Job ID = 5720396 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,801,530 reads read : 5,801,530 reads written : 5,801,530 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289667.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: 00:01:53 5801530 reads; of these: 5801530 (100.00%) were unpaired; of these: 461257 (7.95%) aligned 0 times 4139168 (71.35%) aligned exactly 1 time 1201105 (20.70%) aligned >1 times 92.05% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 895391 / 5340273 = 0.1677 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 00:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.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 00:22:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:13: 1000000 INFO @ Thu, 16 Apr 2020 00:22:18: 2000000 INFO @ Thu, 16 Apr 2020 00:22:24: 3000000 INFO @ Thu, 16 Apr 2020 00:22:29: 4000000 INFO @ Thu, 16 Apr 2020 00:22:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:22:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:22:31: #1 total tags in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:22:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:22:31: #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 00:22:31: #1 tags after filtering in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:22:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:22:31: #1 finished! INFO @ Thu, 16 Apr 2020 00:22:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:22:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:22:32: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 00:22:32: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 00:22:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:22:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:22:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:22:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:22:32: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 00:22:32: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 16 Apr 2020 00:22:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05_model.r WARNING @ Thu, 16 Apr 2020 00:22:32: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:22:32: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 16 Apr 2020 00:22:32: #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 00:22:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:22:32: #3 Pre-compute pvalue-qvalue table... 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 00:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.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 00:22:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:22:43: 1000000 INFO @ Thu, 16 Apr 2020 00:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.05_summits.bed INFO @ Thu, 16 Apr 2020 00:22:47: Done! INFO @ Thu, 16 Apr 2020 00:22:49: 2000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7117 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:22:54: 3000000 INFO @ Thu, 16 Apr 2020 00:22:59: 4000000 INFO @ Thu, 16 Apr 2020 00:23:02: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:23:02: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:23:02: #1 total tags in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:23:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:23:02: #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 00:23:02: #1 tags after filtering in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:23:02: #1 finished! INFO @ Thu, 16 Apr 2020 00:23:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:23:02: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 00:23:02: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 00:23:02: start model_add_line... INFO @ Thu, 16 Apr 2020 00:23:02: start X-correlation... INFO @ Thu, 16 Apr 2020 00:23:02: end of X-cor INFO @ Thu, 16 Apr 2020 00:23:02: #2 finished! INFO @ Thu, 16 Apr 2020 00:23:02: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 00:23:02: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 16 Apr 2020 00:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10_model.r WARNING @ Thu, 16 Apr 2020 00:23:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:23:02: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 16 Apr 2020 00:23:02: #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 00:23:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:23:02: #3 Pre-compute pvalue-qvalue table... 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 00:23:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.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 00:23:07: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:23:07: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:23:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:23:13: 1000000 INFO @ Thu, 16 Apr 2020 00:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.10_summits.bed INFO @ Thu, 16 Apr 2020 00:23:18: Done! INFO @ Thu, 16 Apr 2020 00:23:18: 2000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3709 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:23:24: 3000000 INFO @ Thu, 16 Apr 2020 00:23:29: 4000000 INFO @ Thu, 16 Apr 2020 00:23:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:23:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:23:31: #1 total tags in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:23:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:23:31: #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 00:23:31: #1 tags after filtering in treatment: 4444882 INFO @ Thu, 16 Apr 2020 00:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:23:31: #1 finished! INFO @ Thu, 16 Apr 2020 00:23:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:23:32: #2 number of paired peaks: 461 WARNING @ Thu, 16 Apr 2020 00:23:32: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Thu, 16 Apr 2020 00:23:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:23:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:23:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:23:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:23:32: #2 predicted fragment length is 79 bps INFO @ Thu, 16 Apr 2020 00:23:32: #2 alternative fragment length(s) may be 79 bps INFO @ Thu, 16 Apr 2020 00:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20_model.r WARNING @ Thu, 16 Apr 2020 00:23:32: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:23:32: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Thu, 16 Apr 2020 00:23:32: #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 00:23:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:23:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592390/SRX2592390.20_summits.bed INFO @ Thu, 16 Apr 2020 00:23:47: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1119 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。