Job ID = 6627766 SRX = SRX8521413 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: 00:06:10 48893962 reads; of these: 48893962 (100.00%) were unpaired; of these: 46074631 (94.23%) aligned 0 times 2102731 (4.30%) aligned exactly 1 time 716600 (1.47%) aligned >1 times 5.77% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 307229 / 2819331 = 0.1090 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 @ Tue, 14 Jul 2020 13:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.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 @ Tue, 14 Jul 2020 13:14:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:14:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:14:42: 1000000 INFO @ Tue, 14 Jul 2020 13:14:47: 2000000 INFO @ Tue, 14 Jul 2020 13:14:50: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 13:14:50: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 13:14:50: #1 total tags in treatment: 2512102 INFO @ Tue, 14 Jul 2020 13:14:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:14:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 13:14:50: #1 tags after filtering in treatment: 2511785 INFO @ Tue, 14 Jul 2020 13:14:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:14:50: #1 finished! INFO @ Tue, 14 Jul 2020 13:14:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:14:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:14:50: #2 number of paired peaks: 960 WARNING @ Tue, 14 Jul 2020 13:14:50: Fewer paired peaks (960) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 960 pairs to build model! INFO @ Tue, 14 Jul 2020 13:14:50: start model_add_line... INFO @ Tue, 14 Jul 2020 13:14:50: start X-correlation... INFO @ Tue, 14 Jul 2020 13:14:50: end of X-cor INFO @ Tue, 14 Jul 2020 13:14:50: #2 finished! INFO @ Tue, 14 Jul 2020 13:14:50: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:14:50: #2 alternative fragment length(s) may be 58,542 bps INFO @ Tue, 14 Jul 2020 13:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05_model.r WARNING @ Tue, 14 Jul 2020 13:14:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:14:50: #2 You may need to consider one of the other alternative d(s): 58,542 WARNING @ Tue, 14 Jul 2020 13:14:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 13:14:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:14:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:14:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:14:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:14:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.05_summits.bed INFO @ Tue, 14 Jul 2020 13:14:59: Done! pass1 - making usageList (157 chroms): 1 millis pass2 - checking and writing primary data (730 records, 4 fields): 8 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 @ Tue, 14 Jul 2020 13:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.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 @ Tue, 14 Jul 2020 13:15:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:15:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:15:12: 1000000 INFO @ Tue, 14 Jul 2020 13:15:17: 2000000 INFO @ Tue, 14 Jul 2020 13:15:20: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 13:15:20: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 13:15:20: #1 total tags in treatment: 2512102 INFO @ Tue, 14 Jul 2020 13:15:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:15:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 13:15:20: #1 tags after filtering in treatment: 2511785 INFO @ Tue, 14 Jul 2020 13:15:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:15:20: #1 finished! INFO @ Tue, 14 Jul 2020 13:15:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:15:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:15:20: #2 number of paired peaks: 960 WARNING @ Tue, 14 Jul 2020 13:15:20: Fewer paired peaks (960) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 960 pairs to build model! INFO @ Tue, 14 Jul 2020 13:15:20: start model_add_line... INFO @ Tue, 14 Jul 2020 13:15:20: start X-correlation... INFO @ Tue, 14 Jul 2020 13:15:20: end of X-cor INFO @ Tue, 14 Jul 2020 13:15:20: #2 finished! INFO @ Tue, 14 Jul 2020 13:15:20: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:15:20: #2 alternative fragment length(s) may be 58,542 bps INFO @ Tue, 14 Jul 2020 13:15:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10_model.r WARNING @ Tue, 14 Jul 2020 13:15:20: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:15:20: #2 You may need to consider one of the other alternative d(s): 58,542 WARNING @ Tue, 14 Jul 2020 13:15:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 13:15:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:15:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:15:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.10_summits.bed INFO @ Tue, 14 Jul 2020 13:15:29: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 5 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 @ Tue, 14 Jul 2020 13:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.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 @ Tue, 14 Jul 2020 13:15:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:15:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:15:42: 1000000 INFO @ Tue, 14 Jul 2020 13:15:47: 2000000 INFO @ Tue, 14 Jul 2020 13:15:50: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 13:15:50: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 13:15:50: #1 total tags in treatment: 2512102 INFO @ Tue, 14 Jul 2020 13:15:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:15:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 13:15:50: #1 tags after filtering in treatment: 2511785 INFO @ Tue, 14 Jul 2020 13:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:15:50: #1 finished! INFO @ Tue, 14 Jul 2020 13:15:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:15:51: #2 number of paired peaks: 960 WARNING @ Tue, 14 Jul 2020 13:15:51: Fewer paired peaks (960) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 960 pairs to build model! INFO @ Tue, 14 Jul 2020 13:15:51: start model_add_line... INFO @ Tue, 14 Jul 2020 13:15:51: start X-correlation... INFO @ Tue, 14 Jul 2020 13:15:51: end of X-cor INFO @ Tue, 14 Jul 2020 13:15:51: #2 finished! INFO @ Tue, 14 Jul 2020 13:15:51: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 13:15:51: #2 alternative fragment length(s) may be 58,542 bps INFO @ Tue, 14 Jul 2020 13:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20_model.r WARNING @ Tue, 14 Jul 2020 13:15:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:15:51: #2 You may need to consider one of the other alternative d(s): 58,542 WARNING @ Tue, 14 Jul 2020 13:15:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 13:15:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:15:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:15:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:15:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:15:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:15:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521413/SRX8521413.20_summits.bed INFO @ Tue, 14 Jul 2020 13:15:59: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 3 millis CompletedMACS2peakCalling