Job ID = 6452426 SRX = SRX013049 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:23:33 prefetch.2.10.7: 1) Downloading 'SRR030315'... 2020-06-21T07:23:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:23:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:23:56 prefetch.2.10.7: 'SRR030315' is valid 2020-06-21T07:23:56 prefetch.2.10.7: 1) 'SRR030315' was downloaded successfully Read 1936311 spots for SRR030315/SRR030315.sra Written 1936311 spots for SRR030315/SRR030315.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: 00:00:18 1936311 reads; of these: 1936311 (100.00%) were unpaired; of these: 181321 (9.36%) aligned 0 times 1592866 (82.26%) aligned exactly 1 time 162124 (8.37%) aligned >1 times 90.64% overall alignment rate Time searching: 00:00:18 Overall time: 00:00:18 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] 579158 / 1754990 = 0.3300 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 16:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.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 16:25:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:25:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:25:22: 1000000 INFO @ Sun, 21 Jun 2020 16:25:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:25:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:25:23: #1 total tags in treatment: 1175832 INFO @ Sun, 21 Jun 2020 16:25:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:25:23: #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 16:25:23: #1 tags after filtering in treatment: 1175254 INFO @ Sun, 21 Jun 2020 16:25:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:25:23: #1 finished! INFO @ Sun, 21 Jun 2020 16:25:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:25:24: #2 number of paired peaks: 4628 INFO @ Sun, 21 Jun 2020 16:25:24: start model_add_line... INFO @ Sun, 21 Jun 2020 16:25:24: start X-correlation... INFO @ Sun, 21 Jun 2020 16:25:24: end of X-cor INFO @ Sun, 21 Jun 2020 16:25:24: #2 finished! INFO @ Sun, 21 Jun 2020 16:25:24: #2 predicted fragment length is 257 bps INFO @ Sun, 21 Jun 2020 16:25:24: #2 alternative fragment length(s) may be 257 bps INFO @ Sun, 21 Jun 2020 16:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05_model.r INFO @ Sun, 21 Jun 2020 16:25:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:25:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:25:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:25:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:25:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.05_summits.bed INFO @ Sun, 21 Jun 2020 16:25:29: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 6 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 16:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.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 16:25:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:25:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:25:51: 1000000 INFO @ Sun, 21 Jun 2020 16:25:53: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:25:53: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:25:53: #1 total tags in treatment: 1175832 INFO @ Sun, 21 Jun 2020 16:25:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:25:53: #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 16:25:53: #1 tags after filtering in treatment: 1175254 INFO @ Sun, 21 Jun 2020 16:25:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:25:53: #1 finished! INFO @ Sun, 21 Jun 2020 16:25:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:25:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:25:53: #2 number of paired peaks: 4628 INFO @ Sun, 21 Jun 2020 16:25:53: start model_add_line... INFO @ Sun, 21 Jun 2020 16:25:53: start X-correlation... INFO @ Sun, 21 Jun 2020 16:25:53: end of X-cor INFO @ Sun, 21 Jun 2020 16:25:53: #2 finished! INFO @ Sun, 21 Jun 2020 16:25:53: #2 predicted fragment length is 257 bps INFO @ Sun, 21 Jun 2020 16:25:53: #2 alternative fragment length(s) may be 257 bps INFO @ Sun, 21 Jun 2020 16:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10_model.r INFO @ Sun, 21 Jun 2020 16:25:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:25:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:25:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.10_summits.bed INFO @ Sun, 21 Jun 2020 16:25:58: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (995 records, 4 fields): 3 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 INFO @ Sun, 21 Jun 2020 16:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.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 16:26:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:26:15: #1 read treatment tags... 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 16:26:22: 1000000 INFO @ Sun, 21 Jun 2020 16:26:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:26:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:26:23: #1 total tags in treatment: 1175832 INFO @ Sun, 21 Jun 2020 16:26:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:26:23: #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 16:26:23: #1 tags after filtering in treatment: 1175254 INFO @ Sun, 21 Jun 2020 16:26:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:26:23: #1 finished! INFO @ Sun, 21 Jun 2020 16:26:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:26:24: #2 number of paired peaks: 4628 INFO @ Sun, 21 Jun 2020 16:26:24: start model_add_line... INFO @ Sun, 21 Jun 2020 16:26:24: start X-correlation... INFO @ Sun, 21 Jun 2020 16:26:24: end of X-cor INFO @ Sun, 21 Jun 2020 16:26:24: #2 finished! INFO @ Sun, 21 Jun 2020 16:26:24: #2 predicted fragment length is 257 bps INFO @ Sun, 21 Jun 2020 16:26:24: #2 alternative fragment length(s) may be 257 bps INFO @ Sun, 21 Jun 2020 16:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20_model.r INFO @ Sun, 21 Jun 2020 16:26:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:26:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013049/SRX013049.20_summits.bed INFO @ Sun, 21 Jun 2020 16:26:29: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 millis CompletedMACS2peakCalling