Job ID = 6458724 SRX = SRX5426117 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:47:26 prefetch.2.10.7: 1) Downloading 'SRR8627319'... 2020-06-21T12:47:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:50:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:50:03 prefetch.2.10.7: 'SRR8627319' is valid 2020-06-21T12:50:03 prefetch.2.10.7: 1) 'SRR8627319' was downloaded successfully 2020-06-21T12:50:03 prefetch.2.10.7: 'SRR8627319' has 0 unresolved dependencies Read 17547438 spots for SRR8627319/SRR8627319.sra Written 17547438 spots for SRR8627319/SRR8627319.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:09 17547438 reads; of these: 17547438 (100.00%) were unpaired; of these: 17517971 (99.83%) aligned 0 times 11256 (0.06%) aligned exactly 1 time 18211 (0.10%) aligned >1 times 0.17% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 6520 / 29467 = 0.2213 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 21:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.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 21:53:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:57: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:53:57: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:53:57: #1 total tags in treatment: 22947 INFO @ Sun, 21 Jun 2020 21:53:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:57: #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 21:53:57: #1 tags after filtering in treatment: 22470 INFO @ Sun, 21 Jun 2020 21:53:57: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:53:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:57: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:53:57: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:53:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:57: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 21:53:57: #2 alternative fragment length(s) may be 182,246,297 bps INFO @ Sun, 21 Jun 2020 21:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05_model.r INFO @ Sun, 21 Jun 2020 21:53:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.05_summits.bed INFO @ Sun, 21 Jun 2020 21:53:57: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (57 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 21:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.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 21:54:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:27: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:54:27: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:54:27: #1 total tags in treatment: 22947 INFO @ Sun, 21 Jun 2020 21:54:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:27: #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 21:54:27: #1 tags after filtering in treatment: 22470 INFO @ Sun, 21 Jun 2020 21:54:27: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:54:27: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:27: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:54:27: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:27: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 21:54:27: #2 alternative fragment length(s) may be 182,246,297 bps INFO @ Sun, 21 Jun 2020 21:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10_model.r INFO @ Sun, 21 Jun 2020 21:54:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:27: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (43 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 21:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.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 21:54:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:57: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:54:57: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:54:57: #1 total tags in treatment: 22947 INFO @ Sun, 21 Jun 2020 21:54:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:57: #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 21:54:57: #1 tags after filtering in treatment: 22470 INFO @ Sun, 21 Jun 2020 21:54:57: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 21 Jun 2020 21:54:57: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:57: #2 number of paired peaks: 460 WARNING @ Sun, 21 Jun 2020 21:54:57: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:57: #2 predicted fragment length is 297 bps INFO @ Sun, 21 Jun 2020 21:54:57: #2 alternative fragment length(s) may be 182,246,297 bps INFO @ Sun, 21 Jun 2020 21:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20_model.r INFO @ Sun, 21 Jun 2020 21:54:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5426117/SRX5426117.20_summits.bed INFO @ Sun, 21 Jun 2020 21:54:57: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling