Job ID = 5720929 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,656,458 reads read : 14,656,458 reads written : 14,656,458 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: 00:02:01 14656458 reads; of these: 14656458 (100.00%) were unpaired; of these: 11449834 (78.12%) aligned 0 times 2110349 (14.40%) aligned exactly 1 time 1096275 (7.48%) aligned >1 times 21.88% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 1659565 / 3206624 = 0.5175 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 03:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.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 03:26:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:26:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:26:31: 1000000 INFO @ Thu, 16 Apr 2020 03:26:34: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:26:34: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:26:34: #1 total tags in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:26:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:26:34: #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 03:26:34: #1 tags after filtering in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:26:34: #1 finished! INFO @ Thu, 16 Apr 2020 03:26:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:26:34: #2 number of paired peaks: 374 WARNING @ Thu, 16 Apr 2020 03:26:34: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 16 Apr 2020 03:26:34: start model_add_line... INFO @ Thu, 16 Apr 2020 03:26:34: start X-correlation... INFO @ Thu, 16 Apr 2020 03:26:34: end of X-cor INFO @ Thu, 16 Apr 2020 03:26:34: #2 finished! INFO @ Thu, 16 Apr 2020 03:26:34: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:26:34: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05_model.r WARNING @ Thu, 16 Apr 2020 03:26:34: #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 03:26:34: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:26:34: #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 03:26:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:26:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.05_summits.bed INFO @ Thu, 16 Apr 2020 03:26:39: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (651 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 03:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.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 03:26:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:26:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:27:01: 1000000 INFO @ Thu, 16 Apr 2020 03:27:04: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:27:04: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:27:04: #1 total tags in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:27:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:27:04: #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 03:27:04: #1 tags after filtering in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:27:04: #1 finished! INFO @ Thu, 16 Apr 2020 03:27:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:27:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:27:04: #2 number of paired peaks: 374 WARNING @ Thu, 16 Apr 2020 03:27:04: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 16 Apr 2020 03:27:04: start model_add_line... INFO @ Thu, 16 Apr 2020 03:27:04: start X-correlation... INFO @ Thu, 16 Apr 2020 03:27:04: end of X-cor INFO @ Thu, 16 Apr 2020 03:27:04: #2 finished! INFO @ Thu, 16 Apr 2020 03:27:04: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:27:04: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10_model.r WARNING @ Thu, 16 Apr 2020 03:27:04: #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 03:27:04: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:27:04: #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 03:27:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:27:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.10_summits.bed INFO @ Thu, 16 Apr 2020 03:27:09: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (372 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 03:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.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 03:27:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:27:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:27:33: 1000000 INFO @ Thu, 16 Apr 2020 03:27:36: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 03:27:36: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 03:27:36: #1 total tags in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:27:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:27:36: #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 03:27:36: #1 tags after filtering in treatment: 1547059 INFO @ Thu, 16 Apr 2020 03:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:27:36: #1 finished! INFO @ Thu, 16 Apr 2020 03:27:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:27:36: #2 number of paired peaks: 374 WARNING @ Thu, 16 Apr 2020 03:27:36: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Thu, 16 Apr 2020 03:27:36: start model_add_line... INFO @ Thu, 16 Apr 2020 03:27:36: start X-correlation... INFO @ Thu, 16 Apr 2020 03:27:36: end of X-cor INFO @ Thu, 16 Apr 2020 03:27:36: #2 finished! INFO @ Thu, 16 Apr 2020 03:27:36: #2 predicted fragment length is 52 bps INFO @ Thu, 16 Apr 2020 03:27:36: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 16 Apr 2020 03:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20_model.r WARNING @ Thu, 16 Apr 2020 03:27:36: #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 03:27:36: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 16 Apr 2020 03:27:36: #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 03:27:36: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:27:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 03:27:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 03:27:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:27:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:27:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386730/SRX6386730.20_summits.bed INFO @ Thu, 16 Apr 2020 03:27:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 0 millis CompletedMACS2peakCalling