Job ID = 5720940 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,472,637 reads read : 4,472,637 reads written : 4,472,637 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:29 4472637 reads; of these: 4472637 (100.00%) were unpaired; of these: 331623 (7.41%) aligned 0 times 2696804 (60.30%) aligned exactly 1 time 1444210 (32.29%) aligned >1 times 92.59% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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_rmdupse_core] 561726 / 4141014 = 0.1356 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 03:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.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 03:24:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:24:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:24:48: 1000000 INFO @ Thu, 16 Apr 2020 03:24:52: 2000000 INFO @ Thu, 16 Apr 2020 03:24:57: 3000000 INFO @ Thu, 16 Apr 2020 03:25:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:00: #1 total tags in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:25:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:00: #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 03:25:00: #1 tags after filtering in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:00: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:00: #2 number of paired peaks: 172 WARNING @ Thu, 16 Apr 2020 03:25:00: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:00: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:00: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:00: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:00: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:00: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:25:00: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05_model.r WARNING @ Thu, 16 Apr 2020 03:25:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:25:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:25:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:25:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:25:08: #3 Call peaks for each chromosome... 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 03:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.05_summits.bed INFO @ Thu, 16 Apr 2020 03:25:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (838 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:25:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.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 03:25:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:18: 1000000 INFO @ Thu, 16 Apr 2020 03:25:22: 2000000 INFO @ Thu, 16 Apr 2020 03:25:27: 3000000 INFO @ Thu, 16 Apr 2020 03:25:30: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:25:30: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:25:30: #1 total tags in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:25:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:25:30: #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 03:25:30: #1 tags after filtering in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:25:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:25:30: #1 finished! INFO @ Thu, 16 Apr 2020 03:25:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:25:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:25:30: #2 number of paired peaks: 172 WARNING @ Thu, 16 Apr 2020 03:25:30: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Thu, 16 Apr 2020 03:25:30: start model_add_line... INFO @ Thu, 16 Apr 2020 03:25:30: start X-correlation... INFO @ Thu, 16 Apr 2020 03:25:30: end of X-cor INFO @ Thu, 16 Apr 2020 03:25:30: #2 finished! INFO @ Thu, 16 Apr 2020 03:25:30: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:25:30: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10_model.r WARNING @ Thu, 16 Apr 2020 03:25:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:25:30: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:25:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:25:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:25:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:25:38: #3 Call peaks for each chromosome... 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 03:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.10_summits.bed INFO @ Thu, 16 Apr 2020 03:25:41: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:25:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.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 03:25:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:25:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:25:48: 1000000 INFO @ Thu, 16 Apr 2020 03:25:52: 2000000 INFO @ Thu, 16 Apr 2020 03:25:57: 3000000 INFO @ Thu, 16 Apr 2020 03:26:00: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:26:00: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:26:00: #1 total tags in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:26:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:26:00: #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 03:26:00: #1 tags after filtering in treatment: 3579288 INFO @ Thu, 16 Apr 2020 03:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:26:00: #1 finished! INFO @ Thu, 16 Apr 2020 03:26:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:26:00: #2 number of paired peaks: 172 WARNING @ Thu, 16 Apr 2020 03:26:00: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Thu, 16 Apr 2020 03:26:00: start model_add_line... INFO @ Thu, 16 Apr 2020 03:26:00: start X-correlation... INFO @ Thu, 16 Apr 2020 03:26:00: end of X-cor INFO @ Thu, 16 Apr 2020 03:26:00: #2 finished! INFO @ Thu, 16 Apr 2020 03:26:00: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 03:26:00: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 03:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20_model.r WARNING @ Thu, 16 Apr 2020 03:26:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:26:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 03:26:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 03:26:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:26:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386739/SRX6386739.20_summits.bed INFO @ Thu, 16 Apr 2020 03:26:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。