Job ID = 6453602 SRX = SRX1299928 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:30:41 prefetch.2.10.7: 1) Downloading 'SRR2546847'... 2020-06-21T08:30:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:10 prefetch.2.10.7: 'SRR2546847' is valid 2020-06-21T08:31:10 prefetch.2.10.7: 1) 'SRR2546847' was downloaded successfully 2020-06-21T08:31:10 prefetch.2.10.7: 'SRR2546847' has 0 unresolved dependencies Read 1858993 spots for SRR2546847/SRR2546847.sra Written 1858993 spots for SRR2546847/SRR2546847.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: 00:00:33 1858993 reads; of these: 1858993 (100.00%) were unpaired; of these: 522996 (28.13%) aligned 0 times 687740 (37.00%) aligned exactly 1 time 648257 (34.87%) aligned >1 times 71.87% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 525562 / 1335997 = 0.3934 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 17:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.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 17:32:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:32:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:32:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:32:44: #1 total tags in treatment: 810435 INFO @ Sun, 21 Jun 2020 17:32:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:44: #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 17:32:45: #1 tags after filtering in treatment: 810061 INFO @ Sun, 21 Jun 2020 17:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:45: #2 number of paired peaks: 1697 INFO @ Sun, 21 Jun 2020 17:32:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:45: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:32:45: #2 alternative fragment length(s) may be 82,162,230,279 bps INFO @ Sun, 21 Jun 2020 17:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05_model.r WARNING @ Sun, 21 Jun 2020 17:32:45: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:32:45: #2 You may need to consider one of the other alternative d(s): 82,162,230,279 WARNING @ Sun, 21 Jun 2020 17:32:45: #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 17:32:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.05_summits.bed INFO @ Sun, 21 Jun 2020 17:32:48: Done! pass1 - making usageList (227 chroms): 0 millis pass2 - checking and writing primary data (424 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 17:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.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 17:33:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:33:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:33:15: #1 total tags in treatment: 810435 INFO @ Sun, 21 Jun 2020 17:33:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:15: #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 17:33:15: #1 tags after filtering in treatment: 810061 INFO @ Sun, 21 Jun 2020 17:33:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:15: #2 number of paired peaks: 1697 INFO @ Sun, 21 Jun 2020 17:33:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:15: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:33:15: #2 alternative fragment length(s) may be 82,162,230,279 bps INFO @ Sun, 21 Jun 2020 17:33:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10_model.r WARNING @ Sun, 21 Jun 2020 17:33:15: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:15: #2 You may need to consider one of the other alternative d(s): 82,162,230,279 WARNING @ Sun, 21 Jun 2020 17:33:15: #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 17:33:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.10_summits.bed INFO @ Sun, 21 Jun 2020 17:33:18: Done! pass1 - making usageList (107 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 5 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 17:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.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 17:33:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:33:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:33:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:33:44: #1 total tags in treatment: 810435 INFO @ Sun, 21 Jun 2020 17:33:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:44: #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 17:33:45: #1 tags after filtering in treatment: 810061 INFO @ Sun, 21 Jun 2020 17:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:45: #2 number of paired peaks: 1697 INFO @ Sun, 21 Jun 2020 17:33:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:45: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 17:33:45: #2 alternative fragment length(s) may be 82,162,230,279 bps INFO @ Sun, 21 Jun 2020 17:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20_model.r WARNING @ Sun, 21 Jun 2020 17:33:45: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:45: #2 You may need to consider one of the other alternative d(s): 82,162,230,279 WARNING @ Sun, 21 Jun 2020 17:33:45: #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 17:33:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1299928/SRX1299928.20_summits.bed INFO @ Sun, 21 Jun 2020 17:33:48: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 3 millis CompletedMACS2peakCalling