Job ID = 10224068 SRX = SRX8952625 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12227725 spots for SRR12458261/SRR12458261.sra Written 12227725 spots for SRR12458261/SRR12458261.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 12227725 reads; of these: 12227725 (100.00%) were unpaired; of these: 2755492 (22.53%) aligned 0 times 7593159 (62.10%) aligned exactly 1 time 1879074 (15.37%) aligned >1 times 77.47% 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_rmdupse_core] 7704189 / 9472233 = 0.8133 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 @ Fri, 16 Oct 2020 09:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.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 @ Fri, 16 Oct 2020 09:21:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:21:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:21:42: 1000000 INFO @ Fri, 16 Oct 2020 09:21:47: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 09:21:47: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 09:21:47: #1 total tags in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:21:47: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:21:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:21:47: #1 tags after filtering in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:21:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 09:21:47: #1 finished! INFO @ Fri, 16 Oct 2020 09:21:47: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:21:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:21:47: #2 number of paired peaks: 339 WARNING @ Fri, 16 Oct 2020 09:21:47: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 16 Oct 2020 09:21:47: start model_add_line... INFO @ Fri, 16 Oct 2020 09:21:47: start X-correlation... INFO @ Fri, 16 Oct 2020 09:21:47: end of X-cor INFO @ Fri, 16 Oct 2020 09:21:47: #2 finished! INFO @ Fri, 16 Oct 2020 09:21:47: #2 predicted fragment length is 1 bps INFO @ Fri, 16 Oct 2020 09:21:47: #2 alternative fragment length(s) may be 1,10,41,66,99,124,183,505,575 bps INFO @ Fri, 16 Oct 2020 09:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05_model.r WARNING @ Fri, 16 Oct 2020 09:21:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 09:21:47: #2 You may need to consider one of the other alternative d(s): 1,10,41,66,99,124,183,505,575 WARNING @ Fri, 16 Oct 2020 09:21:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 09:21:47: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:21:50: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:21:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:21:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:21:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.05_summits.bed INFO @ Fri, 16 Oct 2020 09:21:51: 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 @ Fri, 16 Oct 2020 09:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.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 @ Fri, 16 Oct 2020 09:22:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:22:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:22:12: 1000000 INFO @ Fri, 16 Oct 2020 09:22:16: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 09:22:16: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 09:22:16: #1 total tags in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:22:16: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:22:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:22:16: #1 tags after filtering in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 09:22:16: #1 finished! INFO @ Fri, 16 Oct 2020 09:22:16: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:22:16: #2 number of paired peaks: 339 WARNING @ Fri, 16 Oct 2020 09:22:16: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 16 Oct 2020 09:22:16: start model_add_line... INFO @ Fri, 16 Oct 2020 09:22:16: start X-correlation... INFO @ Fri, 16 Oct 2020 09:22:16: end of X-cor INFO @ Fri, 16 Oct 2020 09:22:16: #2 finished! INFO @ Fri, 16 Oct 2020 09:22:16: #2 predicted fragment length is 1 bps INFO @ Fri, 16 Oct 2020 09:22:16: #2 alternative fragment length(s) may be 1,10,41,66,99,124,183,505,575 bps INFO @ Fri, 16 Oct 2020 09:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10_model.r WARNING @ Fri, 16 Oct 2020 09:22:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 09:22:16: #2 You may need to consider one of the other alternative d(s): 1,10,41,66,99,124,183,505,575 WARNING @ Fri, 16 Oct 2020 09:22:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 09:22:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:22:19: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.10_summits.bed INFO @ Fri, 16 Oct 2020 09:22:20: Done! pass1 - making usageList (0 chroms): 1 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 @ Fri, 16 Oct 2020 09:22:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.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 @ Fri, 16 Oct 2020 09:22:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:22:36: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:22:43: 1000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:22:48: #1 tag size is determined as 50 bps INFO @ Fri, 16 Oct 2020 09:22:48: #1 tag size = 50 INFO @ Fri, 16 Oct 2020 09:22:48: #1 total tags in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:22:48: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:22:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:22:48: #1 tags after filtering in treatment: 1768044 INFO @ Fri, 16 Oct 2020 09:22:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Oct 2020 09:22:48: #1 finished! INFO @ Fri, 16 Oct 2020 09:22:48: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:22:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:22:48: #2 number of paired peaks: 339 WARNING @ Fri, 16 Oct 2020 09:22:48: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Fri, 16 Oct 2020 09:22:48: start model_add_line... INFO @ Fri, 16 Oct 2020 09:22:48: start X-correlation... INFO @ Fri, 16 Oct 2020 09:22:48: end of X-cor INFO @ Fri, 16 Oct 2020 09:22:48: #2 finished! INFO @ Fri, 16 Oct 2020 09:22:48: #2 predicted fragment length is 1 bps INFO @ Fri, 16 Oct 2020 09:22:48: #2 alternative fragment length(s) may be 1,10,41,66,99,124,183,505,575 bps INFO @ Fri, 16 Oct 2020 09:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20_model.r WARNING @ Fri, 16 Oct 2020 09:22:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Oct 2020 09:22:48: #2 You may need to consider one of the other alternative d(s): 1,10,41,66,99,124,183,505,575 WARNING @ Fri, 16 Oct 2020 09:22:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Oct 2020 09:22:48: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:22:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:22:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:22:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:22:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952625/SRX8952625.20_summits.bed INFO @ Fri, 16 Oct 2020 09:22:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling