Job ID = 5720574 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,212,934 reads read : 11,212,934 reads written : 11,212,934 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289711.sra.cache’: No such file or directory 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: 00:02:51 11212934 reads; of these: 11212934 (100.00%) were unpaired; of these: 1078920 (9.62%) aligned 0 times 9091649 (81.08%) aligned exactly 1 time 1042365 (9.30%) aligned >1 times 90.38% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5351079 / 10134014 = 0.5280 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 @ Thu, 16 Apr 2020 00:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.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 @ Thu, 16 Apr 2020 00:39:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:50: 1000000 INFO @ Thu, 16 Apr 2020 00:39:56: 2000000 INFO @ Thu, 16 Apr 2020 00:40:02: 3000000 INFO @ Thu, 16 Apr 2020 00:40:08: 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 @ Thu, 16 Apr 2020 00:40:13: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:40:13: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:40:13: #1 total tags in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:40:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:40:13: #1 tags after filtering in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:13: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.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 @ Thu, 16 Apr 2020 00:40:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:14: #2 number of paired peaks: 309 WARNING @ Thu, 16 Apr 2020 00:40:14: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:14: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:14: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:40:14: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05_model.r INFO @ Thu, 16 Apr 2020 00:40:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:19: 1000000 INFO @ Thu, 16 Apr 2020 00:40:26: 2000000 INFO @ Thu, 16 Apr 2020 00:40:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:32: 3000000 INFO @ Thu, 16 Apr 2020 00:40:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.05_summits.bed INFO @ Thu, 16 Apr 2020 00:40:35: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14685 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:40:38: 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 @ Thu, 16 Apr 2020 00:40:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.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 @ Thu, 16 Apr 2020 00:40:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:43: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:40:43: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:40:43: #1 total tags in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:40:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:40:43: #1 tags after filtering in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:40:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:44: #2 number of paired peaks: 309 WARNING @ Thu, 16 Apr 2020 00:40:44: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:44: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:44: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:40:44: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10_model.r INFO @ Thu, 16 Apr 2020 00:40:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:49: 1000000 INFO @ Thu, 16 Apr 2020 00:40:56: 2000000 INFO @ Thu, 16 Apr 2020 00:40:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:02: 3000000 INFO @ Thu, 16 Apr 2020 00:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.10_summits.bed INFO @ Thu, 16 Apr 2020 00:41:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12489 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:09: 4000000 INFO @ Thu, 16 Apr 2020 00:41:13: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:41:13: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:41:13: #1 total tags in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:41:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:41:13: #1 tags after filtering in treatment: 4782935 INFO @ Thu, 16 Apr 2020 00:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:13: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:13: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:14: #2 number of paired peaks: 309 WARNING @ Thu, 16 Apr 2020 00:41:14: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:14: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:14: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:14: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:14: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:14: #2 predicted fragment length is 183 bps INFO @ Thu, 16 Apr 2020 00:41:14: #2 alternative fragment length(s) may be 183 bps INFO @ Thu, 16 Apr 2020 00:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20_model.r INFO @ Thu, 16 Apr 2020 00:41:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:27: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592434/SRX2592434.20_summits.bed INFO @ Thu, 16 Apr 2020 00:41:34: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9602 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。