Job ID = 6459058 SRX = SRX6386736 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:49:52 prefetch.2.10.7: 1) Downloading 'SRR9624468'... 2020-06-21T12:49:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:52:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:52:59 prefetch.2.10.7: 'SRR9624468' is valid 2020-06-21T12:52:59 prefetch.2.10.7: 1) 'SRR9624468' was downloaded successfully Read 13107189 spots for SRR9624468/SRR9624468.sra Written 13107189 spots for SRR9624468/SRR9624468.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: 00:02:41 13107189 reads; of these: 13107189 (100.00%) were unpaired; of these: 5737228 (43.77%) aligned 0 times 5462035 (41.67%) aligned exactly 1 time 1907926 (14.56%) aligned >1 times 56.23% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 2432484 / 7369961 = 0.3301 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 21:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.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 21:58:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:31: 1000000 INFO @ Sun, 21 Jun 2020 21:58:37: 2000000 INFO @ Sun, 21 Jun 2020 21:58:43: 3000000 INFO @ Sun, 21 Jun 2020 21:58:49: 4000000 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 21:58:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:58:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:58:55: #1 total tags in treatment: 4937477 INFO @ Sun, 21 Jun 2020 21:58:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:55: #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 21:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.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 21:58:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:56: #1 tags after filtering in treatment: 4937431 INFO @ Sun, 21 Jun 2020 21:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:56: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 21:58:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:56: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 21:58:56: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 21:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05_model.r INFO @ Sun, 21 Jun 2020 21:58:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:01: 1000000 INFO @ Sun, 21 Jun 2020 21:59:07: 2000000 INFO @ Sun, 21 Jun 2020 21:59:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:12: 3000000 INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.05_summits.bed INFO @ Sun, 21 Jun 2020 21:59:13: Done! pass1 - making usageList (603 chroms): 2 millis pass2 - checking and writing primary data (2198 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:18: 4000000 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 21:59:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:59:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:59:23: #1 total tags in treatment: 4937477 INFO @ Sun, 21 Jun 2020 21:59:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:23: #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 21:59:24: #1 tags after filtering in treatment: 4937431 INFO @ Sun, 21 Jun 2020 21:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:24: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 21:59:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:24: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 21:59:24: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 21:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10_model.r INFO @ Sun, 21 Jun 2020 21:59:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.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 21:59:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:31: 1000000 INFO @ Sun, 21 Jun 2020 21:59:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:37: 2000000 INFO @ Sun, 21 Jun 2020 21:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:40: Done! pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (1496 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:59:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:59:50: 4000000 INFO @ Sun, 21 Jun 2020 21:59:56: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:59:56: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:59:56: #1 total tags in treatment: 4937477 INFO @ Sun, 21 Jun 2020 21:59:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:56: #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 21:59:56: #1 tags after filtering in treatment: 4937431 INFO @ Sun, 21 Jun 2020 21:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:57: #2 number of paired peaks: 1377 INFO @ Sun, 21 Jun 2020 21:59:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:57: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 21:59:57: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 21:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20_model.r INFO @ Sun, 21 Jun 2020 21:59:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:00:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386736/SRX6386736.20_summits.bed INFO @ Sun, 21 Jun 2020 22:00:14: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 11 millis CompletedMACS2peakCalling