Job ID = 6455806 SRX = SRX3009514 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:22:21 prefetch.2.10.7: 1) Downloading 'SRR5832215'... 2020-06-21T10:22:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:49 prefetch.2.10.7: 'SRR5832215' is valid 2020-06-21T10:24:49 prefetch.2.10.7: 1) 'SRR5832215' was downloaded successfully Read 10673586 spots for SRR5832215/SRR5832215.sra Written 10673586 spots for SRR5832215/SRR5832215.sra 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 10673586 reads; of these: 10673586 (100.00%) were unpaired; of these: 4949427 (46.37%) aligned 0 times 4324299 (40.51%) aligned exactly 1 time 1399860 (13.12%) aligned >1 times 53.63% 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] 1536499 / 5724159 = 0.2684 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 @ Sun, 21 Jun 2020 19:29:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.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 @ Sun, 21 Jun 2020 19:29:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:35: 1000000 INFO @ Sun, 21 Jun 2020 19:29:40: 2000000 INFO @ Sun, 21 Jun 2020 19:29:46: 3000000 INFO @ Sun, 21 Jun 2020 19:29:51: 4000000 INFO @ Sun, 21 Jun 2020 19:29:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:29:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:29:52: #1 total tags in treatment: 4187660 INFO @ Sun, 21 Jun 2020 19:29:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:29:53: #1 tags after filtering in treatment: 4187443 INFO @ Sun, 21 Jun 2020 19:29:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:53: #2 number of paired peaks: 676 WARNING @ Sun, 21 Jun 2020 19:29:53: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sun, 21 Jun 2020 19:29:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:53: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 19:29:53: #2 alternative fragment length(s) may be 96,558 bps INFO @ Sun, 21 Jun 2020 19:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05_model.r WARNING @ Sun, 21 Jun 2020 19:29:53: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:53: #2 You may need to consider one of the other alternative d(s): 96,558 WARNING @ Sun, 21 Jun 2020 19:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:29:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:53: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 19:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.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 @ Sun, 21 Jun 2020 19:30:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:06: 1000000 INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.05_summits.bed INFO @ Sun, 21 Jun 2020 19:30:07: Done! pass1 - making usageList (492 chroms): 1 millis pass2 - checking and writing primary data (1496 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:12: 2000000 INFO @ Sun, 21 Jun 2020 19:30:18: 3000000 INFO @ Sun, 21 Jun 2020 19:30:25: 4000000 INFO @ Sun, 21 Jun 2020 19:30:26: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:30:26: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:30:26: #1 total tags in treatment: 4187660 INFO @ Sun, 21 Jun 2020 19:30:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:30:27: #1 tags after filtering in treatment: 4187443 INFO @ Sun, 21 Jun 2020 19:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:27: #2 number of paired peaks: 676 WARNING @ Sun, 21 Jun 2020 19:30:27: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:27: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 19:30:27: #2 alternative fragment length(s) may be 96,558 bps INFO @ Sun, 21 Jun 2020 19:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:27: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:27: #2 You may need to consider one of the other alternative d(s): 96,558 WARNING @ Sun, 21 Jun 2020 19:30:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:30:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:27: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 19:30:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.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 @ Sun, 21 Jun 2020 19:30:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:35: 1000000 INFO @ Sun, 21 Jun 2020 19:30:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:30:40: 2000000 INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.10_summits.bed INFO @ Sun, 21 Jun 2020 19:30:41: Done! pass1 - making usageList (254 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:30:46: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:30:51: 4000000 INFO @ Sun, 21 Jun 2020 19:30:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:30:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:30:52: #1 total tags in treatment: 4187660 INFO @ Sun, 21 Jun 2020 19:30:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:30:53: #1 tags after filtering in treatment: 4187443 INFO @ Sun, 21 Jun 2020 19:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:53: #2 number of paired peaks: 676 WARNING @ Sun, 21 Jun 2020 19:30:53: Fewer paired peaks (676) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 676 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:53: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 19:30:53: #2 alternative fragment length(s) may be 96,558 bps INFO @ Sun, 21 Jun 2020 19:30:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20_model.r WARNING @ Sun, 21 Jun 2020 19:30:53: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:30:53: #2 You may need to consider one of the other alternative d(s): 96,558 WARNING @ Sun, 21 Jun 2020 19:30:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:30:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3009514/SRX3009514.20_summits.bed INFO @ Sun, 21 Jun 2020 19:31:07: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 3 millis CompletedMACS2peakCalling