Job ID = 6454671 SRX = SRX2458932 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:33:44 prefetch.2.10.7: 1) Downloading 'SRR5140281'... 2020-06-21T09:33:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:34:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:34:51 prefetch.2.10.7: 'SRR5140281' is valid 2020-06-21T09:34:51 prefetch.2.10.7: 1) 'SRR5140281' was downloaded successfully 2020-06-21T09:34:51 prefetch.2.10.7: 'SRR5140281' has 0 unresolved dependencies Read 9611221 spots for SRR5140281/SRR5140281.sra Written 9611221 spots for SRR5140281/SRR5140281.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: 00:00:01 Multiseed full-index search: 00:02:39 9611221 reads; of these: 9611221 (100.00%) were unpaired; of these: 550423 (5.73%) aligned 0 times 6947755 (72.29%) aligned exactly 1 time 2113043 (21.99%) aligned >1 times 94.27% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 5658922 / 9060798 = 0.6246 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 18:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.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 18:39:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:02: 1000000 INFO @ Sun, 21 Jun 2020 18:40:07: 2000000 INFO @ Sun, 21 Jun 2020 18:40:13: 3000000 INFO @ Sun, 21 Jun 2020 18:40:15: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:40:15: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:40:15: #1 total tags in treatment: 3401876 INFO @ Sun, 21 Jun 2020 18:40:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:15: #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 18:40:15: #1 tags after filtering in treatment: 3401670 INFO @ Sun, 21 Jun 2020 18:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:15: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 18:40:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:16: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:40:16: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05_model.r INFO @ Sun, 21 Jun 2020 18:40:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:24: #3 Call peaks for each chromosome... 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 18:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.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 18:40:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:28: Done! pass1 - making usageList (246 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:32: 1000000 INFO @ Sun, 21 Jun 2020 18:40:37: 2000000 INFO @ Sun, 21 Jun 2020 18:40:43: 3000000 INFO @ Sun, 21 Jun 2020 18:40:45: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:40:45: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:40:45: #1 total tags in treatment: 3401876 INFO @ Sun, 21 Jun 2020 18:40:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:45: #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 18:40:45: #1 tags after filtering in treatment: 3401670 INFO @ Sun, 21 Jun 2020 18:40:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:46: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 18:40:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:46: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:40:46: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10_model.r INFO @ Sun, 21 Jun 2020 18:40:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:55: #3 Call peaks for each chromosome... 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 18:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.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 18:40:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:40:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:59: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (586 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:02: 1000000 INFO @ Sun, 21 Jun 2020 18:41:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:41:13: 3000000 INFO @ Sun, 21 Jun 2020 18:41:15: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:41:15: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:41:15: #1 total tags in treatment: 3401876 INFO @ Sun, 21 Jun 2020 18:41:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:15: #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 18:41:15: #1 tags after filtering in treatment: 3401670 INFO @ Sun, 21 Jun 2020 18:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:16: #2 number of paired peaks: 2900 INFO @ Sun, 21 Jun 2020 18:41:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:16: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 18:41:16: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 18:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20_model.r INFO @ Sun, 21 Jun 2020 18:41:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:41:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2458932/SRX2458932.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:29: Done! pass1 - making usageList (127 chroms): 0 millis pass2 - checking and writing primary data (268 records, 4 fields): 6 millis CompletedMACS2peakCalling