Job ID = 6528335 SRX = SRX5360589 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:44:25 prefetch.2.10.7: 1) Downloading 'SRR8559065'... 2020-06-29T14:44:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:44:46 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:44:46 prefetch.2.10.7: 'SRR8559065' is valid 2020-06-29T14:44:46 prefetch.2.10.7: 1) 'SRR8559065' was downloaded successfully Read 995528 spots for SRR8559065/SRR8559065.sra Written 995528 spots for SRR8559065/SRR8559065.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: 00:00:08 995528 reads; of these: 995528 (100.00%) were unpaired; of these: 648363 (65.13%) aligned 0 times 330050 (33.15%) aligned exactly 1 time 17115 (1.72%) aligned >1 times 34.87% overall alignment rate Time searching: 00:00:08 Overall time: 00:00:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 280393 / 347165 = 0.8077 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 @ Mon, 29 Jun 2020 23:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.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 @ Mon, 29 Jun 2020 23:45:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:45:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:45:47: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:45:47: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:45:47: #1 total tags in treatment: 66772 INFO @ Mon, 29 Jun 2020 23:45:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:45:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:45:47: #1 tags after filtering in treatment: 66770 INFO @ Mon, 29 Jun 2020 23:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:45:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:45:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:45:47: #2 number of paired peaks: 107 WARNING @ Mon, 29 Jun 2020 23:45:47: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Mon, 29 Jun 2020 23:45:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:45:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:45:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:45:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:45:47: #2 predicted fragment length is 52 bps INFO @ Mon, 29 Jun 2020 23:45:47: #2 alternative fragment length(s) may be 52,160,227,268,327,454,479,540,567 bps INFO @ Mon, 29 Jun 2020 23:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05_model.r WARNING @ Mon, 29 Jun 2020 23:45:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:45:47: #2 You may need to consider one of the other alternative d(s): 52,160,227,268,327,454,479,540,567 WARNING @ Mon, 29 Jun 2020 23:45:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:45:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:47: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.05_summits.bed INFO @ Mon, 29 Jun 2020 23:45:47: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 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 @ Mon, 29 Jun 2020 23:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.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 @ Mon, 29 Jun 2020 23:46:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:46:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:46:17: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:46:17: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:46:17: #1 total tags in treatment: 66772 INFO @ Mon, 29 Jun 2020 23:46:17: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:46:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:46:17: #1 tags after filtering in treatment: 66770 INFO @ Mon, 29 Jun 2020 23:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:46:17: #1 finished! INFO @ Mon, 29 Jun 2020 23:46:17: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:46:17: #2 number of paired peaks: 107 WARNING @ Mon, 29 Jun 2020 23:46:17: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Mon, 29 Jun 2020 23:46:17: start model_add_line... INFO @ Mon, 29 Jun 2020 23:46:17: start X-correlation... INFO @ Mon, 29 Jun 2020 23:46:17: end of X-cor INFO @ Mon, 29 Jun 2020 23:46:17: #2 finished! INFO @ Mon, 29 Jun 2020 23:46:17: #2 predicted fragment length is 52 bps INFO @ Mon, 29 Jun 2020 23:46:17: #2 alternative fragment length(s) may be 52,160,227,268,327,454,479,540,567 bps INFO @ Mon, 29 Jun 2020 23:46:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10_model.r WARNING @ Mon, 29 Jun 2020 23:46:17: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:46:17: #2 You may need to consider one of the other alternative d(s): 52,160,227,268,327,454,479,540,567 WARNING @ Mon, 29 Jun 2020 23:46:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:46:17: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:46:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:46:17: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.10_summits.bed INFO @ Mon, 29 Jun 2020 23:46:17: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 1 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.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 @ Mon, 29 Jun 2020 23:46:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:46:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:46:47: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:46:47: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:46:47: #1 total tags in treatment: 66772 INFO @ Mon, 29 Jun 2020 23:46:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:46:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:46:47: #1 tags after filtering in treatment: 66770 INFO @ Mon, 29 Jun 2020 23:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:46:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:46:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:46:47: #2 number of paired peaks: 107 WARNING @ Mon, 29 Jun 2020 23:46:47: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Mon, 29 Jun 2020 23:46:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:46:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:46:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:46:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:46:47: #2 predicted fragment length is 52 bps INFO @ Mon, 29 Jun 2020 23:46:47: #2 alternative fragment length(s) may be 52,160,227,268,327,454,479,540,567 bps INFO @ Mon, 29 Jun 2020 23:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20_model.r WARNING @ Mon, 29 Jun 2020 23:46:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:46:47: #2 You may need to consider one of the other alternative d(s): 52,160,227,268,327,454,479,540,567 WARNING @ Mon, 29 Jun 2020 23:46:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:46:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:46:47: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360589/SRX5360589.20_summits.bed INFO @ Mon, 29 Jun 2020 23:46:47: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling