Job ID = 6457073 SRX = SRX4375836 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:43:48 prefetch.2.10.7: 1) Downloading 'SRR7506490'... 2020-06-21T11:43:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:50 prefetch.2.10.7: 'SRR7506490' is valid 2020-06-21T11:45:50 prefetch.2.10.7: 1) 'SRR7506490' was downloaded successfully Read 10673586 spots for SRR7506490/SRR7506490.sra Written 10673586 spots for SRR7506490/SRR7506490.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: 00:02:21 10673586 reads; of these: 10673586 (100.00%) were unpaired; of these: 4949447 (46.37%) aligned 0 times 4324292 (40.51%) aligned exactly 1 time 1399847 (13.12%) aligned >1 times 53.63% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 1536669 / 5724139 = 0.2685 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 20:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.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 20:51:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:20: 1000000 INFO @ Sun, 21 Jun 2020 20:51:26: 2000000 INFO @ Sun, 21 Jun 2020 20:51:33: 3000000 INFO @ Sun, 21 Jun 2020 20:51:40: 4000000 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 20:51:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:42: #1 total tags in treatment: 4187470 INFO @ Sun, 21 Jun 2020 20:51:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:42: #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 20:51:42: #1 tags after filtering in treatment: 4187270 INFO @ Sun, 21 Jun 2020 20:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:43: #2 number of paired peaks: 665 WARNING @ Sun, 21 Jun 2020 20:51:43: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sun, 21 Jun 2020 20:51:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:43: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:51:43: #2 alternative fragment length(s) may be 99,579 bps INFO @ Sun, 21 Jun 2020 20:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05_model.r WARNING @ Sun, 21 Jun 2020 20:51:43: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:43: #2 You may need to consider one of the other alternative d(s): 99,579 WARNING @ Sun, 21 Jun 2020 20:51:43: #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 20:51:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.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 20:51:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:51: 1000000 INFO @ Sun, 21 Jun 2020 20:51:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.05_summits.bed INFO @ Sun, 21 Jun 2020 20:51:57: Done! pass1 - making usageList (462 chroms): 2 millis pass2 - checking and writing primary data (1401 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:51:59: 2000000 INFO @ Sun, 21 Jun 2020 20:52:07: 3000000 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 20:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.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 20:52:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:52:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:52:16: 4000000 INFO @ Sun, 21 Jun 2020 20:52:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:18: #1 total tags in treatment: 4187470 INFO @ Sun, 21 Jun 2020 20:52:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:18: #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 20:52:19: #1 tags after filtering in treatment: 4187270 INFO @ Sun, 21 Jun 2020 20:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:19: #2 number of paired peaks: 665 WARNING @ Sun, 21 Jun 2020 20:52:19: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:19: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:19: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:52:19: #2 alternative fragment length(s) may be 99,579 bps INFO @ Sun, 21 Jun 2020 20:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10_model.r WARNING @ Sun, 21 Jun 2020 20:52:19: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:52:19: #2 You may need to consider one of the other alternative d(s): 99,579 WARNING @ Sun, 21 Jun 2020 20:52:19: #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 20:52:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:21: 1000000 INFO @ Sun, 21 Jun 2020 20:52:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:29: 2000000 INFO @ Sun, 21 Jun 2020 20:52:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:33: Done! pass1 - making usageList (271 chroms): 2 millis pass2 - checking and writing primary data (535 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:37: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:46: 4000000 INFO @ Sun, 21 Jun 2020 20:52:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:48: #1 total tags in treatment: 4187470 INFO @ Sun, 21 Jun 2020 20:52:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:48: #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 20:52:48: #1 tags after filtering in treatment: 4187270 INFO @ Sun, 21 Jun 2020 20:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:49: #2 number of paired peaks: 665 WARNING @ Sun, 21 Jun 2020 20:52:49: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sun, 21 Jun 2020 20:52:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:49: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 20:52:49: #2 alternative fragment length(s) may be 99,579 bps INFO @ Sun, 21 Jun 2020 20:52:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20_model.r WARNING @ Sun, 21 Jun 2020 20:52:49: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:52:49: #2 You may need to consider one of the other alternative d(s): 99,579 WARNING @ Sun, 21 Jun 2020 20:52:49: #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 20:52:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:52:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375836/SRX4375836.20_summits.bed INFO @ Sun, 21 Jun 2020 20:53:03: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 7 millis CompletedMACS2peakCalling