Job ID = 6458723 SRX = SRX5426116 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:22 prefetch.2.10.7: 1) Downloading 'SRR8627318'... 2020-06-21T12:34:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:37:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:37:22 prefetch.2.10.7: 1) 'SRR8627318' was downloaded successfully 2020-06-21T12:37:22 prefetch.2.10.7: 'SRR8627318' has 0 unresolved dependencies Read 20662185 spots for SRR8627318/SRR8627318.sra Written 20662185 spots for SRR8627318/SRR8627318.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: 00:02:12 20662185 reads; of these: 20662185 (100.00%) were unpaired; of these: 20635437 (99.87%) aligned 0 times 11559 (0.06%) aligned exactly 1 time 15189 (0.07%) aligned >1 times 0.13% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 3770 / 26748 = 0.1409 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 21:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.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 21:41:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:18: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:41:18: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:41:18: #1 total tags in treatment: 22978 INFO @ Sun, 21 Jun 2020 21:41:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:18: #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 21:41:18: #1 tags after filtering in treatment: 22517 INFO @ Sun, 21 Jun 2020 21:41:18: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:41:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:18: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 21:41:18: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 21:41:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:18: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 21:41:18: #2 alternative fragment length(s) may be 129,140,300 bps INFO @ Sun, 21 Jun 2020 21:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05_model.r INFO @ Sun, 21 Jun 2020 21:41:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.05_summits.bed INFO @ Sun, 21 Jun 2020 21:41:19: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 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 @ Sun, 21 Jun 2020 21:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.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 21:41:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:49: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:41:49: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:41:49: #1 total tags in treatment: 22978 INFO @ Sun, 21 Jun 2020 21:41:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:49: #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 21:41:49: #1 tags after filtering in treatment: 22517 INFO @ Sun, 21 Jun 2020 21:41:49: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:41:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:49: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 21:41:49: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 21:41:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:49: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 21:41:49: #2 alternative fragment length(s) may be 129,140,300 bps INFO @ Sun, 21 Jun 2020 21:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10_model.r INFO @ Sun, 21 Jun 2020 21:41:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:41:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:41:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.10_summits.bed INFO @ Sun, 21 Jun 2020 21:41:49: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (28 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 @ Sun, 21 Jun 2020 21:42:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.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 21:42:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:18: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:42:18: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:42:18: #1 total tags in treatment: 22978 INFO @ Sun, 21 Jun 2020 21:42:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:18: #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 21:42:18: #1 tags after filtering in treatment: 22517 INFO @ Sun, 21 Jun 2020 21:42:18: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:42:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:18: #2 number of paired peaks: 473 WARNING @ Sun, 21 Jun 2020 21:42:18: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 21 Jun 2020 21:42:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:18: #2 predicted fragment length is 300 bps INFO @ Sun, 21 Jun 2020 21:42:18: #2 alternative fragment length(s) may be 129,140,300 bps INFO @ Sun, 21 Jun 2020 21:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20_model.r INFO @ Sun, 21 Jun 2020 21:42:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426116/SRX5426116.20_summits.bed INFO @ Sun, 21 Jun 2020 21:42:19: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling