Job ID = 7108135 SRX = SRX7960934 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12714627 spots for SRR11359439/SRR11359439.sra Written 12714627 spots for SRR11359439/SRR11359439.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: 00:04:07 12714627 reads; of these: 12714627 (100.00%) were unpaired; of these: 1291107 (10.15%) aligned 0 times 7757754 (61.01%) aligned exactly 1 time 3665766 (28.83%) aligned >1 times 89.85% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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_sort_core] merging from 12 files... [bam_rmdupse_core] 7139153 / 11423520 = 0.6250 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 Jul 2020 13:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.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 Jul 2020 13:37:01: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:37:01: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:37:12: 1000000 INFO @ Wed, 22 Jul 2020 13:37:22: 2000000 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 Jul 2020 13:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.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 Jul 2020 13:37:31: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:37:31: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:37:33: 3000000 INFO @ Wed, 22 Jul 2020 13:37:43: 1000000 INFO @ Wed, 22 Jul 2020 13:37:45: 4000000 INFO @ Wed, 22 Jul 2020 13:37:48: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:37:48: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:37:48: #1 total tags in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:37:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:37:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:37:48: #1 tags after filtering in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:37:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:37:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:37:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:37:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:37:48: #2 number of paired peaks: 157 WARNING @ Wed, 22 Jul 2020 13:37:48: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Wed, 22 Jul 2020 13:37:48: start model_add_line... INFO @ Wed, 22 Jul 2020 13:37:48: start X-correlation... INFO @ Wed, 22 Jul 2020 13:37:48: end of X-cor INFO @ Wed, 22 Jul 2020 13:37:48: #2 finished! INFO @ Wed, 22 Jul 2020 13:37:48: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Jul 2020 13:37:48: #2 alternative fragment length(s) may be 2,57,81,89,97,118 bps INFO @ Wed, 22 Jul 2020 13:37:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05_model.r WARNING @ Wed, 22 Jul 2020 13:37:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:37:48: #2 You may need to consider one of the other alternative d(s): 2,57,81,89,97,118 WARNING @ Wed, 22 Jul 2020 13:37:48: #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 Jul 2020 13:37:48: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:37:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:37:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:37:54: 2000000 INFO @ Wed, 22 Jul 2020 13:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.05_summits.bed INFO @ Wed, 22 Jul 2020 13:37:55: 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 @ Wed, 22 Jul 2020 13:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.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 Jul 2020 13:38:01: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:38:01: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:38:05: 3000000 INFO @ Wed, 22 Jul 2020 13:38:13: 1000000 INFO @ Wed, 22 Jul 2020 13:38:16: 4000000 INFO @ Wed, 22 Jul 2020 13:38:19: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:38:19: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:38:19: #1 total tags in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:38:19: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:38:19: #1 tags after filtering in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:19: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:19: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:19: #2 number of paired peaks: 157 WARNING @ Wed, 22 Jul 2020 13:38:19: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:19: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:19: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:19: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:19: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:19: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Jul 2020 13:38:19: #2 alternative fragment length(s) may be 2,57,81,89,97,118 bps INFO @ Wed, 22 Jul 2020 13:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10_model.r WARNING @ Wed, 22 Jul 2020 13:38:19: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:19: #2 You may need to consider one of the other alternative d(s): 2,57,81,89,97,118 WARNING @ Wed, 22 Jul 2020 13:38:19: #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 Jul 2020 13:38:19: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:38:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:38:24: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 13:38:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:38:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.10_summits.bed INFO @ Wed, 22 Jul 2020 13:38:26: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:38:35: 3000000 INFO @ Wed, 22 Jul 2020 13:38:46: 4000000 INFO @ Wed, 22 Jul 2020 13:38:48: #1 tag size is determined as 151 bps INFO @ Wed, 22 Jul 2020 13:38:48: #1 tag size = 151 INFO @ Wed, 22 Jul 2020 13:38:48: #1 total tags in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:38:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:38:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:38:48: #1 tags after filtering in treatment: 4284367 INFO @ Wed, 22 Jul 2020 13:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 13:38:48: #1 finished! INFO @ Wed, 22 Jul 2020 13:38:48: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:38:49: #2 number of paired peaks: 157 WARNING @ Wed, 22 Jul 2020 13:38:49: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Wed, 22 Jul 2020 13:38:49: start model_add_line... INFO @ Wed, 22 Jul 2020 13:38:49: start X-correlation... INFO @ Wed, 22 Jul 2020 13:38:49: end of X-cor INFO @ Wed, 22 Jul 2020 13:38:49: #2 finished! INFO @ Wed, 22 Jul 2020 13:38:49: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Jul 2020 13:38:49: #2 alternative fragment length(s) may be 2,57,81,89,97,118 bps INFO @ Wed, 22 Jul 2020 13:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20_model.r WARNING @ Wed, 22 Jul 2020 13:38:49: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 13:38:49: #2 You may need to consider one of the other alternative d(s): 2,57,81,89,97,118 WARNING @ Wed, 22 Jul 2020 13:38:49: #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 Jul 2020 13:38:49: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:38:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7960934/SRX7960934.20_summits.bed INFO @ Wed, 22 Jul 2020 13:38:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling