Job ID = 14521924 SRX = SRX11539775 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16025938 spots for SRR15233870/SRR15233870.sra Written 16025938 spots for SRR15233870/SRR15233870.sra 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: 00:01:46 16025938 reads; of these: 16025938 (100.00%) were paired; of these: 15686156 (97.88%) aligned concordantly 0 times 265023 (1.65%) aligned concordantly exactly 1 time 74759 (0.47%) aligned concordantly >1 times ---- 15686156 pairs aligned concordantly 0 times; of these: 238546 (1.52%) aligned discordantly 1 time ---- 15447610 pairs aligned 0 times concordantly or discordantly; of these: 30895220 mates make up the pairs; of these: 30525774 (98.80%) aligned 0 times 262581 (0.85%) aligned exactly 1 time 106865 (0.35%) aligned >1 times 4.76% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 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] 456377 / 568109 = 0.8033 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.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 @ Sat, 15 Jan 2022 21:53:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:53:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:53:40: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 21:53:40: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 21:53:40: #1 total tags in treatment: 66356 INFO @ Sat, 15 Jan 2022 21:53:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:53:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:53:40: #1 tags after filtering in treatment: 62670 INFO @ Sat, 15 Jan 2022 21:53:40: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Jan 2022 21:53:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:53:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:53:40: #2 number of paired peaks: 238 WARNING @ Sat, 15 Jan 2022 21:53:40: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 15 Jan 2022 21:53:40: start model_add_line... INFO @ Sat, 15 Jan 2022 21:53:40: start X-correlation... INFO @ Sat, 15 Jan 2022 21:53:40: end of X-cor INFO @ Sat, 15 Jan 2022 21:53:40: #2 finished! INFO @ Sat, 15 Jan 2022 21:53:40: #2 predicted fragment length is 56 bps INFO @ Sat, 15 Jan 2022 21:53:40: #2 alternative fragment length(s) may be 7,56,78,107,176,210,232,262,300,382,425,474,545 bps INFO @ Sat, 15 Jan 2022 21:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05_model.r WARNING @ Sat, 15 Jan 2022 21:53:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:53:40: #2 You may need to consider one of the other alternative d(s): 7,56,78,107,176,210,232,262,300,382,425,474,545 WARNING @ Sat, 15 Jan 2022 21:53:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:53:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:53:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:53:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.05_summits.bed INFO @ Sat, 15 Jan 2022 21:53:40: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:54:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.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 @ Sat, 15 Jan 2022 21:54:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:54:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:54:10: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 21:54:10: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 21:54:10: #1 total tags in treatment: 66356 INFO @ Sat, 15 Jan 2022 21:54:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:54:10: #1 tags after filtering in treatment: 62670 INFO @ Sat, 15 Jan 2022 21:54:10: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Jan 2022 21:54:10: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:10: #2 number of paired peaks: 238 WARNING @ Sat, 15 Jan 2022 21:54:10: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:10: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:10: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:10: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:10: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:10: #2 predicted fragment length is 56 bps INFO @ Sat, 15 Jan 2022 21:54:10: #2 alternative fragment length(s) may be 7,56,78,107,176,210,232,262,300,382,425,474,545 bps INFO @ Sat, 15 Jan 2022 21:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10_model.r WARNING @ Sat, 15 Jan 2022 21:54:10: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:54:10: #2 You may need to consider one of the other alternative d(s): 7,56,78,107,176,210,232,262,300,382,425,474,545 WARNING @ Sat, 15 Jan 2022 21:54:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:54:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.10_summits.bed INFO @ Sat, 15 Jan 2022 21:54:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.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 @ Sat, 15 Jan 2022 21:54:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:54:37: #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 @ Sat, 15 Jan 2022 21:54:40: #1 tag size is determined as 39 bps INFO @ Sat, 15 Jan 2022 21:54:40: #1 tag size = 39 INFO @ Sat, 15 Jan 2022 21:54:40: #1 total tags in treatment: 66356 INFO @ Sat, 15 Jan 2022 21:54:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:54:40: #1 tags after filtering in treatment: 62670 INFO @ Sat, 15 Jan 2022 21:54:40: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 15 Jan 2022 21:54:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:40: #2 number of paired peaks: 238 WARNING @ Sat, 15 Jan 2022 21:54:40: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:40: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:40: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:40: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:40: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:40: #2 predicted fragment length is 56 bps INFO @ Sat, 15 Jan 2022 21:54:40: #2 alternative fragment length(s) may be 7,56,78,107,176,210,232,262,300,382,425,474,545 bps INFO @ Sat, 15 Jan 2022 21:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20_model.r WARNING @ Sat, 15 Jan 2022 21:54:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:54:40: #2 You may need to consider one of the other alternative d(s): 7,56,78,107,176,210,232,262,300,382,425,474,545 WARNING @ Sat, 15 Jan 2022 21:54:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:54:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539775/SRX11539775.20_summits.bed INFO @ Sat, 15 Jan 2022 21:54:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling