Job ID = 6458898 SRX = SRX5775907 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:50:52 prefetch.2.10.7: 1) Downloading 'SRR8997110'... 2020-06-21T12:50:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:53:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:53:30 prefetch.2.10.7: 1) 'SRR8997110' was downloaded successfully Read 20513666 spots for SRR8997110/SRR8997110.sra Written 20513666 spots for SRR8997110/SRR8997110.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: 00:03:57 20513666 reads; of these: 20513666 (100.00%) were unpaired; of these: 15406277 (75.10%) aligned 0 times 3779219 (18.42%) aligned exactly 1 time 1328170 (6.47%) aligned >1 times 24.90% overall alignment rate Time searching: 00:03:57 Overall time: 00:03:57 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] 1641458 / 5107389 = 0.3214 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 22:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.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 22:00:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:21: 1000000 INFO @ Sun, 21 Jun 2020 22:00:29: 2000000 INFO @ Sun, 21 Jun 2020 22:00:38: 3000000 INFO @ Sun, 21 Jun 2020 22:00:41: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:00:41: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:00:41: #1 total tags in treatment: 3465931 INFO @ Sun, 21 Jun 2020 22:00:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:41: #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 22:00:41: #1 tags after filtering in treatment: 3465910 INFO @ Sun, 21 Jun 2020 22:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:41: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:42: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:00:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:42: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 22:00:42: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 22:00:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05_model.r WARNING @ Sun, 21 Jun 2020 22:00:42: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:42: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 22:00:42: #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 22:00:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:42: #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 22:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.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 22:00:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:51: 1000000 INFO @ Sun, 21 Jun 2020 22:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:54: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (1683 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:59: 2000000 INFO @ Sun, 21 Jun 2020 22:01:07: 3000000 INFO @ Sun, 21 Jun 2020 22:01:11: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:01:11: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:01:11: #1 total tags in treatment: 3465931 INFO @ Sun, 21 Jun 2020 22:01:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:11: #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 22:01:11: #1 tags after filtering in treatment: 3465910 INFO @ Sun, 21 Jun 2020 22:01:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:11: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:11: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:01:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:11: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 22:01:11: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 22:01:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10_model.r WARNING @ Sun, 21 Jun 2020 22:01:11: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:11: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 22:01:11: #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 22:01:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:11: #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 22:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.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 22:01:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:21: 1000000 INFO @ Sun, 21 Jun 2020 22:01:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.10_summits.bed INFO @ Sun, 21 Jun 2020 22:01:23: Done! pass1 - making usageList (388 chroms): 0 millis pass2 - checking and writing primary data (929 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:29: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:01:38: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:42: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:01:42: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:01:42: #1 total tags in treatment: 3465931 INFO @ Sun, 21 Jun 2020 22:01:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:42: #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 22:01:42: #1 tags after filtering in treatment: 3465910 INFO @ Sun, 21 Jun 2020 22:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:42: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:42: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:01:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:42: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 22:01:42: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 22:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20_model.r WARNING @ Sun, 21 Jun 2020 22:01:42: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:42: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sun, 21 Jun 2020 22:01:42: #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 22:01:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775907/SRX5775907.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:54: Done! pass1 - making usageList (181 chroms): 2 millis pass2 - checking and writing primary data (335 records, 4 fields): 6 millis CompletedMACS2peakCalling