Job ID = 6454253 SRX = SRX193329 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:04 prefetch.2.10.7: 1) Downloading 'SRR585062'... 2020-06-21T08:54:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:07 prefetch.2.10.7: 'SRR585062' is valid 2020-06-21T08:56:07 prefetch.2.10.7: 1) 'SRR585062' was downloaded successfully Read 15694616 spots for SRR585062/SRR585062.sra Written 15694616 spots for SRR585062/SRR585062.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: 00:04:52 15694616 reads; of these: 15694616 (100.00%) were unpaired; of these: 551799 (3.52%) aligned 0 times 10572726 (67.37%) aligned exactly 1 time 4570091 (29.12%) aligned >1 times 96.48% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 2160195 / 15142817 = 0.1427 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 18:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.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 18:05:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:40: 1000000 INFO @ Sun, 21 Jun 2020 18:05:45: 2000000 INFO @ Sun, 21 Jun 2020 18:05:50: 3000000 INFO @ Sun, 21 Jun 2020 18:05:55: 4000000 INFO @ Sun, 21 Jun 2020 18:06:01: 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 18:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.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 18:06:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:06: 6000000 INFO @ Sun, 21 Jun 2020 18:06:10: 1000000 INFO @ Sun, 21 Jun 2020 18:06:11: 7000000 INFO @ Sun, 21 Jun 2020 18:06:15: 2000000 INFO @ Sun, 21 Jun 2020 18:06:16: 8000000 INFO @ Sun, 21 Jun 2020 18:06:21: 3000000 INFO @ Sun, 21 Jun 2020 18:06:21: 9000000 INFO @ Sun, 21 Jun 2020 18:06:26: 4000000 INFO @ Sun, 21 Jun 2020 18:06:27: 10000000 INFO @ Sun, 21 Jun 2020 18:06:32: 5000000 INFO @ Sun, 21 Jun 2020 18:06:32: 11000000 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 18:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.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 18:06:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:37: 6000000 INFO @ Sun, 21 Jun 2020 18:06:38: 12000000 INFO @ Sun, 21 Jun 2020 18:06:39: 1000000 INFO @ Sun, 21 Jun 2020 18:06:42: 7000000 INFO @ Sun, 21 Jun 2020 18:06:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:06:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:06:43: #1 total tags in treatment: 12982622 INFO @ Sun, 21 Jun 2020 18:06:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:43: #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 18:06:44: #1 tags after filtering in treatment: 12982543 INFO @ Sun, 21 Jun 2020 18:06:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:44: 2000000 INFO @ Sun, 21 Jun 2020 18:06:45: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 18:06:45: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 18:06:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:45: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:06:45: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 18:06:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05_model.r WARNING @ Sun, 21 Jun 2020 18:06:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:06:45: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 18:06:45: #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 18:06:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:06:48: 8000000 INFO @ Sun, 21 Jun 2020 18:06:49: 3000000 INFO @ Sun, 21 Jun 2020 18:06:53: 9000000 INFO @ Sun, 21 Jun 2020 18:06:53: 4000000 INFO @ Sun, 21 Jun 2020 18:06:58: 5000000 INFO @ Sun, 21 Jun 2020 18:06:58: 10000000 INFO @ Sun, 21 Jun 2020 18:07:03: 6000000 INFO @ Sun, 21 Jun 2020 18:07:04: 11000000 INFO @ Sun, 21 Jun 2020 18:07:08: 7000000 INFO @ Sun, 21 Jun 2020 18:07:09: 12000000 INFO @ Sun, 21 Jun 2020 18:07:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:12: 8000000 INFO @ Sun, 21 Jun 2020 18:07:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:15: #1 total tags in treatment: 12982622 INFO @ Sun, 21 Jun 2020 18:07:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:15: #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 18:07:15: #1 tags after filtering in treatment: 12982543 INFO @ Sun, 21 Jun 2020 18:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:16: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 18:07:16: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:16: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:07:16: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 18:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10_model.r WARNING @ Sun, 21 Jun 2020 18:07:16: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:16: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 18:07:16: #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 18:07:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:17: 9000000 INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:22: 10000000 INFO @ Sun, 21 Jun 2020 18:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:22: Done! pass1 - making usageList (654 chroms): 2 millis pass2 - checking and writing primary data (2902 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:27: 11000000 INFO @ Sun, 21 Jun 2020 18:07:31: 12000000 INFO @ Sun, 21 Jun 2020 18:07:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:36: #1 total tags in treatment: 12982622 INFO @ Sun, 21 Jun 2020 18:07:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:36: #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 18:07:37: #1 tags after filtering in treatment: 12982543 INFO @ Sun, 21 Jun 2020 18:07:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:37: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:38: #2 number of paired peaks: 794 WARNING @ Sun, 21 Jun 2020 18:07:38: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:38: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 18:07:38: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 18:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20_model.r WARNING @ Sun, 21 Jun 2020 18:07:38: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:38: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 18:07:38: #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 18:07:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:55: Done! pass1 - making usageList (460 chroms): 2 millis pass2 - checking and writing primary data (1358 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193329/SRX193329.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:15: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (491 records, 4 fields): 7 millis CompletedMACS2peakCalling