Job ID = 7098775 SRX = SRX6473468 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2644061 spots for SRR9715591/SRR9715591.sra Written 2644061 spots for SRR9715591/SRR9715591.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: 00:00:32 2644061 reads; of these: 2644061 (100.00%) were unpaired; of these: 491210 (18.58%) aligned 0 times 1870411 (70.74%) aligned exactly 1 time 282440 (10.68%) aligned >1 times 81.42% overall alignment rate Time searching: 00:00:32 Overall time: 00:00:32 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] 827997 / 2152851 = 0.3846 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 12:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.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 12:00:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:00:13: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:00:20: 1000000 INFO @ Wed, 22 Jul 2020 12:00:22: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:00:22: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:00:22: #1 total tags in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:00:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:00:22: #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 12:00:22: #1 tags after filtering in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:00:22: #1 finished! INFO @ Wed, 22 Jul 2020 12:00:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:00:22: #2 number of paired peaks: 394 WARNING @ Wed, 22 Jul 2020 12:00:22: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Wed, 22 Jul 2020 12:00:22: start model_add_line... INFO @ Wed, 22 Jul 2020 12:00:22: start X-correlation... INFO @ Wed, 22 Jul 2020 12:00:22: end of X-cor INFO @ Wed, 22 Jul 2020 12:00:22: #2 finished! INFO @ Wed, 22 Jul 2020 12:00:22: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Jul 2020 12:00:22: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Jul 2020 12:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05_model.r WARNING @ Wed, 22 Jul 2020 12:00:22: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:00:22: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Wed, 22 Jul 2020 12:00:22: #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 12:00:22: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:00:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.05_summits.bed INFO @ Wed, 22 Jul 2020 12:00:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (732 records, 4 fields): 2 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 Jul 2020 12:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.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 12:00:43: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:00:43: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:00:50: 1000000 INFO @ Wed, 22 Jul 2020 12:00:52: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:00:52: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:00:52: #1 total tags in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:00:52: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:00:52: #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 12:00:52: #1 tags after filtering in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:00:52: #1 finished! INFO @ Wed, 22 Jul 2020 12:00:52: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:00:52: #2 number of paired peaks: 394 WARNING @ Wed, 22 Jul 2020 12:00:52: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Wed, 22 Jul 2020 12:00:52: start model_add_line... INFO @ Wed, 22 Jul 2020 12:00:52: start X-correlation... INFO @ Wed, 22 Jul 2020 12:00:52: end of X-cor INFO @ Wed, 22 Jul 2020 12:00:52: #2 finished! INFO @ Wed, 22 Jul 2020 12:00:52: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Jul 2020 12:00:52: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Jul 2020 12:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10_model.r WARNING @ Wed, 22 Jul 2020 12:00:52: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:00:52: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Wed, 22 Jul 2020 12:00:52: #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 12:00:52: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:00:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.10_summits.bed INFO @ Wed, 22 Jul 2020 12:00:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (488 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 Jul 2020 12:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.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 12:01:13: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:01:13: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:01:20: 1000000 INFO @ Wed, 22 Jul 2020 12:01:22: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 12:01:22: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 12:01:22: #1 total tags in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:01:22: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:01:22: #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 12:01:22: #1 tags after filtering in treatment: 1324854 INFO @ Wed, 22 Jul 2020 12:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:01:22: #1 finished! INFO @ Wed, 22 Jul 2020 12:01:22: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:01:22: #2 number of paired peaks: 394 WARNING @ Wed, 22 Jul 2020 12:01:22: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Wed, 22 Jul 2020 12:01:22: start model_add_line... INFO @ Wed, 22 Jul 2020 12:01:22: start X-correlation... INFO @ Wed, 22 Jul 2020 12:01:22: end of X-cor INFO @ Wed, 22 Jul 2020 12:01:22: #2 finished! INFO @ Wed, 22 Jul 2020 12:01:22: #2 predicted fragment length is 182 bps INFO @ Wed, 22 Jul 2020 12:01:22: #2 alternative fragment length(s) may be 182 bps INFO @ Wed, 22 Jul 2020 12:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20_model.r BigWig に変換しました。 WARNING @ Wed, 22 Jul 2020 12:01:22: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:01:22: #2 You may need to consider one of the other alternative d(s): 182 WARNING @ Wed, 22 Jul 2020 12:01:22: #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 12:01:22: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:01:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6473468/SRX6473468.20_summits.bed INFO @ Wed, 22 Jul 2020 12:01:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 2 millis CompletedMACS2peakCalling