Job ID = 6458975 SRX = SRX5827840 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:46:41 prefetch.2.10.7: 1) Downloading 'SRR9051591'... 2020-06-21T12:46:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:48:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:48:07 prefetch.2.10.7: 'SRR9051591' is valid 2020-06-21T12:48:07 prefetch.2.10.7: 1) 'SRR9051591' was downloaded successfully 2020-06-21T12:48:07 prefetch.2.10.7: 'SRR9051591' has 0 unresolved dependencies Read 13849687 spots for SRR9051591/SRR9051591.sra Written 13849687 spots for SRR9051591/SRR9051591.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: 00:02:40 13849687 reads; of these: 13849687 (100.00%) were unpaired; of these: 5332627 (38.50%) aligned 0 times 6860391 (49.53%) aligned exactly 1 time 1656669 (11.96%) aligned >1 times 61.50% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 5496139 / 8517060 = 0.6453 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 21:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.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 21:53:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:52: 1000000 INFO @ Sun, 21 Jun 2020 21:53:58: 2000000 INFO @ Sun, 21 Jun 2020 21:54:04: 3000000 INFO @ Sun, 21 Jun 2020 21:54:04: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:54:04: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:54:04: #1 total tags in treatment: 3020921 INFO @ Sun, 21 Jun 2020 21:54:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:04: #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 21:54:04: #1 tags after filtering in treatment: 3020884 INFO @ Sun, 21 Jun 2020 21:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:04: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #2 number of paired peaks: 1059 INFO @ Sun, 21 Jun 2020 21:54:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:05: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2 alternative fragment length(s) may be 57,572 bps INFO @ Sun, 21 Jun 2020 21:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:05: #2 You may need to consider one of the other alternative d(s): 57,572 WARNING @ Sun, 21 Jun 2020 21:54:05: #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 21:54:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:15: 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 (479 chroms): 1 millis pass2 - checking and writing primary data (1637 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.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 21:54:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:22: 1000000 INFO @ Sun, 21 Jun 2020 21:54:28: 2000000 INFO @ Sun, 21 Jun 2020 21:54:34: 3000000 INFO @ Sun, 21 Jun 2020 21:54:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:54:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:54:34: #1 total tags in treatment: 3020921 INFO @ Sun, 21 Jun 2020 21:54:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:34: #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 21:54:34: #1 tags after filtering in treatment: 3020884 INFO @ Sun, 21 Jun 2020 21:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:34: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:35: #2 number of paired peaks: 1059 INFO @ Sun, 21 Jun 2020 21:54:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:35: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:54:35: #2 alternative fragment length(s) may be 57,572 bps INFO @ Sun, 21 Jun 2020 21:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:35: #2 You may need to consider one of the other alternative d(s): 57,572 WARNING @ Sun, 21 Jun 2020 21:54:35: #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 21:54:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:42: #3 Call peaks for each chromosome... 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 21:54:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:45: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.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 21:54:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:53: 1000000 INFO @ Sun, 21 Jun 2020 21:54:58: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:04: 3000000 INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:55:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:55:05: #1 total tags in treatment: 3020921 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: 3020884 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: 1059 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 57 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2 alternative fragment length(s) may be 57,572 bps INFO @ Sun, 21 Jun 2020 21:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:05: #2 Since the d (57) 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): 57,572 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... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827840/SRX5827840.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:15: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 4 millis CompletedMACS2peakCalling