Job ID = 6458391 SRX = SRX511131 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:25:19 prefetch.2.10.7: 1) Downloading 'SRR1217236'... 2020-06-21T12:25:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:27:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:27:21 prefetch.2.10.7: 'SRR1217236' is valid 2020-06-21T12:27:21 prefetch.2.10.7: 1) 'SRR1217236' was downloaded successfully Read 10341191 spots for SRR1217236/SRR1217236.sra Written 10341191 spots for SRR1217236/SRR1217236.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: 00:03:03 10341191 reads; of these: 10341191 (100.00%) were unpaired; of these: 354284 (3.43%) aligned 0 times 6865582 (66.39%) aligned exactly 1 time 3121325 (30.18%) aligned >1 times 96.57% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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 8 files... [bam_rmdupse_core] 1757611 / 9986907 = 0.1760 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 21:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.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 21:33:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:55: 1000000 INFO @ Sun, 21 Jun 2020 21:34:01: 2000000 INFO @ Sun, 21 Jun 2020 21:34:07: 3000000 INFO @ Sun, 21 Jun 2020 21:34:14: 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 21:34:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.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 21:34:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:20: 5000000 INFO @ Sun, 21 Jun 2020 21:34:25: 1000000 INFO @ Sun, 21 Jun 2020 21:34:27: 6000000 INFO @ Sun, 21 Jun 2020 21:34:32: 2000000 INFO @ Sun, 21 Jun 2020 21:34:34: 7000000 INFO @ Sun, 21 Jun 2020 21:34:39: 3000000 INFO @ Sun, 21 Jun 2020 21:34:41: 8000000 INFO @ Sun, 21 Jun 2020 21:34:42: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:42: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:42: #1 total tags in treatment: 8229296 INFO @ Sun, 21 Jun 2020 21:34:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:42: #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 21:34:43: #1 tags after filtering in treatment: 8229194 INFO @ Sun, 21 Jun 2020 21:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:43: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:44: #2 number of paired peaks: 4588 INFO @ Sun, 21 Jun 2020 21:34:44: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:44: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:44: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:44: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:44: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 21:34:44: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 21:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05_model.r INFO @ Sun, 21 Jun 2020 21:34:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:46: 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 21:34:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.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 21:34:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:53: 5000000 INFO @ Sun, 21 Jun 2020 21:34:55: 1000000 INFO @ Sun, 21 Jun 2020 21:35:00: 6000000 INFO @ Sun, 21 Jun 2020 21:35:01: 2000000 INFO @ Sun, 21 Jun 2020 21:35:07: 3000000 INFO @ Sun, 21 Jun 2020 21:35:07: 7000000 INFO @ Sun, 21 Jun 2020 21:35:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:13: 4000000 INFO @ Sun, 21 Jun 2020 21:35:14: 8000000 INFO @ Sun, 21 Jun 2020 21:35:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:16: #1 total tags in treatment: 8229296 INFO @ Sun, 21 Jun 2020 21:35:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:16: #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 21:35:16: #1 tags after filtering in treatment: 8229194 INFO @ Sun, 21 Jun 2020 21:35:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:16: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:17: #2 number of paired peaks: 4588 INFO @ Sun, 21 Jun 2020 21:35:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:17: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 21:35:17: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 21:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10_model.r INFO @ Sun, 21 Jun 2020 21:35:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:19: 5000000 INFO @ Sun, 21 Jun 2020 21:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:20: Done! pass1 - making usageList (603 chroms): 2 millis pass2 - checking and writing primary data (6255 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:31: 7000000 INFO @ Sun, 21 Jun 2020 21:35:36: 8000000 INFO @ Sun, 21 Jun 2020 21:35:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:38: #1 total tags in treatment: 8229296 INFO @ Sun, 21 Jun 2020 21:35:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:38: #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 21:35:38: #1 tags after filtering in treatment: 8229194 INFO @ Sun, 21 Jun 2020 21:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:38: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:39: #2 number of paired peaks: 4588 INFO @ Sun, 21 Jun 2020 21:35:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:39: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 21:35:39: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 21:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20_model.r INFO @ Sun, 21 Jun 2020 21:35:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.10_summits.bed INFO @ Sun, 21 Jun 2020 21:35:53: Done! pass1 - making usageList (403 chroms): 2 millis pass2 - checking and writing primary data (4825 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511131/SRX511131.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:14: Done! pass1 - making usageList (182 chroms): 1 millis pass2 - checking and writing primary data (3642 records, 4 fields): 10 millis CompletedMACS2peakCalling