020 09:13:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:13:56: #2 number of paired peaks: 108 WARNING @ Wed, 22 Apr 2020 09:13:56: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 22 Apr 2020 09:13:56: start model_add_line... INFO @ Wed, 22 Apr 2020 09:13:56: start X-correlation... INFO @ Wed, 22 Apr 2020 09:13:56: end of X-cor INFO @ Wed, 22 Apr 2020 09:13:56: #2 finished! INFO @ Wed, 22 Apr 2020 09:13:56: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 09:13:56: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 09:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05_model.r WARNING @ Wed, 22 Apr 2020 09:13:56: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:13:56: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 22 Apr 2020 09:13:56: #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 09:13:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:13:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.05_summits.bed INFO @ Wed, 22 Apr 2020 09:13:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (110 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 09:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.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 09:14:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:14:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:14:26: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:14:26: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:14:26: #1 total tags in treatment: 69630 INFO @ Wed, 22 Apr 2020 09:14:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:26: #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 09:14:26: #1 tags after filtering in treatment: 55853 INFO @ Wed, 22 Apr 2020 09:14:26: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:14:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:26: #2 number of paired peaks: 108 WARNING @ Wed, 22 Apr 2020 09:14:26: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 22 Apr 2020 09:14:26: start model_add_line... INFO @ Wed, 22 Apr 2020 09:14:26: start X-correlation... INFO @ Wed, 22 Apr 2020 09:14:26: end of X-cor INFO @ Wed, 22 Apr 2020 09:14:26: #2 finished! INFO @ Wed, 22 Apr 2020 09:14:26: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 09:14:26: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 09:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10_model.r WARNING @ Wed, 22 Apr 2020 09:14:26: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:14:26: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 22 Apr 2020 09:14:26: #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 09:14:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:14:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.10_summits.bed INFO @ Wed, 22 Apr 2020 09:14:26: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (59 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 09:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.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 09:14:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:14:54: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:14:56: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:14:56: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:14:56: #1 total tags in treatment: 69630 INFO @ Wed, 22 Apr 2020 09:14:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:56: #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 09:14:56: #1 tags after filtering in treatment: 55853 INFO @ Wed, 22 Apr 2020 09:14:56: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 09:14:56: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:56: #2 number of paired peaks: 108 WARNING @ Wed, 22 Apr 2020 09:14:56: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Wed, 22 Apr 2020 09:14:56: start model_add_line... INFO @ Wed, 22 Apr 2020 09:14:56: start X-correlation... INFO @ Wed, 22 Apr 2020 09:14:56: end of X-cor INFO @ Wed, 22 Apr 2020 09:14:56: #2 finished! INFO @ Wed, 22 Apr 2020 09:14:56: #2 predicted fragment length is 216 bps INFO @ Wed, 22 Apr 2020 09:14:56: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 22 Apr 2020 09:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20_model.r WARNING @ Wed, 22 Apr 2020 09:14:56: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:14:56: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 22 Apr 2020 09:14:56: #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 09:14:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:14:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:14:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:14:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:14:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255999/SRX7255999.20_summits.bed INFO @ Wed, 22 Apr 2020 09:14:56: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 millis CompletedMACS2peakCalling