Job ID = 6458654 SRX = SRX5360583 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:26 prefetch.2.10.7: 1) Downloading 'SRR8559089'... 2020-06-21T12:43:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:44:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:44:20 prefetch.2.10.7: 'SRR8559089' is valid 2020-06-21T12:44:20 prefetch.2.10.7: 1) 'SRR8559089' was downloaded successfully Read 5117467 spots for SRR8559089/SRR8559089.sra Written 5117467 spots for SRR8559089/SRR8559089.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: 00:00:46 5117467 reads; of these: 5117467 (100.00%) were unpaired; of these: 1556361 (30.41%) aligned 0 times 3519126 (68.77%) aligned exactly 1 time 41980 (0.82%) aligned >1 times 69.59% overall alignment rate Time searching: 00:00:47 Overall time: 00:00:47 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] 3391825 / 3561106 = 0.9525 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 21:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.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 21:46:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:18: #1 total tags in treatment: 169281 INFO @ Sun, 21 Jun 2020 21:46:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:18: #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 21:46:18: #1 tags after filtering in treatment: 168635 INFO @ Sun, 21 Jun 2020 21:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:18: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 21:46:18: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 21:46:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:18: #2 predicted fragment length is 302 bps INFO @ Sun, 21 Jun 2020 21:46:18: #2 alternative fragment length(s) may be 110,179,232,283,302,417 bps INFO @ Sun, 21 Jun 2020 21:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05_model.r INFO @ Sun, 21 Jun 2020 21:46:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.05_summits.bed INFO @ Sun, 21 Jun 2020 21:46:19: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (23 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 21:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.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 21:46:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:46:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:46:48: #1 total tags in treatment: 169281 INFO @ Sun, 21 Jun 2020 21:46:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:48: #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 21:46:48: #1 tags after filtering in treatment: 168635 INFO @ Sun, 21 Jun 2020 21:46:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 21:46:48: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 21:46:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:48: #2 predicted fragment length is 302 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2 alternative fragment length(s) may be 110,179,232,283,302,417 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10_model.r INFO @ Sun, 21 Jun 2020 21:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:46:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.10_summits.bed INFO @ Sun, 21 Jun 2020 21:46:49: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (17 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 21:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.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 21:47:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:47:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:47:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:47:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:47:18: #1 total tags in treatment: 169281 INFO @ Sun, 21 Jun 2020 21:47:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:18: #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 21:47:18: #1 tags after filtering in treatment: 168635 INFO @ Sun, 21 Jun 2020 21:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:18: #2 number of paired peaks: 457 WARNING @ Sun, 21 Jun 2020 21:47:18: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Sun, 21 Jun 2020 21:47:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:18: #2 predicted fragment length is 302 bps INFO @ Sun, 21 Jun 2020 21:47:18: #2 alternative fragment length(s) may be 110,179,232,283,302,417 bps INFO @ Sun, 21 Jun 2020 21:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20_model.r INFO @ Sun, 21 Jun 2020 21:47:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360583/SRX5360583.20_summits.bed INFO @ Sun, 21 Jun 2020 21:47:20: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 1 millis CompletedMACS2peakCalling