Job ID = 14167749 SRX = SRX6407590 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:10 4822856 reads; of these: 4822856 (100.00%) were unpaired; of these: 601097 (12.46%) aligned 0 times 3414441 (70.80%) aligned exactly 1 time 807318 (16.74%) aligned >1 times 87.54% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 359964 / 4221759 = 0.0853 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 @ Fri, 10 Dec 2021 13:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 10 Dec 2021 13:21:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:21:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:21:54: 1000000 INFO @ Fri, 10 Dec 2021 13:22:03: 2000000 INFO @ Fri, 10 Dec 2021 13:22:12: 3000000 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 @ Fri, 10 Dec 2021 13:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 10 Dec 2021 13:22:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:22:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:22:21: #1 tag size is determined as 97 bps INFO @ Fri, 10 Dec 2021 13:22:21: #1 tag size = 97 INFO @ Fri, 10 Dec 2021 13:22:21: #1 total tags in treatment: 3861795 INFO @ Fri, 10 Dec 2021 13:22:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:22:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:22:21: #1 tags after filtering in treatment: 3861541 INFO @ Fri, 10 Dec 2021 13:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:22:21: #1 finished! INFO @ Fri, 10 Dec 2021 13:22:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:22:21: #2 number of paired peaks: 702 WARNING @ Fri, 10 Dec 2021 13:22:21: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Fri, 10 Dec 2021 13:22:21: start model_add_line... INFO @ Fri, 10 Dec 2021 13:22:21: start X-correlation... INFO @ Fri, 10 Dec 2021 13:22:21: end of X-cor INFO @ Fri, 10 Dec 2021 13:22:21: #2 finished! INFO @ Fri, 10 Dec 2021 13:22:21: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 13:22:21: #2 alternative fragment length(s) may be 107,541 bps INFO @ Fri, 10 Dec 2021 13:22:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05_model.r WARNING @ Fri, 10 Dec 2021 13:22:21: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:22:21: #2 You may need to consider one of the other alternative d(s): 107,541 WARNING @ Fri, 10 Dec 2021 13:22:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:22:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:22:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:22:24: 1000000 INFO @ Fri, 10 Dec 2021 13:22:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:22:31: 2000000 INFO @ Fri, 10 Dec 2021 13:22:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:22:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:22:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.05_summits.bed INFO @ Fri, 10 Dec 2021 13:22:34: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:22:38: 3000000 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 @ Fri, 10 Dec 2021 13:22:45: #1 tag size is determined as 97 bps INFO @ Fri, 10 Dec 2021 13:22:45: #1 tag size = 97 INFO @ Fri, 10 Dec 2021 13:22:45: #1 total tags in treatment: 3861795 INFO @ Fri, 10 Dec 2021 13:22:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:22:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:22:45: #1 tags after filtering in treatment: 3861541 INFO @ Fri, 10 Dec 2021 13:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:22:45: #1 finished! INFO @ Fri, 10 Dec 2021 13:22:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 10 Dec 2021 13:22:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:22:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:22:45: #2 number of paired peaks: 702 WARNING @ Fri, 10 Dec 2021 13:22:45: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Fri, 10 Dec 2021 13:22:45: start model_add_line... INFO @ Fri, 10 Dec 2021 13:22:45: start X-correlation... INFO @ Fri, 10 Dec 2021 13:22:45: end of X-cor INFO @ Fri, 10 Dec 2021 13:22:45: #2 finished! INFO @ Fri, 10 Dec 2021 13:22:45: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 13:22:45: #2 alternative fragment length(s) may be 107,541 bps INFO @ Fri, 10 Dec 2021 13:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10_model.r WARNING @ Fri, 10 Dec 2021 13:22:45: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:22:45: #2 You may need to consider one of the other alternative d(s): 107,541 WARNING @ Fri, 10 Dec 2021 13:22:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:22:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:22:54: 1000000 INFO @ Fri, 10 Dec 2021 13:22:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:22:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:22:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:22:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.10_summits.bed INFO @ Fri, 10 Dec 2021 13:22:59: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:23:03: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:23:12: 3000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:23:19: #1 tag size is determined as 97 bps INFO @ Fri, 10 Dec 2021 13:23:19: #1 tag size = 97 INFO @ Fri, 10 Dec 2021 13:23:19: #1 total tags in treatment: 3861795 INFO @ Fri, 10 Dec 2021 13:23:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:23:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:23:20: #1 tags after filtering in treatment: 3861541 INFO @ Fri, 10 Dec 2021 13:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:23:20: #1 finished! INFO @ Fri, 10 Dec 2021 13:23:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:23:20: #2 number of paired peaks: 702 WARNING @ Fri, 10 Dec 2021 13:23:20: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Fri, 10 Dec 2021 13:23:20: start model_add_line... INFO @ Fri, 10 Dec 2021 13:23:20: start X-correlation... INFO @ Fri, 10 Dec 2021 13:23:20: end of X-cor INFO @ Fri, 10 Dec 2021 13:23:20: #2 finished! INFO @ Fri, 10 Dec 2021 13:23:20: #2 predicted fragment length is 107 bps INFO @ Fri, 10 Dec 2021 13:23:20: #2 alternative fragment length(s) may be 107,541 bps INFO @ Fri, 10 Dec 2021 13:23:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20_model.r WARNING @ Fri, 10 Dec 2021 13:23:20: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:23:20: #2 You may need to consider one of the other alternative d(s): 107,541 WARNING @ Fri, 10 Dec 2021 13:23:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:23:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:23:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407590/SRX6407590.20_summits.bed INFO @ Fri, 10 Dec 2021 13:23:33: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 6 millis CompletedMACS2peakCalling