Job ID = 14168973 SRX = SRX8688986 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: 00:01:33 5985350 reads; of these: 5985350 (100.00%) were unpaired; of these: 208271 (3.48%) aligned 0 times 4398574 (73.49%) aligned exactly 1 time 1378505 (23.03%) aligned >1 times 96.52% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 373950 / 5777079 = 0.0647 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 22:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.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 22:33:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:33:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:33:58: 1000000 INFO @ Fri, 10 Dec 2021 22:34:03: 2000000 INFO @ Fri, 10 Dec 2021 22:34:08: 3000000 INFO @ Fri, 10 Dec 2021 22:34:13: 4000000 INFO @ Fri, 10 Dec 2021 22:34:18: 5000000 INFO @ Fri, 10 Dec 2021 22:34:20: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:34:20: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:34:20: #1 total tags in treatment: 5403129 INFO @ Fri, 10 Dec 2021 22:34:20: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:34:20: #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 22:34:20: #1 tags after filtering in treatment: 5402898 INFO @ Fri, 10 Dec 2021 22:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:34:20: #1 finished! INFO @ Fri, 10 Dec 2021 22:34:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:34:21: #2 number of paired peaks: 994 WARNING @ Fri, 10 Dec 2021 22:34:21: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Fri, 10 Dec 2021 22:34:21: start model_add_line... INFO @ Fri, 10 Dec 2021 22:34:21: start X-correlation... INFO @ Fri, 10 Dec 2021 22:34:21: end of X-cor INFO @ Fri, 10 Dec 2021 22:34:21: #2 finished! INFO @ Fri, 10 Dec 2021 22:34:21: #2 predicted fragment length is 68 bps INFO @ Fri, 10 Dec 2021 22:34:21: #2 alternative fragment length(s) may be 68 bps INFO @ Fri, 10 Dec 2021 22:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05_model.r WARNING @ Fri, 10 Dec 2021 22:34:21: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:34:21: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Fri, 10 Dec 2021 22:34:21: #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 22:34:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:34:21: #3 Pre-compute pvalue-qvalue table... 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 22:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.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 22:34:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:34:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:34:28: 1000000 INFO @ Fri, 10 Dec 2021 22:34:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:34:33: 2000000 INFO @ Fri, 10 Dec 2021 22:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.05_summits.bed INFO @ Fri, 10 Dec 2021 22:34:38: Done! pass1 - making usageList (384 chroms): 1 millis pass2 - checking and writing primary data (2585 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:34:38: 3000000 INFO @ Fri, 10 Dec 2021 22:34:43: 4000000 INFO @ Fri, 10 Dec 2021 22:34:48: 5000000 INFO @ Fri, 10 Dec 2021 22:34:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:34:50: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:34:50: #1 total tags in treatment: 5403129 INFO @ Fri, 10 Dec 2021 22:34:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:34:50: #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 22:34:50: #1 tags after filtering in treatment: 5402898 INFO @ Fri, 10 Dec 2021 22:34:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:34:50: #1 finished! INFO @ Fri, 10 Dec 2021 22:34:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:34:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:34:51: #2 number of paired peaks: 994 WARNING @ Fri, 10 Dec 2021 22:34:51: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Fri, 10 Dec 2021 22:34:51: start model_add_line... INFO @ Fri, 10 Dec 2021 22:34:51: start X-correlation... INFO @ Fri, 10 Dec 2021 22:34:51: end of X-cor INFO @ Fri, 10 Dec 2021 22:34:51: #2 finished! INFO @ Fri, 10 Dec 2021 22:34:51: #2 predicted fragment length is 68 bps INFO @ Fri, 10 Dec 2021 22:34:51: #2 alternative fragment length(s) may be 68 bps INFO @ Fri, 10 Dec 2021 22:34:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10_model.r WARNING @ Fri, 10 Dec 2021 22:34:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:34:51: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Fri, 10 Dec 2021 22:34:51: #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 22:34:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:34:51: #3 Pre-compute pvalue-qvalue table... 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 22:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.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 22:34:54: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:34:54: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:34:59: 1000000 INFO @ Fri, 10 Dec 2021 22:35:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:35:04: 2000000 INFO @ Fri, 10 Dec 2021 22:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.10_summits.bed INFO @ Fri, 10 Dec 2021 22:35:08: Done! pass1 - making usageList (252 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:35:09: 3000000 INFO @ Fri, 10 Dec 2021 22:35:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:35:20: 5000000 INFO @ Fri, 10 Dec 2021 22:35:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:35:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:35:22: #1 total tags in treatment: 5403129 INFO @ Fri, 10 Dec 2021 22:35:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:35:22: #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 22:35:22: #1 tags after filtering in treatment: 5402898 INFO @ Fri, 10 Dec 2021 22:35:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:35:22: #1 finished! INFO @ Fri, 10 Dec 2021 22:35:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:35:23: #2 number of paired peaks: 994 WARNING @ Fri, 10 Dec 2021 22:35:23: Fewer paired peaks (994) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 994 pairs to build model! INFO @ Fri, 10 Dec 2021 22:35:23: start model_add_line... INFO @ Fri, 10 Dec 2021 22:35:23: start X-correlation... INFO @ Fri, 10 Dec 2021 22:35:23: end of X-cor INFO @ Fri, 10 Dec 2021 22:35:23: #2 finished! INFO @ Fri, 10 Dec 2021 22:35:23: #2 predicted fragment length is 68 bps INFO @ Fri, 10 Dec 2021 22:35:23: #2 alternative fragment length(s) may be 68 bps INFO @ Fri, 10 Dec 2021 22:35:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20_model.r WARNING @ Fri, 10 Dec 2021 22:35:23: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:35:23: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Fri, 10 Dec 2021 22:35:23: #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 22:35:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:35:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:35:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:35:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:35:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:35:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688986/SRX8688986.20_summits.bed INFO @ Fri, 10 Dec 2021 22:35:41: Done! pass1 - making usageList (160 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 7 millis CompletedMACS2peakCalling