Job ID = 6454686 SRX = SRX2520635 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:25 prefetch.2.10.7: 1) Downloading 'SRR5206754'... 2020-06-21T09:35:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:40:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:40:48 prefetch.2.10.7: 1) 'SRR5206754' was downloaded successfully Read 33295538 spots for SRR5206754/SRR5206754.sra Written 33295538 spots for SRR5206754/SRR5206754.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: 00:07:14 33295538 reads; of these: 33295538 (100.00%) were unpaired; of these: 8339443 (25.05%) aligned 0 times 20299955 (60.97%) aligned exactly 1 time 4656140 (13.98%) aligned >1 times 74.95% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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_sort_core] merging from 12 files... [bam_rmdupse_core] 10527584 / 24956095 = 0.4218 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 18:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.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 18:56:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:09: 1000000 INFO @ Sun, 21 Jun 2020 18:56:15: 2000000 INFO @ Sun, 21 Jun 2020 18:56:21: 3000000 INFO @ Sun, 21 Jun 2020 18:56:27: 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 18:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.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 18:56:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:56:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:56:33: 5000000 INFO @ Sun, 21 Jun 2020 18:56:40: 1000000 INFO @ Sun, 21 Jun 2020 18:56:40: 6000000 INFO @ Sun, 21 Jun 2020 18:56:46: 2000000 INFO @ Sun, 21 Jun 2020 18:56:46: 7000000 INFO @ Sun, 21 Jun 2020 18:56:53: 8000000 INFO @ Sun, 21 Jun 2020 18:56:53: 3000000 INFO @ Sun, 21 Jun 2020 18:57:00: 9000000 INFO @ Sun, 21 Jun 2020 18:57:00: 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 18:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.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 18:57:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:07: 5000000 INFO @ Sun, 21 Jun 2020 18:57:07: 10000000 INFO @ Sun, 21 Jun 2020 18:57:11: 1000000 INFO @ Sun, 21 Jun 2020 18:57:14: 6000000 INFO @ Sun, 21 Jun 2020 18:57:14: 11000000 INFO @ Sun, 21 Jun 2020 18:57:18: 2000000 INFO @ Sun, 21 Jun 2020 18:57:21: 7000000 INFO @ Sun, 21 Jun 2020 18:57:22: 12000000 INFO @ Sun, 21 Jun 2020 18:57:25: 3000000 INFO @ Sun, 21 Jun 2020 18:57:28: 8000000 INFO @ Sun, 21 Jun 2020 18:57:29: 13000000 INFO @ Sun, 21 Jun 2020 18:57:33: 4000000 INFO @ Sun, 21 Jun 2020 18:57:35: 9000000 INFO @ Sun, 21 Jun 2020 18:57:37: 14000000 INFO @ Sun, 21 Jun 2020 18:57:40: 5000000 INFO @ Sun, 21 Jun 2020 18:57:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:40: #1 total tags in treatment: 14428511 INFO @ Sun, 21 Jun 2020 18:57:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:40: #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 18:57:41: #1 tags after filtering in treatment: 14428408 INFO @ Sun, 21 Jun 2020 18:57:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:42: #2 number of paired peaks: 2576 INFO @ Sun, 21 Jun 2020 18:57:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:42: 10000000 INFO @ Sun, 21 Jun 2020 18:57:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:42: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 18:57:42: #2 alternative fragment length(s) may be 236 bps INFO @ Sun, 21 Jun 2020 18:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05_model.r INFO @ Sun, 21 Jun 2020 18:57:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:47: 6000000 INFO @ Sun, 21 Jun 2020 18:57:49: 11000000 INFO @ Sun, 21 Jun 2020 18:57:53: 7000000 INFO @ Sun, 21 Jun 2020 18:57:56: 12000000 INFO @ Sun, 21 Jun 2020 18:58:00: 8000000 INFO @ Sun, 21 Jun 2020 18:58:03: 13000000 INFO @ Sun, 21 Jun 2020 18:58:07: 9000000 INFO @ Sun, 21 Jun 2020 18:58:10: 14000000 INFO @ Sun, 21 Jun 2020 18:58:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:13: #1 total tags in treatment: 14428511 INFO @ Sun, 21 Jun 2020 18:58:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:13: #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 18:58:13: 10000000 INFO @ Sun, 21 Jun 2020 18:58:14: #1 tags after filtering in treatment: 14428408 INFO @ Sun, 21 Jun 2020 18:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:15: #2 number of paired peaks: 2576 INFO @ Sun, 21 Jun 2020 18:58:15: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:15: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:15: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:15: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:15: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 18:58:15: #2 alternative fragment length(s) may be 236 bps INFO @ Sun, 21 Jun 2020 18:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10_model.r INFO @ Sun, 21 Jun 2020 18:58:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:26: 12000000 INFO @ Sun, 21 Jun 2020 18:58:32: 13000000 INFO @ Sun, 21 Jun 2020 18:58:38: 14000000 INFO @ Sun, 21 Jun 2020 18:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.05_summits.bed INFO @ Sun, 21 Jun 2020 18:58:39: Done! pass1 - making usageList (216 chroms): 2 millis pass2 - checking and writing primary data (6278 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:41: #1 total tags in treatment: 14428511 INFO @ Sun, 21 Jun 2020 18:58:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:41: #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 18:58:42: #1 tags after filtering in treatment: 14428408 INFO @ Sun, 21 Jun 2020 18:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:43: #2 number of paired peaks: 2576 INFO @ Sun, 21 Jun 2020 18:58:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:43: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 18:58:43: #2 alternative fragment length(s) may be 236 bps INFO @ Sun, 21 Jun 2020 18:58:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20_model.r INFO @ Sun, 21 Jun 2020 18:58:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.10_summits.bed INFO @ Sun, 21 Jun 2020 18:59:12: Done! pass1 - making usageList (184 chroms): 2 millis pass2 - checking and writing primary data (4073 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2520635/SRX2520635.20_summits.bed INFO @ Sun, 21 Jun 2020 18:59:39: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (2094 records, 4 fields): 12 millis CompletedMACS2peakCalling