Job ID = 6456882 SRX = SRX4047180 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:08:39 prefetch.2.10.7: 1) Downloading 'SRR7126161'... 2020-06-21T11:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:53 prefetch.2.10.7: 'SRR7126161' is valid 2020-06-21T11:11:53 prefetch.2.10.7: 1) 'SRR7126161' was downloaded successfully Read 22145669 spots for SRR7126161/SRR7126161.sra Written 22145669 spots for SRR7126161/SRR7126161.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: 00:02:46 22145669 reads; of these: 22145669 (100.00%) were unpaired; of these: 9826518 (44.37%) aligned 0 times 10415584 (47.03%) aligned exactly 1 time 1903567 (8.60%) aligned >1 times 55.63% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 7336468 / 12319151 = 0.5955 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 20:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.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 20:17:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:17:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:00: 1000000 INFO @ Sun, 21 Jun 2020 20:18:05: 2000000 INFO @ Sun, 21 Jun 2020 20:18:10: 3000000 INFO @ Sun, 21 Jun 2020 20:18:15: 4000000 INFO @ Sun, 21 Jun 2020 20:18:19: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:18:19: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:18:19: #1 total tags in treatment: 4982683 INFO @ Sun, 21 Jun 2020 20:18:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:19: #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 20:18:20: #1 tags after filtering in treatment: 4982637 INFO @ Sun, 21 Jun 2020 20:18:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:20: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 20:18:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:20: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:18:20: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:18:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05_model.r INFO @ Sun, 21 Jun 2020 20:18:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:20: #3 Pre-compute pvalue-qvalue table... 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 20:18:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.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 20:18:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:18:30: 1000000 INFO @ Sun, 21 Jun 2020 20:18:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:18:35: 2000000 INFO @ Sun, 21 Jun 2020 20:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:18:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:18:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.05_summits.bed INFO @ Sun, 21 Jun 2020 20:18:37: Done! pass1 - making usageList (584 chroms): 1 millis pass2 - checking and writing primary data (5885 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:18:40: 3000000 INFO @ Sun, 21 Jun 2020 20:18:45: 4000000 INFO @ Sun, 21 Jun 2020 20:18:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:18:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:18:50: #1 total tags in treatment: 4982683 INFO @ Sun, 21 Jun 2020 20:18:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:18:50: #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 20:18:50: #1 tags after filtering in treatment: 4982637 INFO @ Sun, 21 Jun 2020 20:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:18:50: #1 finished! INFO @ Sun, 21 Jun 2020 20:18:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:18:50: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 20:18:50: start model_add_line... INFO @ Sun, 21 Jun 2020 20:18:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:18:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:18:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:18:51: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:18:51: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10_model.r INFO @ Sun, 21 Jun 2020 20:18:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:18:51: #3 Pre-compute pvalue-qvalue table... 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 20:18:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.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 20:18:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:18:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:19:00: 1000000 INFO @ Sun, 21 Jun 2020 20:19:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:05: 2000000 INFO @ Sun, 21 Jun 2020 20:19:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.10_summits.bed INFO @ Sun, 21 Jun 2020 20:19:07: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (2512 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:19:10: 3000000 INFO @ Sun, 21 Jun 2020 20:19:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:19:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:19:20: #1 total tags in treatment: 4982683 INFO @ Sun, 21 Jun 2020 20:19:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:19:20: #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 20:19:20: #1 tags after filtering in treatment: 4982637 INFO @ Sun, 21 Jun 2020 20:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:19:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:19:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #2 number of paired peaks: 1492 INFO @ Sun, 21 Jun 2020 20:19:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:19:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:19:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:19:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:19:21: #2 predicted fragment length is 83 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2 alternative fragment length(s) may be 83 bps INFO @ Sun, 21 Jun 2020 20:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20_model.r INFO @ Sun, 21 Jun 2020 20:19:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:19:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:19:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:19:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:19:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:19:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047180/SRX4047180.20_summits.bed INFO @ Sun, 21 Jun 2020 20:19:38: Done! pass1 - making usageList (154 chroms): 1 millis pass2 - checking and writing primary data (986 records, 4 fields): 6 millis CompletedMACS2peakCalling