Job ID = 6453163 SRX = SRX104978 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:07:33 prefetch.2.10.7: 1) Downloading 'SRR363422'... 2020-06-21T08:07:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:09:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:09:13 prefetch.2.10.7: 'SRR363422' is valid 2020-06-21T08:09:13 prefetch.2.10.7: 1) 'SRR363422' was downloaded successfully Read 22233630 spots for SRR363422/SRR363422.sra Written 22233630 spots for SRR363422/SRR363422.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: 00:04:39 22233630 reads; of these: 22233630 (100.00%) were unpaired; of these: 789883 (3.55%) aligned 0 times 16948883 (76.23%) aligned exactly 1 time 4494864 (20.22%) aligned >1 times 96.45% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 3150800 / 21443747 = 0.1469 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 17:19:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.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 17:19:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:19:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:19:46: 1000000 INFO @ Sun, 21 Jun 2020 17:19:51: 2000000 INFO @ Sun, 21 Jun 2020 17:19:56: 3000000 INFO @ Sun, 21 Jun 2020 17:20:01: 4000000 INFO @ Sun, 21 Jun 2020 17:20:06: 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 17:20:11: 6000000 INFO @ Sun, 21 Jun 2020 17:20:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.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 17:20:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:16: 7000000 INFO @ Sun, 21 Jun 2020 17:20:16: 1000000 INFO @ Sun, 21 Jun 2020 17:20:21: 8000000 INFO @ Sun, 21 Jun 2020 17:20:21: 2000000 INFO @ Sun, 21 Jun 2020 17:20:26: 9000000 INFO @ Sun, 21 Jun 2020 17:20:26: 3000000 INFO @ Sun, 21 Jun 2020 17:20:31: 10000000 INFO @ Sun, 21 Jun 2020 17:20:31: 4000000 INFO @ Sun, 21 Jun 2020 17:20:36: 11000000 INFO @ Sun, 21 Jun 2020 17:20:36: 5000000 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 17:20:41: 6000000 INFO @ Sun, 21 Jun 2020 17:20:41: 12000000 INFO @ Sun, 21 Jun 2020 17:20:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.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 17:20:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:46: 7000000 INFO @ Sun, 21 Jun 2020 17:20:46: 13000000 INFO @ Sun, 21 Jun 2020 17:20:47: 1000000 INFO @ Sun, 21 Jun 2020 17:20:51: 8000000 INFO @ Sun, 21 Jun 2020 17:20:51: 14000000 INFO @ Sun, 21 Jun 2020 17:20:53: 2000000 INFO @ Sun, 21 Jun 2020 17:20:56: 9000000 INFO @ Sun, 21 Jun 2020 17:20:56: 15000000 INFO @ Sun, 21 Jun 2020 17:20:58: 3000000 INFO @ Sun, 21 Jun 2020 17:21:01: 10000000 INFO @ Sun, 21 Jun 2020 17:21:02: 16000000 INFO @ Sun, 21 Jun 2020 17:21:04: 4000000 INFO @ Sun, 21 Jun 2020 17:21:06: 11000000 INFO @ Sun, 21 Jun 2020 17:21:07: 17000000 INFO @ Sun, 21 Jun 2020 17:21:10: 5000000 INFO @ Sun, 21 Jun 2020 17:21:11: 12000000 INFO @ Sun, 21 Jun 2020 17:21:12: 18000000 INFO @ Sun, 21 Jun 2020 17:21:14: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:14: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:14: #1 total tags in treatment: 18292947 INFO @ Sun, 21 Jun 2020 17:21:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:14: #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 17:21:14: #1 tags after filtering in treatment: 18292940 INFO @ Sun, 21 Jun 2020 17:21:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:15: 6000000 INFO @ Sun, 21 Jun 2020 17:21:16: #2 number of paired peaks: 548 WARNING @ Sun, 21 Jun 2020 17:21:16: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Sun, 21 Jun 2020 17:21:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:16: 13000000 INFO @ Sun, 21 Jun 2020 17:21:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:16: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 17:21:16: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 17:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05_model.r INFO @ Sun, 21 Jun 2020 17:21:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:21: 14000000 INFO @ Sun, 21 Jun 2020 17:21:21: 7000000 INFO @ Sun, 21 Jun 2020 17:21:26: 15000000 INFO @ Sun, 21 Jun 2020 17:21:27: 8000000 INFO @ Sun, 21 Jun 2020 17:21:31: 16000000 INFO @ Sun, 21 Jun 2020 17:21:32: 9000000 INFO @ Sun, 21 Jun 2020 17:21:36: 17000000 INFO @ Sun, 21 Jun 2020 17:21:38: 10000000 INFO @ Sun, 21 Jun 2020 17:21:41: 18000000 INFO @ Sun, 21 Jun 2020 17:21:42: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:21:42: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:21:42: #1 total tags in treatment: 18292947 INFO @ Sun, 21 Jun 2020 17:21:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:42: #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 17:21:43: #1 tags after filtering in treatment: 18292940 INFO @ Sun, 21 Jun 2020 17:21:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:43: 11000000 INFO @ Sun, 21 Jun 2020 17:21:45: #2 number of paired peaks: 548 WARNING @ Sun, 21 Jun 2020 17:21:45: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Sun, 21 Jun 2020 17:21:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:45: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 17:21:45: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 17:21:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10_model.r INFO @ Sun, 21 Jun 2020 17:21:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:21:49: 12000000 INFO @ Sun, 21 Jun 2020 17:21:55: 13000000 INFO @ Sun, 21 Jun 2020 17:22:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:00: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:22:06: 15000000 INFO @ Sun, 21 Jun 2020 17:22:11: 16000000 INFO @ Sun, 21 Jun 2020 17:22:17: 17000000 INFO @ Sun, 21 Jun 2020 17:22:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.05_summits.bed INFO @ Sun, 21 Jun 2020 17:22:21: Done! pass1 - making usageList (277 chroms): 2 millis pass2 - checking and writing primary data (4541 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:22:22: 18000000 INFO @ Sun, 21 Jun 2020 17:22:24: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:22:24: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:22:24: #1 total tags in treatment: 18292947 INFO @ Sun, 21 Jun 2020 17:22:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:22:24: #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 17:22:25: #1 tags after filtering in treatment: 18292940 INFO @ Sun, 21 Jun 2020 17:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:22:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:22:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:22:26: #2 number of paired peaks: 548 WARNING @ Sun, 21 Jun 2020 17:22:26: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Sun, 21 Jun 2020 17:22:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:22:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:22:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:22:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:22:26: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 17:22:26: #2 alternative fragment length(s) may be 4,130 bps INFO @ Sun, 21 Jun 2020 17:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20_model.r INFO @ Sun, 21 Jun 2020 17:22:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:22:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.10_summits.bed INFO @ Sun, 21 Jun 2020 17:22:49: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX104978/SRX104978.20_summits.bed INFO @ Sun, 21 Jun 2020 17:23:30: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 4 millis CompletedMACS2peakCalling