Job ID = 6529161 SRX = SRX017473 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:03:37 15540073 reads; of these: 15540073 (100.00%) were unpaired; of these: 544148 (3.50%) aligned 0 times 11044886 (71.07%) aligned exactly 1 time 3951039 (25.42%) aligned >1 times 96.50% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2167716 / 14995925 = 0.1446 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 @ Tue, 30 Jun 2020 01:26:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.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 @ Tue, 30 Jun 2020 01:26:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:02: 1000000 INFO @ Tue, 30 Jun 2020 01:27:07: 2000000 INFO @ Tue, 30 Jun 2020 01:27:12: 3000000 INFO @ Tue, 30 Jun 2020 01:27:17: 4000000 INFO @ Tue, 30 Jun 2020 01:27:22: 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 @ Tue, 30 Jun 2020 01:27:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.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 @ Tue, 30 Jun 2020 01:27:27: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:27: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:27: 6000000 INFO @ Tue, 30 Jun 2020 01:27:32: 1000000 INFO @ Tue, 30 Jun 2020 01:27:32: 7000000 INFO @ Tue, 30 Jun 2020 01:27:37: 2000000 INFO @ Tue, 30 Jun 2020 01:27:37: 8000000 INFO @ Tue, 30 Jun 2020 01:27:42: 3000000 INFO @ Tue, 30 Jun 2020 01:27:42: 9000000 INFO @ Tue, 30 Jun 2020 01:27:47: 4000000 INFO @ Tue, 30 Jun 2020 01:27:48: 10000000 INFO @ Tue, 30 Jun 2020 01:27:52: 5000000 INFO @ Tue, 30 Jun 2020 01:27:54: 11000000 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 @ Tue, 30 Jun 2020 01:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.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 @ Tue, 30 Jun 2020 01:27:57: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:57: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:57: 6000000 INFO @ Tue, 30 Jun 2020 01:27:59: 12000000 INFO @ Tue, 30 Jun 2020 01:28:02: 7000000 INFO @ Tue, 30 Jun 2020 01:28:03: 1000000 INFO @ Tue, 30 Jun 2020 01:28:04: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:28:04: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:28:04: #1 total tags in treatment: 12828209 INFO @ Tue, 30 Jun 2020 01:28:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:28:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:28:05: #1 tags after filtering in treatment: 12828138 INFO @ Tue, 30 Jun 2020 01:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:28:05: #1 finished! INFO @ Tue, 30 Jun 2020 01:28:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:28:06: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 01:28:06: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 01:28:06: start model_add_line... INFO @ Tue, 30 Jun 2020 01:28:06: start X-correlation... INFO @ Tue, 30 Jun 2020 01:28:06: end of X-cor INFO @ Tue, 30 Jun 2020 01:28:06: #2 finished! INFO @ Tue, 30 Jun 2020 01:28:06: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 01:28:06: #2 alternative fragment length(s) may be 51,538 bps INFO @ Tue, 30 Jun 2020 01:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05_model.r WARNING @ Tue, 30 Jun 2020 01:28:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:28:06: #2 You may need to consider one of the other alternative d(s): 51,538 WARNING @ Tue, 30 Jun 2020 01:28:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:28:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:28:08: 8000000 INFO @ Tue, 30 Jun 2020 01:28:08: 2000000 INFO @ Tue, 30 Jun 2020 01:28:13: 9000000 INFO @ Tue, 30 Jun 2020 01:28:13: 3000000 INFO @ Tue, 30 Jun 2020 01:28:18: 4000000 INFO @ Tue, 30 Jun 2020 01:28:18: 10000000 INFO @ Tue, 30 Jun 2020 01:28:23: 5000000 INFO @ Tue, 30 Jun 2020 01:28:24: 11000000 INFO @ Tue, 30 Jun 2020 01:28:28: 6000000 INFO @ Tue, 30 Jun 2020 01:28:29: 12000000 INFO @ Tue, 30 Jun 2020 01:28:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:28:33: 7000000 INFO @ Tue, 30 Jun 2020 01:28:33: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:28:33: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:28:33: #1 total tags in treatment: 12828209 INFO @ Tue, 30 Jun 2020 01:28:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:28:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:28:34: #1 tags after filtering in treatment: 12828138 INFO @ Tue, 30 Jun 2020 01:28:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:28:34: #1 finished! INFO @ Tue, 30 Jun 2020 01:28:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:28:35: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 01:28:35: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 01:28:35: start model_add_line... INFO @ Tue, 30 Jun 2020 01:28:35: start X-correlation... INFO @ Tue, 30 Jun 2020 01:28:35: end of X-cor INFO @ Tue, 30 Jun 2020 01:28:35: #2 finished! INFO @ Tue, 30 Jun 2020 01:28:35: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 01:28:35: #2 alternative fragment length(s) may be 51,538 bps INFO @ Tue, 30 Jun 2020 01:28:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10_model.r WARNING @ Tue, 30 Jun 2020 01:28:35: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:28:35: #2 You may need to consider one of the other alternative d(s): 51,538 WARNING @ Tue, 30 Jun 2020 01:28:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:28:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:28:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:28:38: 8000000 INFO @ Tue, 30 Jun 2020 01:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.05_summits.bed INFO @ Tue, 30 Jun 2020 01:28:43: Done! INFO @ Tue, 30 Jun 2020 01:28:44: 9000000 pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (3136 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:28:49: 10000000 INFO @ Tue, 30 Jun 2020 01:28:54: 11000000 INFO @ Tue, 30 Jun 2020 01:28:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:29:00: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:29:04: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:29:04: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:29:04: #1 total tags in treatment: 12828209 INFO @ Tue, 30 Jun 2020 01:29:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:29:05: #1 tags after filtering in treatment: 12828138 INFO @ Tue, 30 Jun 2020 01:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:05: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:06: #2 number of paired peaks: 292 WARNING @ Tue, 30 Jun 2020 01:29:06: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:06: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:06: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:06: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:06: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:06: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 01:29:06: #2 alternative fragment length(s) may be 51,538 bps INFO @ Tue, 30 Jun 2020 01:29:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20_model.r WARNING @ Tue, 30 Jun 2020 01:29:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:29:06: #2 You may need to consider one of the other alternative d(s): 51,538 WARNING @ Tue, 30 Jun 2020 01:29:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:29:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.10_summits.bed INFO @ Tue, 30 Jun 2020 01:29:12: Done! pass1 - making usageList (288 chroms): 1 millis pass2 - checking and writing primary data (1060 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:29:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX017473/SRX017473.20_summits.bed INFO @ Tue, 30 Jun 2020 01:29:43: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 63 millis CompletedMACS2peakCalling