Job ID = 6454789 SRX = SRX2592392 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:39:25 prefetch.2.10.7: 1) Downloading 'SRR5289669'... 2020-06-21T09:39:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:57 prefetch.2.10.7: 'SRR5289669' is valid 2020-06-21T09:40:57 prefetch.2.10.7: 1) 'SRR5289669' was downloaded successfully Read 7050454 spots for SRR5289669/SRR5289669.sra Written 7050454 spots for SRR5289669/SRR5289669.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: 00:01:58 7050454 reads; of these: 7050454 (100.00%) were unpaired; of these: 503345 (7.14%) aligned 0 times 5359420 (76.02%) aligned exactly 1 time 1187689 (16.85%) aligned >1 times 92.86% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 1330926 / 6547109 = 0.2033 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 18:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.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 18:45:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:33: 1000000 INFO @ Sun, 21 Jun 2020 18:45:37: 2000000 INFO @ Sun, 21 Jun 2020 18:45:42: 3000000 INFO @ Sun, 21 Jun 2020 18:45:47: 4000000 INFO @ Sun, 21 Jun 2020 18:45:52: 5000000 INFO @ Sun, 21 Jun 2020 18:45:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:45:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:45:53: #1 total tags in treatment: 5216183 INFO @ Sun, 21 Jun 2020 18:45:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:53: #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 18:45:53: #1 tags after filtering in treatment: 5215882 INFO @ Sun, 21 Jun 2020 18:45:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:54: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 18:45:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:54: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:45:54: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:45:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05_model.r INFO @ Sun, 21 Jun 2020 18:45:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:54: #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 18:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.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 18:45:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:03: 1000000 INFO @ Sun, 21 Jun 2020 18:46:07: 2000000 INFO @ Sun, 21 Jun 2020 18:46:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:12: 3000000 INFO @ Sun, 21 Jun 2020 18:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.05_summits.bed INFO @ Sun, 21 Jun 2020 18:46:15: Done! pass1 - making usageList (119 chroms): 2 millis pass2 - checking and writing primary data (9372 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:17: 4000000 INFO @ Sun, 21 Jun 2020 18:46:22: 5000000 INFO @ Sun, 21 Jun 2020 18:46:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:46:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:46:23: #1 total tags in treatment: 5216183 INFO @ Sun, 21 Jun 2020 18:46:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:23: #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 18:46:23: #1 tags after filtering in treatment: 5215882 INFO @ Sun, 21 Jun 2020 18:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:24: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 18:46:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:24: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:46:24: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10_model.r INFO @ Sun, 21 Jun 2020 18:46:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:24: #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 18:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.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 18:46:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:33: 1000000 INFO @ Sun, 21 Jun 2020 18:46:38: 2000000 INFO @ Sun, 21 Jun 2020 18:46:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:43: 3000000 INFO @ Sun, 21 Jun 2020 18:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:45: Done! pass1 - making usageList (80 chroms): 2 millis pass2 - checking and writing primary data (4963 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:47: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:52: 5000000 INFO @ Sun, 21 Jun 2020 18:46:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:46:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:46:54: #1 total tags in treatment: 5216183 INFO @ Sun, 21 Jun 2020 18:46:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:54: #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 18:46:54: #1 tags after filtering in treatment: 5215882 INFO @ Sun, 21 Jun 2020 18:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:55: #2 number of paired peaks: 2295 INFO @ Sun, 21 Jun 2020 18:46:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:55: #2 predicted fragment length is 204 bps INFO @ Sun, 21 Jun 2020 18:46:55: #2 alternative fragment length(s) may be 204 bps INFO @ Sun, 21 Jun 2020 18:46:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20_model.r INFO @ Sun, 21 Jun 2020 18:46:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592392/SRX2592392.20_summits.bed INFO @ Sun, 21 Jun 2020 18:47:16: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2067 records, 4 fields): 6 millis CompletedMACS2peakCalling