Job ID = 6458637 SRX = SRX5360569 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:45:25 prefetch.2.10.7: 1) Downloading 'SRR8559059'... 2020-06-21T12:45:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:14 prefetch.2.10.7: 'SRR8559059' is valid 2020-06-21T12:46:14 prefetch.2.10.7: 1) 'SRR8559059' was downloaded successfully Read 2543465 spots for SRR8559059/SRR8559059.sra Written 2543465 spots for SRR8559059/SRR8559059.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: 00:00:25 2543465 reads; of these: 2543465 (100.00%) were unpaired; of these: 846171 (33.27%) aligned 0 times 1665452 (65.48%) aligned exactly 1 time 31842 (1.25%) aligned >1 times 66.73% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 1585881 / 1697294 = 0.9344 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 21:47:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.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 21:47:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:37: #1 total tags in treatment: 111413 INFO @ Sun, 21 Jun 2020 21:47:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:37: #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 21:47:37: #1 tags after filtering in treatment: 110959 INFO @ Sun, 21 Jun 2020 21:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:38: #2 number of paired peaks: 215 WARNING @ Sun, 21 Jun 2020 21:47:38: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sun, 21 Jun 2020 21:47:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:38: #2 predicted fragment length is 280 bps INFO @ Sun, 21 Jun 2020 21:47:38: #2 alternative fragment length(s) may be 0,46,84,122,169,206,253,280,353,389,437,484,501 bps INFO @ Sun, 21 Jun 2020 21:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05_model.r INFO @ Sun, 21 Jun 2020 21:47:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:39: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (17 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 21:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.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 21:48:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:07: #1 total tags in treatment: 111413 INFO @ Sun, 21 Jun 2020 21:48:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:07: #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 21:48:07: #1 tags after filtering in treatment: 110959 INFO @ Sun, 21 Jun 2020 21:48:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:07: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:08: #2 number of paired peaks: 215 WARNING @ Sun, 21 Jun 2020 21:48:08: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sun, 21 Jun 2020 21:48:08: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:08: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:08: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:08: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:08: #2 predicted fragment length is 280 bps INFO @ Sun, 21 Jun 2020 21:48:08: #2 alternative fragment length(s) may be 0,46,84,122,169,206,253,280,353,389,437,484,501 bps INFO @ Sun, 21 Jun 2020 21:48:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10_model.r INFO @ Sun, 21 Jun 2020 21:48:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.10_summits.bed INFO @ Sun, 21 Jun 2020 21:48:09: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 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 21:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.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 21:48:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:48:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:48:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:48:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:48:38: #1 total tags in treatment: 111413 INFO @ Sun, 21 Jun 2020 21:48:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:48:38: #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 21:48:38: #1 tags after filtering in treatment: 110959 INFO @ Sun, 21 Jun 2020 21:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:48:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:48:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:48:38: #2 number of paired peaks: 215 WARNING @ Sun, 21 Jun 2020 21:48:38: Fewer paired peaks (215) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 215 pairs to build model! INFO @ Sun, 21 Jun 2020 21:48:38: start model_add_line... INFO @ Sun, 21 Jun 2020 21:48:38: start X-correlation... INFO @ Sun, 21 Jun 2020 21:48:38: end of X-cor INFO @ Sun, 21 Jun 2020 21:48:38: #2 finished! INFO @ Sun, 21 Jun 2020 21:48:38: #2 predicted fragment length is 280 bps INFO @ Sun, 21 Jun 2020 21:48:38: #2 alternative fragment length(s) may be 0,46,84,122,169,206,253,280,353,389,437,484,501 bps INFO @ Sun, 21 Jun 2020 21:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20_model.r INFO @ Sun, 21 Jun 2020 21:48:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:48:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360569/SRX5360569.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:39: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling