Job ID = 5720894 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,299,501 reads read : 24,299,501 reads written : 24,299,501 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: 00:05:44 24299501 reads; of these: 24299501 (100.00%) were unpaired; of these: 18037841 (74.23%) aligned 0 times 4039061 (16.62%) aligned exactly 1 time 2222599 (9.15%) aligned >1 times 25.77% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 3019102 / 6261660 = 0.4822 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 03:13:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.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 03:13:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:13:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:13:44: 1000000 INFO @ Thu, 16 Apr 2020 03:13:49: 2000000 INFO @ Thu, 16 Apr 2020 03:13:55: 3000000 INFO @ Thu, 16 Apr 2020 03:13:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:13:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:13:56: #1 total tags in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:13:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:13:56: #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 03:13:56: #1 tags after filtering in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:13:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:13:56: #1 finished! INFO @ Thu, 16 Apr 2020 03:13:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:13:56: #2 number of paired peaks: 946 WARNING @ Thu, 16 Apr 2020 03:13:56: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Thu, 16 Apr 2020 03:13:56: start model_add_line... INFO @ Thu, 16 Apr 2020 03:13:56: start X-correlation... INFO @ Thu, 16 Apr 2020 03:13:56: end of X-cor INFO @ Thu, 16 Apr 2020 03:13:56: #2 finished! INFO @ Thu, 16 Apr 2020 03:13:56: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:13:56: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05_model.r WARNING @ Thu, 16 Apr 2020 03:13:56: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:13:56: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:13:56: #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 03:13:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:14:03: #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 03:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.05_summits.bed INFO @ Thu, 16 Apr 2020 03:14:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2073 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:14:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.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 03:14:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:14:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:14:14: 1000000 INFO @ Thu, 16 Apr 2020 03:14:21: 2000000 INFO @ Thu, 16 Apr 2020 03:14:27: 3000000 INFO @ Thu, 16 Apr 2020 03:14:29: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:14:29: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:14:29: #1 total tags in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:14:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:14:29: #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 03:14:29: #1 tags after filtering in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:14:29: #1 finished! INFO @ Thu, 16 Apr 2020 03:14:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:14:29: #2 number of paired peaks: 946 WARNING @ Thu, 16 Apr 2020 03:14:29: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Thu, 16 Apr 2020 03:14:29: start model_add_line... INFO @ Thu, 16 Apr 2020 03:14:29: start X-correlation... INFO @ Thu, 16 Apr 2020 03:14:29: end of X-cor INFO @ Thu, 16 Apr 2020 03:14:29: #2 finished! INFO @ Thu, 16 Apr 2020 03:14:29: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:14:29: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10_model.r WARNING @ Thu, 16 Apr 2020 03:14:29: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:14:29: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:14:29: #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 03:14:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:14:36: #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 03:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.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 03:14:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:14:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:14:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:14:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:14:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.10_summits.bed INFO @ Thu, 16 Apr 2020 03:14:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1216 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:14:44: 1000000 INFO @ Thu, 16 Apr 2020 03:14:49: 2000000 INFO @ Thu, 16 Apr 2020 03:14:55: 3000000 INFO @ Thu, 16 Apr 2020 03:14:56: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:14:56: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:14:56: #1 total tags in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:14:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:14:56: #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 03:14:56: #1 tags after filtering in treatment: 3242558 INFO @ Thu, 16 Apr 2020 03:14:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:14:56: #1 finished! INFO @ Thu, 16 Apr 2020 03:14:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:14:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:14:56: #2 number of paired peaks: 946 WARNING @ Thu, 16 Apr 2020 03:14:56: Fewer paired peaks (946) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 946 pairs to build model! INFO @ Thu, 16 Apr 2020 03:14:56: start model_add_line... INFO @ Thu, 16 Apr 2020 03:14:56: start X-correlation... INFO @ Thu, 16 Apr 2020 03:14:56: end of X-cor INFO @ Thu, 16 Apr 2020 03:14:56: #2 finished! INFO @ Thu, 16 Apr 2020 03:14:56: #2 predicted fragment length is 72 bps INFO @ Thu, 16 Apr 2020 03:14:56: #2 alternative fragment length(s) may be 72 bps INFO @ Thu, 16 Apr 2020 03:14:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20_model.r WARNING @ Thu, 16 Apr 2020 03:14:56: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:14:56: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Thu, 16 Apr 2020 03:14:56: #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 03:14:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:14:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:15:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775922/SRX5775922.20_summits.bed INFO @ Thu, 16 Apr 2020 03:15:07: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。