Job ID = 5720927 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,925,858 reads read : 18,925,858 reads written : 18,925,858 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: 00:03:12 18925858 reads; of these: 18925858 (100.00%) were unpaired; of these: 13073705 (69.08%) aligned 0 times 3928464 (20.76%) aligned exactly 1 time 1923689 (10.16%) aligned >1 times 30.92% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 3004496 / 5852153 = 0.5134 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 03:29:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.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 03:29:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:28: 1000000 INFO @ Thu, 16 Apr 2020 03:29:35: 2000000 INFO @ Thu, 16 Apr 2020 03:29:41: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:29:41: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:29:41: #1 total tags in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:29:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:29:41: #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 03:29:41: #1 tags after filtering in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:29:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:29:41: #1 finished! INFO @ Thu, 16 Apr 2020 03:29:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:29:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:29:41: #2 number of paired peaks: 286 WARNING @ Thu, 16 Apr 2020 03:29:41: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Thu, 16 Apr 2020 03:29:41: start model_add_line... INFO @ Thu, 16 Apr 2020 03:29:41: start X-correlation... INFO @ Thu, 16 Apr 2020 03:29:41: end of X-cor INFO @ Thu, 16 Apr 2020 03:29:41: #2 finished! INFO @ Thu, 16 Apr 2020 03:29:41: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:29:41: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05_model.r WARNING @ Thu, 16 Apr 2020 03:29:41: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:29:41: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:29:41: #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 03:29:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:29:47: #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 03:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.05_summits.bed INFO @ Thu, 16 Apr 2020 03:29:50: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (897 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:29:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.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 03:29:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:29:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:29:58: 1000000 INFO @ Thu, 16 Apr 2020 03:30:05: 2000000 INFO @ Thu, 16 Apr 2020 03:30:11: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:30:11: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:30:11: #1 total tags in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:30:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:30:11: #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 03:30:11: #1 tags after filtering in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:30:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:30:11: #1 finished! INFO @ Thu, 16 Apr 2020 03:30:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:30:11: #2 number of paired peaks: 286 WARNING @ Thu, 16 Apr 2020 03:30:11: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Thu, 16 Apr 2020 03:30:11: start model_add_line... INFO @ Thu, 16 Apr 2020 03:30:11: start X-correlation... INFO @ Thu, 16 Apr 2020 03:30:11: end of X-cor INFO @ Thu, 16 Apr 2020 03:30:11: #2 finished! INFO @ Thu, 16 Apr 2020 03:30:11: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:30:11: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10_model.r WARNING @ Thu, 16 Apr 2020 03:30:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:30:11: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:30:11: #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 03:30:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:30:18: #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 03:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.10_summits.bed INFO @ Thu, 16 Apr 2020 03:30:21: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (525 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.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 03:30:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:30:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:30:28: 1000000 INFO @ Thu, 16 Apr 2020 03:30:34: 2000000 INFO @ Thu, 16 Apr 2020 03:30:40: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:30:40: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:30:40: #1 total tags in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:30:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:30:40: #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 03:30:40: #1 tags after filtering in treatment: 2847657 INFO @ Thu, 16 Apr 2020 03:30:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:30:40: #1 finished! INFO @ Thu, 16 Apr 2020 03:30:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:30:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:30:40: #2 number of paired peaks: 286 WARNING @ Thu, 16 Apr 2020 03:30:40: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Thu, 16 Apr 2020 03:30:40: start model_add_line... INFO @ Thu, 16 Apr 2020 03:30:40: start X-correlation... INFO @ Thu, 16 Apr 2020 03:30:40: end of X-cor INFO @ Thu, 16 Apr 2020 03:30:40: #2 finished! INFO @ Thu, 16 Apr 2020 03:30:40: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:30:40: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20_model.r WARNING @ Thu, 16 Apr 2020 03:30:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:30:40: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:30:40: #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 03:30:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:30:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:30:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:30:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:30:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386728/SRX6386728.20_summits.bed INFO @ Thu, 16 Apr 2020 03:30:50: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (248 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。