Job ID = 6454866 SRX = SRX2592455 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:36:44 prefetch.2.10.7: 1) Downloading 'SRR5289732'... 2020-06-21T09:36:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:11 prefetch.2.10.7: 'SRR5289732' is valid 2020-06-21T09:40:11 prefetch.2.10.7: 1) 'SRR5289732' was downloaded successfully Read 13485645 spots for SRR5289732/SRR5289732.sra Written 13485645 spots for SRR5289732/SRR5289732.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: 00:04:26 13485645 reads; of these: 13485645 (100.00%) were unpaired; of these: 1424141 (10.56%) aligned 0 times 8559568 (63.47%) aligned exactly 1 time 3501936 (25.97%) aligned >1 times 89.44% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 5653896 / 12061504 = 0.4688 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 18:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.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 18:48:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:49: 1000000 INFO @ Sun, 21 Jun 2020 18:48:55: 2000000 INFO @ Sun, 21 Jun 2020 18:49:01: 3000000 INFO @ Sun, 21 Jun 2020 18:49:08: 4000000 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 18:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.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 18:49:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:15: 5000000 INFO @ Sun, 21 Jun 2020 18:49:19: 1000000 INFO @ Sun, 21 Jun 2020 18:49:21: 6000000 INFO @ Sun, 21 Jun 2020 18:49:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:24: #1 total tags in treatment: 6407608 INFO @ Sun, 21 Jun 2020 18:49:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:24: #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 18:49:24: #1 tags after filtering in treatment: 6407447 INFO @ Sun, 21 Jun 2020 18:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:25: #2 number of paired peaks: 603 WARNING @ Sun, 21 Jun 2020 18:49:25: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:25: 2000000 INFO @ Sun, 21 Jun 2020 18:49:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:26: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 18:49:26: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 18:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05_model.r INFO @ Sun, 21 Jun 2020 18:49:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:32: 3000000 INFO @ Sun, 21 Jun 2020 18:49:38: 4000000 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 18:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.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 18:49:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:49:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:49:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:45: 5000000 INFO @ Sun, 21 Jun 2020 18:49:49: 1000000 INFO @ Sun, 21 Jun 2020 18:49:51: 6000000 INFO @ Sun, 21 Jun 2020 18:49:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:49:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:49:54: #1 total tags in treatment: 6407608 INFO @ Sun, 21 Jun 2020 18:49:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:54: #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 18:49:54: #1 tags after filtering in treatment: 6407447 INFO @ Sun, 21 Jun 2020 18:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.05_summits.bed INFO @ Sun, 21 Jun 2020 18:49:55: Done! INFO @ Sun, 21 Jun 2020 18:49:55: 2000000 pass1 - making usageList (589 chroms): 3 millis pass2 - checking and writing primary data (15340 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:49:55: #2 number of paired peaks: 603 WARNING @ Sun, 21 Jun 2020 18:49:55: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 21 Jun 2020 18:49:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:56: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 18:49:56: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 18:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10_model.r INFO @ Sun, 21 Jun 2020 18:49:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:01: 3000000 INFO @ Sun, 21 Jun 2020 18:50:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:14: 5000000 INFO @ Sun, 21 Jun 2020 18:50:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:20: 6000000 INFO @ Sun, 21 Jun 2020 18:50:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:50:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:50:23: #1 total tags in treatment: 6407608 INFO @ Sun, 21 Jun 2020 18:50:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:23: #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 18:50:23: #1 tags after filtering in treatment: 6407447 INFO @ Sun, 21 Jun 2020 18:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:23: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:24: #2 number of paired peaks: 603 WARNING @ Sun, 21 Jun 2020 18:50:24: Fewer paired peaks (603) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 603 pairs to build model! INFO @ Sun, 21 Jun 2020 18:50:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:24: #2 predicted fragment length is 225 bps INFO @ Sun, 21 Jun 2020 18:50:24: #2 alternative fragment length(s) may be 225 bps INFO @ Sun, 21 Jun 2020 18:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20_model.r INFO @ Sun, 21 Jun 2020 18:50:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.10_summits.bed INFO @ Sun, 21 Jun 2020 18:50:26: Done! pass1 - making usageList (440 chroms): 2 millis pass2 - checking and writing primary data (12881 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592455/SRX2592455.20_summits.bed INFO @ Sun, 21 Jun 2020 18:50:52: Done! pass1 - making usageList (302 chroms): 3 millis pass2 - checking and writing primary data (10012 records, 4 fields): 21 millis CompletedMACS2peakCalling