Job ID = 6459914 SRX = SRX994742 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:55:49 prefetch.2.10.7: 1) Downloading 'SRR1973460'... 2020-06-21T13:55:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:58:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:58:00 prefetch.2.10.7: 1) 'SRR1973460' was downloaded successfully Read 19469994 spots for SRR1973460/SRR1973460.sra Written 19469994 spots for SRR1973460/SRR1973460.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: 00:05:12 19469994 reads; of these: 19469994 (100.00%) were unpaired; of these: 3370913 (17.31%) aligned 0 times 11567354 (59.41%) aligned exactly 1 time 4531727 (23.28%) aligned >1 times 82.69% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 2512030 / 16099081 = 0.1560 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 23:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.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 23:08:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:08:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:08:49: 1000000 INFO @ Sun, 21 Jun 2020 23:08:54: 2000000 INFO @ Sun, 21 Jun 2020 23:09:00: 3000000 INFO @ Sun, 21 Jun 2020 23:09:06: 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 23:09:12: 5000000 INFO @ Sun, 21 Jun 2020 23:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.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 23:09:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:09:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:09:19: 6000000 INFO @ Sun, 21 Jun 2020 23:09:19: 1000000 INFO @ Sun, 21 Jun 2020 23:09:25: 7000000 INFO @ Sun, 21 Jun 2020 23:09:26: 2000000 INFO @ Sun, 21 Jun 2020 23:09:32: 8000000 INFO @ Sun, 21 Jun 2020 23:09:33: 3000000 INFO @ Sun, 21 Jun 2020 23:09:39: 9000000 INFO @ Sun, 21 Jun 2020 23:09:39: 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 23:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.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 23:09:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:09:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:09:45: 10000000 INFO @ Sun, 21 Jun 2020 23:09:46: 5000000 INFO @ Sun, 21 Jun 2020 23:09:50: 1000000 INFO @ Sun, 21 Jun 2020 23:09:52: 11000000 INFO @ Sun, 21 Jun 2020 23:09:53: 6000000 INFO @ Sun, 21 Jun 2020 23:09:57: 2000000 INFO @ Sun, 21 Jun 2020 23:10:00: 12000000 INFO @ Sun, 21 Jun 2020 23:10:00: 7000000 INFO @ Sun, 21 Jun 2020 23:10:04: 3000000 INFO @ Sun, 21 Jun 2020 23:10:07: 13000000 INFO @ Sun, 21 Jun 2020 23:10:07: 8000000 INFO @ Sun, 21 Jun 2020 23:10:11: 4000000 INFO @ Sun, 21 Jun 2020 23:10:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:10:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:10:11: #1 total tags in treatment: 13587051 INFO @ Sun, 21 Jun 2020 23:10:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:11: #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 23:10:11: #1 tags after filtering in treatment: 13587050 INFO @ Sun, 21 Jun 2020 23:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:11: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:12: #2 number of paired peaks: 401 WARNING @ Sun, 21 Jun 2020 23:10:12: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:12: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:13: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:13: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:13: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:13: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 23:10:13: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 23:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05_model.r INFO @ Sun, 21 Jun 2020 23:10:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:14: 9000000 INFO @ Sun, 21 Jun 2020 23:10:18: 5000000 INFO @ Sun, 21 Jun 2020 23:10:21: 10000000 INFO @ Sun, 21 Jun 2020 23:10:25: 6000000 INFO @ Sun, 21 Jun 2020 23:10:28: 11000000 INFO @ Sun, 21 Jun 2020 23:10:32: 7000000 INFO @ Sun, 21 Jun 2020 23:10:35: 12000000 INFO @ Sun, 21 Jun 2020 23:10:39: 8000000 INFO @ Sun, 21 Jun 2020 23:10:42: 13000000 INFO @ Sun, 21 Jun 2020 23:10:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:10:46: 9000000 INFO @ Sun, 21 Jun 2020 23:10:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:10:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:10:47: #1 total tags in treatment: 13587051 INFO @ Sun, 21 Jun 2020 23:10:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:47: #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 23:10:47: #1 tags after filtering in treatment: 13587050 INFO @ Sun, 21 Jun 2020 23:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:47: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:48: #2 number of paired peaks: 401 WARNING @ Sun, 21 Jun 2020 23:10:48: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:48: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:48: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:48: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:48: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:48: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 23:10:48: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 23:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10_model.r INFO @ Sun, 21 Jun 2020 23:10:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:53: 10000000 INFO @ Sun, 21 Jun 2020 23:10:59: 11000000 INFO @ Sun, 21 Jun 2020 23:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.05_summits.bed INFO @ Sun, 21 Jun 2020 23:11:02: Done! pass1 - making usageList (715 chroms): 1 millis pass2 - checking and writing primary data (4500 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:11:06: 12000000 INFO @ Sun, 21 Jun 2020 23:11:13: 13000000 INFO @ Sun, 21 Jun 2020 23:11:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:11:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:11:17: #1 total tags in treatment: 13587051 INFO @ Sun, 21 Jun 2020 23:11:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:11:17: #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 23:11:17: #1 tags after filtering in treatment: 13587050 INFO @ Sun, 21 Jun 2020 23:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:11:17: #1 finished! INFO @ Sun, 21 Jun 2020 23:11:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:11:18: #2 number of paired peaks: 401 WARNING @ Sun, 21 Jun 2020 23:11:18: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Sun, 21 Jun 2020 23:11:18: start model_add_line... INFO @ Sun, 21 Jun 2020 23:11:19: start X-correlation... INFO @ Sun, 21 Jun 2020 23:11:19: end of X-cor INFO @ Sun, 21 Jun 2020 23:11:19: #2 finished! INFO @ Sun, 21 Jun 2020 23:11:19: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 23:11:19: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 23:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20_model.r INFO @ Sun, 21 Jun 2020 23:11:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:11:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.10_summits.bed INFO @ Sun, 21 Jun 2020 23:11:35: Done! pass1 - making usageList (534 chroms): 2 millis pass2 - checking and writing primary data (2344 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:11:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX994742/SRX994742.20_summits.bed INFO @ Sun, 21 Jun 2020 23:12:05: Done! pass1 - making usageList (252 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 9 millis CompletedMACS2peakCalling