Job ID = 6458633 SRX = SRX5360565 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:33:22 prefetch.2.10.7: 1) Downloading 'SRR8559055'... 2020-06-21T12:33:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:58 prefetch.2.10.7: 'SRR8559055' is valid 2020-06-21T12:33:58 prefetch.2.10.7: 1) 'SRR8559055' was downloaded successfully Read 2448916 spots for SRR8559055/SRR8559055.sra Written 2448916 spots for SRR8559055/SRR8559055.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: 00:00:21 2448916 reads; of these: 2448916 (100.00%) were unpaired; of these: 813823 (33.23%) aligned 0 times 1606623 (65.61%) aligned exactly 1 time 28470 (1.16%) aligned >1 times 66.77% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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_rmdupse_core] 1529188 / 1635093 = 0.9352 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 21:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.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 21:35:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:11: #1 total tags in treatment: 105905 INFO @ Sun, 21 Jun 2020 21:35:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:11: #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 21:35:11: #1 tags after filtering in treatment: 105509 INFO @ Sun, 21 Jun 2020 21:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:11: #2 number of paired peaks: 155 WARNING @ Sun, 21 Jun 2020 21:35:11: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sun, 21 Jun 2020 21:35:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:11: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 21:35:11: #2 alternative fragment length(s) may be 45,104,126,148,168,204,236,271,311,336,400,454,499,545,579 bps INFO @ Sun, 21 Jun 2020 21:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05_model.r INFO @ Sun, 21 Jun 2020 21:35:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.05_summits.bed INFO @ Sun, 21 Jun 2020 21:35:12: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 21:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.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 21:35:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:35:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:35:41: #1 total tags in treatment: 105905 INFO @ Sun, 21 Jun 2020 21:35:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:41: #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 21:35:41: #1 tags after filtering in treatment: 105509 INFO @ Sun, 21 Jun 2020 21:35:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:41: #2 number of paired peaks: 155 WARNING @ Sun, 21 Jun 2020 21:35:41: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sun, 21 Jun 2020 21:35:41: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:41: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:41: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:41: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:41: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 21:35:41: #2 alternative fragment length(s) may be 45,104,126,148,168,204,236,271,311,336,400,454,499,545,579 bps INFO @ Sun, 21 Jun 2020 21:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10_model.r INFO @ Sun, 21 Jun 2020 21:35:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.10_summits.bed INFO @ Sun, 21 Jun 2020 21:35:42: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.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 21:36:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:36:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:36:11: #1 total tags in treatment: 105905 INFO @ Sun, 21 Jun 2020 21:36:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:36:11: #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 21:36:11: #1 tags after filtering in treatment: 105509 INFO @ Sun, 21 Jun 2020 21:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:36:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:36:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:36:12: #2 number of paired peaks: 155 WARNING @ Sun, 21 Jun 2020 21:36:12: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sun, 21 Jun 2020 21:36:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:36:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:36:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:36:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:36:12: #2 predicted fragment length is 236 bps INFO @ Sun, 21 Jun 2020 21:36:12: #2 alternative fragment length(s) may be 45,104,126,148,168,204,236,271,311,336,400,454,499,545,579 bps INFO @ Sun, 21 Jun 2020 21:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20_model.r INFO @ Sun, 21 Jun 2020 21:36:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:36:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5360565/SRX5360565.20_summits.bed INFO @ Sun, 21 Jun 2020 21:36:12: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling