Job ID = 6458242 SRX = SRX5011009 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:37 prefetch.2.10.7: 1) Downloading 'SRR8191458'... 2020-06-21T12:17:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:30 prefetch.2.10.7: 1) 'SRR8191458' was downloaded successfully 2020-06-21T12:20:30 prefetch.2.10.7: 'SRR8191458' has 0 unresolved dependencies Read 32843529 spots for SRR8191458/SRR8191458.sra Written 32843529 spots for SRR8191458/SRR8191458.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 32843529 reads; of these: 32843529 (100.00%) were unpaired; of these: 6048495 (18.42%) aligned 0 times 21002940 (63.95%) aligned exactly 1 time 5792094 (17.64%) aligned >1 times 81.58% 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] 14230806 / 26795034 = 0.5311 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 21:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.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 21:33:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:31: 1000000 INFO @ Sun, 21 Jun 2020 21:33:36: 2000000 INFO @ Sun, 21 Jun 2020 21:33:41: 3000000 INFO @ Sun, 21 Jun 2020 21:33:46: 4000000 INFO @ Sun, 21 Jun 2020 21:33:51: 5000000 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 21:33:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.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 21:33:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:33:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:33:57: 6000000 INFO @ Sun, 21 Jun 2020 21:34:03: 1000000 INFO @ Sun, 21 Jun 2020 21:34:03: 7000000 INFO @ Sun, 21 Jun 2020 21:34:10: 8000000 INFO @ Sun, 21 Jun 2020 21:34:10: 2000000 INFO @ Sun, 21 Jun 2020 21:34:16: 9000000 INFO @ Sun, 21 Jun 2020 21:34:18: 3000000 INFO @ Sun, 21 Jun 2020 21:34:23: 10000000 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 21:34:25: 4000000 INFO @ Sun, 21 Jun 2020 21:34:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.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 21:34:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:29: 11000000 INFO @ Sun, 21 Jun 2020 21:34:32: 1000000 INFO @ Sun, 21 Jun 2020 21:34:33: 5000000 INFO @ Sun, 21 Jun 2020 21:34:36: 12000000 INFO @ Sun, 21 Jun 2020 21:34:39: 2000000 INFO @ Sun, 21 Jun 2020 21:34:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:34:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:34:40: #1 total tags in treatment: 12564228 INFO @ Sun, 21 Jun 2020 21:34:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:40: #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 21:34:40: #1 tags after filtering in treatment: 12564162 INFO @ Sun, 21 Jun 2020 21:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:41: 6000000 INFO @ Sun, 21 Jun 2020 21:34:41: #2 number of paired peaks: 2328 INFO @ Sun, 21 Jun 2020 21:34:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:41: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 21:34:41: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 21:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05_model.r INFO @ Sun, 21 Jun 2020 21:34:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:46: 3000000 INFO @ Sun, 21 Jun 2020 21:34:49: 7000000 INFO @ Sun, 21 Jun 2020 21:34:52: 4000000 INFO @ Sun, 21 Jun 2020 21:34:56: 8000000 INFO @ Sun, 21 Jun 2020 21:34:58: 5000000 INFO @ Sun, 21 Jun 2020 21:35:04: 9000000 INFO @ Sun, 21 Jun 2020 21:35:05: 6000000 INFO @ Sun, 21 Jun 2020 21:35:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:11: 7000000 INFO @ Sun, 21 Jun 2020 21:35:11: 10000000 INFO @ Sun, 21 Jun 2020 21:35:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:35:18: 11000000 INFO @ Sun, 21 Jun 2020 21:35:24: 9000000 INFO @ Sun, 21 Jun 2020 21:35:25: 12000000 INFO @ Sun, 21 Jun 2020 21:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:26: Done! pass1 - making usageList (752 chroms): 3 millis pass2 - checking and writing primary data (10380 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:29: #1 total tags in treatment: 12564228 INFO @ Sun, 21 Jun 2020 21:35:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:29: #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 21:35:30: #1 tags after filtering in treatment: 12564162 INFO @ Sun, 21 Jun 2020 21:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:30: 10000000 INFO @ Sun, 21 Jun 2020 21:35:31: #2 number of paired peaks: 2328 INFO @ Sun, 21 Jun 2020 21:35:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:31: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 21:35:31: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 21:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10_model.r INFO @ Sun, 21 Jun 2020 21:35:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:36: 11000000 INFO @ Sun, 21 Jun 2020 21:35:41: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:44: #1 total tags in treatment: 12564228 INFO @ Sun, 21 Jun 2020 21:35:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:44: #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 21:35:45: #1 tags after filtering in treatment: 12564162 INFO @ Sun, 21 Jun 2020 21:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:46: #2 number of paired peaks: 2328 INFO @ Sun, 21 Jun 2020 21:35:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:46: #2 predicted fragment length is 182 bps INFO @ Sun, 21 Jun 2020 21:35:46: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 21 Jun 2020 21:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20_model.r INFO @ Sun, 21 Jun 2020 21:35:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.10_summits.bed INFO @ Sun, 21 Jun 2020 21:36:15: Done! pass1 - making usageList (657 chroms): 2 millis pass2 - checking and writing primary data (6866 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011009/SRX5011009.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:29: Done! pass1 - making usageList (492 chroms): 2 millis pass2 - checking and writing primary data (3660 records, 4 fields): 17 millis CompletedMACS2peakCalling