Job ID = 5721038 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,440,766 reads read : 10,440,766 reads written : 10,440,766 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: 00:02:36 10440766 reads; of these: 10440766 (100.00%) were unpaired; of these: 3428707 (32.84%) aligned 0 times 4893466 (46.87%) aligned exactly 1 time 2118593 (20.29%) aligned >1 times 67.16% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 1616727 / 7012059 = 0.2306 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 03:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.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 03:44:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:44:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:44:07: 1000000 INFO @ Thu, 16 Apr 2020 03:44:13: 2000000 INFO @ Thu, 16 Apr 2020 03:44:18: 3000000 INFO @ Thu, 16 Apr 2020 03:44:24: 4000000 INFO @ Thu, 16 Apr 2020 03:44:29: 5000000 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 03:44:32: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:44:32: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:44:32: #1 total tags in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:44:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:44:32: #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 03:44:32: #1 tags after filtering in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:44:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:44:32: #1 finished! INFO @ Thu, 16 Apr 2020 03:44:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.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 03:44:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:44:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:44:32: #2 number of paired peaks: 179 WARNING @ Thu, 16 Apr 2020 03:44:32: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Thu, 16 Apr 2020 03:44:32: start model_add_line... INFO @ Thu, 16 Apr 2020 03:44:32: start X-correlation... INFO @ Thu, 16 Apr 2020 03:44:32: end of X-cor INFO @ Thu, 16 Apr 2020 03:44:32: #2 finished! INFO @ Thu, 16 Apr 2020 03:44:32: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 03:44:32: #2 alternative fragment length(s) may be 53,543 bps INFO @ Thu, 16 Apr 2020 03:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05_model.r WARNING @ Thu, 16 Apr 2020 03:44:32: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:44:32: #2 You may need to consider one of the other alternative d(s): 53,543 WARNING @ Thu, 16 Apr 2020 03:44:32: #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 03:44:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:44:37: 1000000 INFO @ Thu, 16 Apr 2020 03:44:43: 2000000 INFO @ Thu, 16 Apr 2020 03:44:43: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:44:48: 3000000 INFO @ Thu, 16 Apr 2020 03:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.05_summits.bed INFO @ Thu, 16 Apr 2020 03:44:49: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1031 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:44:54: 4000000 INFO @ Thu, 16 Apr 2020 03:45:00: 5000000 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 03:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.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 03:45:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:45:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:45:02: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:02: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:02: #1 total tags in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:45:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:02: #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 03:45:02: #1 tags after filtering in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:45:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:02: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:02: #2 number of paired peaks: 179 WARNING @ Thu, 16 Apr 2020 03:45:02: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:02: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:02: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:02: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:02: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:02: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 03:45:02: #2 alternative fragment length(s) may be 53,543 bps INFO @ Thu, 16 Apr 2020 03:45:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10_model.r WARNING @ Thu, 16 Apr 2020 03:45:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:45:02: #2 You may need to consider one of the other alternative d(s): 53,543 WARNING @ Thu, 16 Apr 2020 03:45:02: #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 03:45:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:08: 1000000 INFO @ Thu, 16 Apr 2020 03:45:13: 2000000 INFO @ Thu, 16 Apr 2020 03:45:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.10_summits.bed INFO @ Thu, 16 Apr 2020 03:45:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:45:19: 3000000 INFO @ Thu, 16 Apr 2020 03:45:25: 4000000 INFO @ Thu, 16 Apr 2020 03:45:31: 5000000 INFO @ Thu, 16 Apr 2020 03:45:33: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:45:33: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:45:33: #1 total tags in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:45:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:45:33: #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 03:45:33: #1 tags after filtering in treatment: 5395332 INFO @ Thu, 16 Apr 2020 03:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:45:33: #1 finished! INFO @ Thu, 16 Apr 2020 03:45:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:45:34: #2 number of paired peaks: 179 WARNING @ Thu, 16 Apr 2020 03:45:34: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Thu, 16 Apr 2020 03:45:34: start model_add_line... INFO @ Thu, 16 Apr 2020 03:45:34: start X-correlation... INFO @ Thu, 16 Apr 2020 03:45:34: end of X-cor INFO @ Thu, 16 Apr 2020 03:45:34: #2 finished! INFO @ Thu, 16 Apr 2020 03:45:34: #2 predicted fragment length is 53 bps INFO @ Thu, 16 Apr 2020 03:45:34: #2 alternative fragment length(s) may be 53,543 bps INFO @ Thu, 16 Apr 2020 03:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20_model.r WARNING @ Thu, 16 Apr 2020 03:45:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:45:34: #2 You may need to consider one of the other alternative d(s): 53,543 WARNING @ Thu, 16 Apr 2020 03:45:34: #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 03:45:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:45:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:45:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386773/SRX6386773.20_summits.bed INFO @ Thu, 16 Apr 2020 03:45:50: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (309 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。