Job ID = 6456638 SRX = SRX386287 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:53:47 prefetch.2.10.7: 1) Downloading 'SRR1041952'... 2020-06-21T10:53:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:45 prefetch.2.10.7: 'SRR1041952' is valid 2020-06-21T10:54:45 prefetch.2.10.7: 1) 'SRR1041952' was downloaded successfully Read 9469024 spots for SRR1041952/SRR1041952.sra Written 9469024 spots for SRR1041952/SRR1041952.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: 00:00:37 9469024 reads; of these: 9469024 (100.00%) were unpaired; of these: 9178830 (96.94%) aligned 0 times 238172 (2.52%) aligned exactly 1 time 52022 (0.55%) aligned >1 times 3.06% overall alignment rate Time searching: 00:00:37 Overall time: 00:00:37 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] 32122 / 290194 = 0.1107 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 19:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.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 19:56:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:22: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 19:56:22: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 19:56:22: #1 total tags in treatment: 258072 INFO @ Sun, 21 Jun 2020 19:56:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:22: #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 19:56:22: #1 tags after filtering in treatment: 257183 INFO @ Sun, 21 Jun 2020 19:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:22: #2 number of paired peaks: 3932 INFO @ Sun, 21 Jun 2020 19:56:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:22: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 19:56:22: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 19:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05_model.r INFO @ Sun, 21 Jun 2020 19:56:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:23: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (397 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 19:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.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 19:56:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:52: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 19:56:52: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 19:56:52: #1 total tags in treatment: 258072 INFO @ Sun, 21 Jun 2020 19:56:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:52: #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 19:56:52: #1 tags after filtering in treatment: 257183 INFO @ Sun, 21 Jun 2020 19:56:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:52: #2 number of paired peaks: 3932 INFO @ Sun, 21 Jun 2020 19:56:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:52: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 19:56:52: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 19:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10_model.r INFO @ Sun, 21 Jun 2020 19:56:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (86 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... INFO @ Sun, 21 Jun 2020 19:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.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 19:57:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:20: #1 read treatment tags... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:57:22: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 19:57:22: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 19:57:22: #1 total tags in treatment: 258072 INFO @ Sun, 21 Jun 2020 19:57:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:22: #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 19:57:22: #1 tags after filtering in treatment: 257183 INFO @ Sun, 21 Jun 2020 19:57:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:22: #2 number of paired peaks: 3932 INFO @ Sun, 21 Jun 2020 19:57:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:22: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 19:57:22: #2 alternative fragment length(s) may be 93 bps INFO @ Sun, 21 Jun 2020 19:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20_model.r INFO @ Sun, 21 Jun 2020 19:57:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX386287/SRX386287.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 1 millis CompletedMACS2peakCalling