Job ID = 6456671 SRX = SRX3937197 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:08:24 prefetch.2.10.7: 1) Downloading 'SRR7004617'... 2020-06-21T11:08:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:00 prefetch.2.10.7: 'SRR7004617' is valid 2020-06-21T11:09:00 prefetch.2.10.7: 1) 'SRR7004617' was downloaded successfully 2020-06-21T11:09:00 prefetch.2.10.7: 'SRR7004617' has 0 unresolved dependencies Read 2056059 spots for SRR7004617/SRR7004617.sra Written 2056059 spots for SRR7004617/SRR7004617.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: 00:00:53 2056059 reads; of these: 2056059 (100.00%) were unpaired; of these: 114228 (5.56%) aligned 0 times 1470652 (71.53%) aligned exactly 1 time 471179 (22.92%) aligned >1 times 94.44% overall alignment rate Time searching: 00:00:53 Overall time: 00:00:53 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] 30665 / 1941831 = 0.0158 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 20:11:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.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 20:11:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:25: 1000000 INFO @ Sun, 21 Jun 2020 20:11:32: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:11:32: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:11:32: #1 total tags in treatment: 1911166 INFO @ Sun, 21 Jun 2020 20:11:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:32: #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 20:11:32: #1 tags after filtering in treatment: 1911083 INFO @ Sun, 21 Jun 2020 20:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:33: #2 number of paired peaks: 493 WARNING @ Sun, 21 Jun 2020 20:11:33: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sun, 21 Jun 2020 20:11:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:33: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 20:11:33: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 20:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05_model.r WARNING @ Sun, 21 Jun 2020 20:11:33: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:11:33: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 20:11:33: #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 20:11:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:11:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.05_summits.bed INFO @ Sun, 21 Jun 2020 20:11:40: Done! pass1 - making usageList (208 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 26 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 20:11:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.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 20:11:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:11:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:11:55: 1000000 INFO @ Sun, 21 Jun 2020 20:12:02: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:12:02: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:12:02: #1 total tags in treatment: 1911166 INFO @ Sun, 21 Jun 2020 20:12:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:02: #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 20:12:03: #1 tags after filtering in treatment: 1911083 INFO @ Sun, 21 Jun 2020 20:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:03: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:03: #2 number of paired peaks: 493 WARNING @ Sun, 21 Jun 2020 20:12:03: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:03: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 20:12:03: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 20:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10_model.r WARNING @ Sun, 21 Jun 2020 20:12:03: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:03: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 20:12:03: #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 20:12:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:12:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.10_summits.bed INFO @ Sun, 21 Jun 2020 20:12:10: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (206 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 20:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.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 20:12:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:12:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:12:25: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:12:32: #1 tag size is determined as 98 bps INFO @ Sun, 21 Jun 2020 20:12:32: #1 tag size = 98 INFO @ Sun, 21 Jun 2020 20:12:32: #1 total tags in treatment: 1911166 INFO @ Sun, 21 Jun 2020 20:12:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:12:32: #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 20:12:32: #1 tags after filtering in treatment: 1911083 INFO @ Sun, 21 Jun 2020 20:12:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:12:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:12:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:12:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:12:32: #2 number of paired peaks: 493 WARNING @ Sun, 21 Jun 2020 20:12:32: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Sun, 21 Jun 2020 20:12:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:12:32: start X-correlation... INFO @ Sun, 21 Jun 2020 20:12:32: end of X-cor INFO @ Sun, 21 Jun 2020 20:12:32: #2 finished! INFO @ Sun, 21 Jun 2020 20:12:32: #2 predicted fragment length is 107 bps INFO @ Sun, 21 Jun 2020 20:12:32: #2 alternative fragment length(s) may be 107 bps INFO @ Sun, 21 Jun 2020 20:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20_model.r WARNING @ Sun, 21 Jun 2020 20:12:32: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:12:32: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sun, 21 Jun 2020 20:12:32: #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 20:12:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:12:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:12:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:12:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:12:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:12:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3937197/SRX3937197.20_summits.bed INFO @ Sun, 21 Jun 2020 20:12:39: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 3 millis CompletedMACS2peakCalling