Job ID = 6458911 SRX = SRX5775917 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:25 prefetch.2.10.7: 1) Downloading 'SRR8997120'... 2020-06-21T12:43:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:05 prefetch.2.10.7: 1) 'SRR8997120' was downloaded successfully Read 21443327 spots for SRR8997120/SRR8997120.sra Written 21443327 spots for SRR8997120/SRR8997120.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: 00:04:12 21443327 reads; of these: 21443327 (100.00%) were unpaired; of these: 15396852 (71.80%) aligned 0 times 4293792 (20.02%) aligned exactly 1 time 1752683 (8.17%) aligned >1 times 28.20% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 3490310 / 6046475 = 0.5772 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 21:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.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 21:54:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:24: 1000000 INFO @ Sun, 21 Jun 2020 21:54:32: 2000000 INFO @ Sun, 21 Jun 2020 21:54:36: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:54:36: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:54:36: #1 total tags in treatment: 2556165 INFO @ Sun, 21 Jun 2020 21:54:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:36: #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 21:54:36: #1 tags after filtering in treatment: 2556117 INFO @ Sun, 21 Jun 2020 21:54:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:36: #2 number of paired peaks: 1238 INFO @ Sun, 21 Jun 2020 21:54:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:36: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 21:54:36: #2 alternative fragment length(s) may be 78,546 bps INFO @ Sun, 21 Jun 2020 21:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:36: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:36: #2 You may need to consider one of the other alternative d(s): 78,546 WARNING @ Sun, 21 Jun 2020 21:54:36: #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 21:54:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:45: Done! 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 pass1 - making usageList (597 chroms): 2 millis pass2 - checking and writing primary data (1765 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.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 21:54:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:54: 1000000 INFO @ Sun, 21 Jun 2020 21:55:01: 2000000 INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:55:05: #1 total tags in treatment: 2556165 INFO @ Sun, 21 Jun 2020 21:55:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:05: #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 21:55:05: #1 tags after filtering in treatment: 2556117 INFO @ Sun, 21 Jun 2020 21:55:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:05: #2 number of paired peaks: 1238 INFO @ Sun, 21 Jun 2020 21:55:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:05: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2 alternative fragment length(s) may be 78,546 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:05: #2 You may need to consider one of the other alternative d(s): 78,546 WARNING @ Sun, 21 Jun 2020 21:55:05: #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 21:55:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:14: Done! pass1 - making usageList (455 chroms): 1 millis pass2 - checking and writing primary data (1168 records, 4 fields): 13 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 @ Sun, 21 Jun 2020 21:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.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 21:55:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:24: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:31: 2000000 INFO @ Sun, 21 Jun 2020 21:55:34: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:55:34: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:55:34: #1 total tags in treatment: 2556165 INFO @ Sun, 21 Jun 2020 21:55:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:34: #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 21:55:35: #1 tags after filtering in treatment: 2556117 INFO @ Sun, 21 Jun 2020 21:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:35: #2 number of paired peaks: 1238 INFO @ Sun, 21 Jun 2020 21:55:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:35: #2 predicted fragment length is 78 bps INFO @ Sun, 21 Jun 2020 21:55:35: #2 alternative fragment length(s) may be 78,546 bps INFO @ Sun, 21 Jun 2020 21:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:35: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:35: #2 You may need to consider one of the other alternative d(s): 78,546 WARNING @ Sun, 21 Jun 2020 21:55:35: #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 21:55:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775917/SRX5775917.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:44: Done! pass1 - making usageList (317 chroms): 1 millis pass2 - checking and writing primary data (543 records, 4 fields): 10 millis CompletedMACS2peakCalling