Job ID = 6627383 SRX = SRX8521284 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: 00:09:17 57659654 reads; of these: 57659654 (100.00%) were unpaired; of these: 49636430 (86.09%) aligned 0 times 6211780 (10.77%) aligned exactly 1 time 1811444 (3.14%) aligned >1 times 13.91% overall alignment rate Time searching: 00:09:17 Overall time: 00:09:17 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] 1491203 / 8023224 = 0.1859 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 11:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.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 11:25:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:25:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:25:33: 1000000 INFO @ Tue, 14 Jul 2020 11:25:39: 2000000 INFO @ Tue, 14 Jul 2020 11:25:47: 3000000 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 11:25:54: 4000000 INFO @ Tue, 14 Jul 2020 11:25:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.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 11:25:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:25:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:26:02: 5000000 INFO @ Tue, 14 Jul 2020 11:26:04: 1000000 INFO @ Tue, 14 Jul 2020 11:26:10: 6000000 INFO @ Tue, 14 Jul 2020 11:26:12: 2000000 INFO @ Tue, 14 Jul 2020 11:26:14: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:26:14: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:26:14: #1 total tags in treatment: 6532021 INFO @ Tue, 14 Jul 2020 11:26:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:26:14: #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 11:26:14: #1 tags after filtering in treatment: 6531815 INFO @ Tue, 14 Jul 2020 11:26:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:26:14: #1 finished! INFO @ Tue, 14 Jul 2020 11:26:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:26:15: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 11:26:15: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 11:26:15: start model_add_line... INFO @ Tue, 14 Jul 2020 11:26:15: start X-correlation... INFO @ Tue, 14 Jul 2020 11:26:15: end of X-cor INFO @ Tue, 14 Jul 2020 11:26:15: #2 finished! INFO @ Tue, 14 Jul 2020 11:26:15: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:26:15: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 14 Jul 2020 11:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05_model.r WARNING @ Tue, 14 Jul 2020 11:26:15: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:26:15: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 14 Jul 2020 11:26:15: #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 11:26:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:26:20: 3000000 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 11:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.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 11:26:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:26:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:26:28: 4000000 INFO @ Tue, 14 Jul 2020 11:26:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:26:33: 1000000 INFO @ Tue, 14 Jul 2020 11:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.05_summits.bed INFO @ Tue, 14 Jul 2020 11:26:35: Done! pass1 - making usageList (277 chroms): 1 millis pass2 - checking and writing primary data (1766 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:26:36: 5000000 INFO @ Tue, 14 Jul 2020 11:26:41: 2000000 INFO @ Tue, 14 Jul 2020 11:26:45: 6000000 INFO @ Tue, 14 Jul 2020 11:26:48: 3000000 INFO @ Tue, 14 Jul 2020 11:26:49: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:26:49: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:26:49: #1 total tags in treatment: 6532021 INFO @ Tue, 14 Jul 2020 11:26:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:26:49: #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 11:26:49: #1 tags after filtering in treatment: 6531815 INFO @ Tue, 14 Jul 2020 11:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:26:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:26:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:26:50: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 11:26:50: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 11:26:50: start model_add_line... INFO @ Tue, 14 Jul 2020 11:26:50: start X-correlation... INFO @ Tue, 14 Jul 2020 11:26:50: end of X-cor INFO @ Tue, 14 Jul 2020 11:26:50: #2 finished! INFO @ Tue, 14 Jul 2020 11:26:50: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:26:50: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 14 Jul 2020 11:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10_model.r WARNING @ Tue, 14 Jul 2020 11:26:50: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:26:50: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 14 Jul 2020 11:26:50: #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 11:26:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:26:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:27:02: 5000000 INFO @ Tue, 14 Jul 2020 11:27:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:27:09: 6000000 INFO @ Tue, 14 Jul 2020 11:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.10_summits.bed INFO @ Tue, 14 Jul 2020 11:27:12: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:27:13: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 11:27:13: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 11:27:13: #1 total tags in treatment: 6532021 INFO @ Tue, 14 Jul 2020 11:27:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:27:13: #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 11:27:13: #1 tags after filtering in treatment: 6531815 INFO @ Tue, 14 Jul 2020 11:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:27:13: #1 finished! INFO @ Tue, 14 Jul 2020 11:27:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:27:13: #2 number of paired peaks: 650 WARNING @ Tue, 14 Jul 2020 11:27:13: Fewer paired peaks (650) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 650 pairs to build model! INFO @ Tue, 14 Jul 2020 11:27:13: start model_add_line... INFO @ Tue, 14 Jul 2020 11:27:14: start X-correlation... INFO @ Tue, 14 Jul 2020 11:27:14: end of X-cor INFO @ Tue, 14 Jul 2020 11:27:14: #2 finished! INFO @ Tue, 14 Jul 2020 11:27:14: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 11:27:14: #2 alternative fragment length(s) may be 67 bps INFO @ Tue, 14 Jul 2020 11:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20_model.r WARNING @ Tue, 14 Jul 2020 11:27:14: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:27:14: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Tue, 14 Jul 2020 11:27:14: #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 11:27:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:27:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:27:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521284/SRX8521284.20_summits.bed INFO @ Tue, 14 Jul 2020 11:27:35: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 3 millis CompletedMACS2peakCalling