Job ID = 6455312 SRX = SRX287686 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:48:40 prefetch.2.10.7: 1) Downloading 'SRR869874'... 2020-06-21T09:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:50:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:50:24 prefetch.2.10.7: 'SRR869874' is valid 2020-06-21T09:50:24 prefetch.2.10.7: 1) 'SRR869874' was downloaded successfully Read 11258758 spots for SRR869874/SRR869874.sra Written 11258758 spots for SRR869874/SRR869874.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:19 11258758 reads; of these: 11258758 (100.00%) were unpaired; of these: 690831 (6.14%) aligned 0 times 7184268 (63.81%) aligned exactly 1 time 3383659 (30.05%) aligned >1 times 93.86% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1456456 / 10567927 = 0.1378 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 18:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.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 18:57:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:27: 1000000 INFO @ Sun, 21 Jun 2020 18:57:32: 2000000 INFO @ Sun, 21 Jun 2020 18:57:37: 3000000 INFO @ Sun, 21 Jun 2020 18:57:42: 4000000 INFO @ Sun, 21 Jun 2020 18:57:47: 5000000 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 18:57:52: 6000000 INFO @ Sun, 21 Jun 2020 18:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.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 18:57:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:57: 7000000 INFO @ Sun, 21 Jun 2020 18:57:57: 1000000 INFO @ Sun, 21 Jun 2020 18:58:02: 2000000 INFO @ Sun, 21 Jun 2020 18:58:03: 8000000 INFO @ Sun, 21 Jun 2020 18:58:08: 3000000 INFO @ Sun, 21 Jun 2020 18:58:08: 9000000 INFO @ Sun, 21 Jun 2020 18:58:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:09: #1 total tags in treatment: 9111471 INFO @ Sun, 21 Jun 2020 18:58:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:09: #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 18:58:09: #1 tags after filtering in treatment: 9111469 INFO @ Sun, 21 Jun 2020 18:58:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:10: #2 number of paired peaks: 853 WARNING @ Sun, 21 Jun 2020 18:58:10: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:10: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:58:10: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 18:58:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05_model.r WARNING @ Sun, 21 Jun 2020 18:58:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:10: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 18:58:10: #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 18:58:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:13: 4000000 INFO @ Sun, 21 Jun 2020 18:58:18: 5000000 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 18:58:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.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 18:58:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:23: 6000000 INFO @ Sun, 21 Jun 2020 18:58:27: 1000000 INFO @ Sun, 21 Jun 2020 18:58:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:28: 7000000 INFO @ Sun, 21 Jun 2020 18:58:32: 2000000 INFO @ Sun, 21 Jun 2020 18:58:34: 8000000 INFO @ Sun, 21 Jun 2020 18:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:37: Done! INFO @ Sun, 21 Jun 2020 18:58:38: 3000000 pass1 - making usageList (592 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:39: 9000000 INFO @ Sun, 21 Jun 2020 18:58:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:40: #1 total tags in treatment: 9111471 INFO @ Sun, 21 Jun 2020 18:58:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:40: #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 18:58:41: #1 tags after filtering in treatment: 9111469 INFO @ Sun, 21 Jun 2020 18:58:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:41: #2 number of paired peaks: 853 WARNING @ Sun, 21 Jun 2020 18:58:41: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:41: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:58:41: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 18:58:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10_model.r WARNING @ Sun, 21 Jun 2020 18:58:41: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:41: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 18:58:41: #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 18:58:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:43: 4000000 INFO @ Sun, 21 Jun 2020 18:58:48: 5000000 INFO @ Sun, 21 Jun 2020 18:58:53: 6000000 INFO @ Sun, 21 Jun 2020 18:58:58: 7000000 INFO @ Sun, 21 Jun 2020 18:59:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:03: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:59:08: 9000000 INFO @ Sun, 21 Jun 2020 18:59:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:09: Done! INFO @ Sun, 21 Jun 2020 18:59:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:09: #1 total tags in treatment: 9111471 INFO @ Sun, 21 Jun 2020 18:59:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (491 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:09: #1 tags after filtering in treatment: 9111469 INFO @ Sun, 21 Jun 2020 18:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:10: #2 number of paired peaks: 853 WARNING @ Sun, 21 Jun 2020 18:59:10: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Sun, 21 Jun 2020 18:59:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:10: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 18:59:10: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 18:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20_model.r WARNING @ Sun, 21 Jun 2020 18:59:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:10: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 18:59:10: #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 18:59:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:59:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287686/SRX287686.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:37: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (704 records, 4 fields): 10 millis CompletedMACS2peakCalling