Job ID = 6455057 SRX = SRX2642404 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:59 prefetch.2.10.7: 1) Downloading 'SRR5345744'... 2020-06-21T09:31:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:00 prefetch.2.10.7: 'SRR5345744' is valid 2020-06-21T09:33:00 prefetch.2.10.7: 1) 'SRR5345744' was downloaded successfully 2020-06-21T09:33:00 prefetch.2.10.7: 'SRR5345744' has 0 unresolved dependencies Read 3667111 spots for SRR5345744/SRR5345744.sra Written 3667111 spots for SRR5345744/SRR5345744.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: 00:01:33 3667111 reads; of these: 3667111 (100.00%) were unpaired; of these: 811485 (22.13%) aligned 0 times 2169616 (59.16%) aligned exactly 1 time 686010 (18.71%) aligned >1 times 77.87% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 101654 / 2855626 = 0.0356 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 18:36:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.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 18:36:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:27: 1000000 INFO @ Sun, 21 Jun 2020 18:36:35: 2000000 INFO @ Sun, 21 Jun 2020 18:36:42: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 18:36:42: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 18:36:42: #1 total tags in treatment: 2753972 INFO @ Sun, 21 Jun 2020 18:36:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:42: #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 18:36:42: #1 tags after filtering in treatment: 2753923 INFO @ Sun, 21 Jun 2020 18:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:42: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:36:42: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:36:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:43: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:36:43: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 18:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05_model.r WARNING @ Sun, 21 Jun 2020 18:36:43: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:36:43: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 18:36:43: #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 18:36:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:43: #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 18:36:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.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 18:36:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.05_summits.bed INFO @ Sun, 21 Jun 2020 18:36:52: Done! pass1 - making usageList (305 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:36:57: 1000000 INFO @ Sun, 21 Jun 2020 18:37:06: 2000000 INFO @ Sun, 21 Jun 2020 18:37:13: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 18:37:13: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 18:37:13: #1 total tags in treatment: 2753972 INFO @ Sun, 21 Jun 2020 18:37:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:13: #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 18:37:13: #1 tags after filtering in treatment: 2753923 INFO @ Sun, 21 Jun 2020 18:37:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:13: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:37:13: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:13: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:37:13: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 18:37:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10_model.r WARNING @ Sun, 21 Jun 2020 18:37:13: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:37:13: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 18:37:13: #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 18:37:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:13: #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 18:37:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.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 18:37:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.10_summits.bed INFO @ Sun, 21 Jun 2020 18:37:23: Done! pass1 - making usageList (162 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:37:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:37:36: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:37:43: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 18:37:43: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 18:37:43: #1 total tags in treatment: 2753972 INFO @ Sun, 21 Jun 2020 18:37:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:37:43: #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 18:37:43: #1 tags after filtering in treatment: 2753923 INFO @ Sun, 21 Jun 2020 18:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:37:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:37:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:37:43: #2 number of paired peaks: 391 WARNING @ Sun, 21 Jun 2020 18:37:43: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Sun, 21 Jun 2020 18:37:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:37:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:37:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:37:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:37:43: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 18:37:43: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 18:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20_model.r WARNING @ Sun, 21 Jun 2020 18:37:43: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:37:43: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 18:37:43: #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 18:37:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:37:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642404/SRX2642404.20_summits.bed INFO @ Sun, 21 Jun 2020 18:37:53: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 3 millis CompletedMACS2peakCalling