Job ID = 6627755 SRX = SRX8521402 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: 00:06:41 54562636 reads; of these: 54562636 (100.00%) were unpaired; of these: 48762926 (89.37%) aligned 0 times 4391632 (8.05%) aligned exactly 1 time 1408078 (2.58%) aligned >1 times 10.63% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 751105 / 5799710 = 0.1295 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 13:11:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.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 13:11:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:11:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:11:34: 1000000 INFO @ Tue, 14 Jul 2020 13:11:40: 2000000 INFO @ Tue, 14 Jul 2020 13:11:46: 3000000 INFO @ Tue, 14 Jul 2020 13:11:52: 4000000 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 13:11:58: 5000000 INFO @ Tue, 14 Jul 2020 13:11:58: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 13:11:58: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 13:11:58: #1 total tags in treatment: 5048605 INFO @ Tue, 14 Jul 2020 13:11:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:11:58: #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 13:11:58: #1 tags after filtering in treatment: 5048385 INFO @ Tue, 14 Jul 2020 13:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:11:58: #1 finished! INFO @ Tue, 14 Jul 2020 13:11:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:11:59: #2 number of paired peaks: 756 WARNING @ Tue, 14 Jul 2020 13:11:59: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 14 Jul 2020 13:11:59: start model_add_line... INFO @ Tue, 14 Jul 2020 13:11:59: start X-correlation... INFO @ Tue, 14 Jul 2020 13:11:59: end of X-cor INFO @ Tue, 14 Jul 2020 13:11:59: #2 finished! INFO @ Tue, 14 Jul 2020 13:11:59: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:11:59: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 13:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05_model.r WARNING @ Tue, 14 Jul 2020 13:11:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:11:59: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 13:11:59: #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 13:11:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:11:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.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 13:11:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:11:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:12:05: 1000000 INFO @ Tue, 14 Jul 2020 13:12:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:12:10: 2000000 INFO @ Tue, 14 Jul 2020 13:12:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05_peaks.xls INFO @ Tue, 14 Jul 2020 13:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.05_summits.bed INFO @ Tue, 14 Jul 2020 13:12:16: Done! INFO @ Tue, 14 Jul 2020 13:12:16: 3000000 pass1 - making usageList (171 chroms): 1 millis pass2 - checking and writing primary data (873 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:12:22: 4000000 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 13:12:28: 5000000 INFO @ Tue, 14 Jul 2020 13:12:28: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 13:12:28: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 13:12:28: #1 total tags in treatment: 5048605 INFO @ Tue, 14 Jul 2020 13:12:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:12:28: #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 13:12:28: #1 tags after filtering in treatment: 5048385 INFO @ Tue, 14 Jul 2020 13:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:12:28: #1 finished! INFO @ Tue, 14 Jul 2020 13:12:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:12:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.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 13:12:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 13:12:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 13:12:29: #2 number of paired peaks: 756 WARNING @ Tue, 14 Jul 2020 13:12:29: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 14 Jul 2020 13:12:29: start model_add_line... INFO @ Tue, 14 Jul 2020 13:12:29: start X-correlation... INFO @ Tue, 14 Jul 2020 13:12:29: end of X-cor INFO @ Tue, 14 Jul 2020 13:12:29: #2 finished! INFO @ Tue, 14 Jul 2020 13:12:29: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:12:29: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 13:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10_model.r WARNING @ Tue, 14 Jul 2020 13:12:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:12:29: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 13:12:29: #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 13:12:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 13:12:35: 1000000 INFO @ Tue, 14 Jul 2020 13:12:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:12:40: 2000000 INFO @ Tue, 14 Jul 2020 13:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10_peaks.xls INFO @ Tue, 14 Jul 2020 13:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.10_summits.bed INFO @ Tue, 14 Jul 2020 13:12:45: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 13:12:46: 3000000 INFO @ Tue, 14 Jul 2020 13:12:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 13:12:58: 5000000 INFO @ Tue, 14 Jul 2020 13:12:58: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 13:12:58: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 13:12:58: #1 total tags in treatment: 5048605 INFO @ Tue, 14 Jul 2020 13:12:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 13:12:58: #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 13:12:58: #1 tags after filtering in treatment: 5048385 INFO @ Tue, 14 Jul 2020 13:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 13:12:58: #1 finished! INFO @ Tue, 14 Jul 2020 13:12:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 13:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 13:12:59: #2 number of paired peaks: 756 WARNING @ Tue, 14 Jul 2020 13:12:59: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Tue, 14 Jul 2020 13:12:59: start model_add_line... INFO @ Tue, 14 Jul 2020 13:12:59: start X-correlation... INFO @ Tue, 14 Jul 2020 13:12:59: end of X-cor INFO @ Tue, 14 Jul 2020 13:12:59: #2 finished! INFO @ Tue, 14 Jul 2020 13:12:59: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 13:12:59: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 13:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20_model.r WARNING @ Tue, 14 Jul 2020 13:12:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 13:12:59: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 13:12:59: #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 13:12:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 13:12:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 13:13:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 13:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20_peaks.xls INFO @ Tue, 14 Jul 2020 13:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 13:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521402/SRX8521402.20_summits.bed INFO @ Tue, 14 Jul 2020 13:13:15: Done! pass1 - making usageList (75 chroms): 0 millis pass2 - checking and writing primary data (131 records, 4 fields): 4 millis CompletedMACS2peakCalling