Job ID = 6529390 SRX = SRX2325650 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: 00:10:09 45978696 reads; of these: 45978696 (100.00%) were unpaired; of these: 26908256 (58.52%) aligned 0 times 14692333 (31.95%) aligned exactly 1 time 4378107 (9.52%) aligned >1 times 41.48% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8540885 / 19070440 = 0.4479 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 02:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.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 02:23:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:25: 1000000 INFO @ Tue, 30 Jun 2020 02:23:32: 2000000 INFO @ Tue, 30 Jun 2020 02:23:40: 3000000 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 02:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.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 02:23:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:47: 4000000 INFO @ Tue, 30 Jun 2020 02:23:56: 1000000 INFO @ Tue, 30 Jun 2020 02:23:56: 5000000 INFO @ Tue, 30 Jun 2020 02:24:04: 2000000 INFO @ Tue, 30 Jun 2020 02:24:05: 6000000 INFO @ Tue, 30 Jun 2020 02:24:13: 3000000 INFO @ Tue, 30 Jun 2020 02:24:13: 7000000 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 02:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.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 02:24:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:22: 4000000 INFO @ Tue, 30 Jun 2020 02:24:22: 8000000 INFO @ Tue, 30 Jun 2020 02:24:25: 1000000 INFO @ Tue, 30 Jun 2020 02:24:30: 5000000 INFO @ Tue, 30 Jun 2020 02:24:31: 9000000 INFO @ Tue, 30 Jun 2020 02:24:33: 2000000 INFO @ Tue, 30 Jun 2020 02:24:39: 6000000 INFO @ Tue, 30 Jun 2020 02:24:39: 10000000 INFO @ Tue, 30 Jun 2020 02:24:41: 3000000 INFO @ Tue, 30 Jun 2020 02:24:44: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:24:44: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:24:44: #1 total tags in treatment: 10529555 INFO @ Tue, 30 Jun 2020 02:24:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:44: #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 02:24:44: #1 tags after filtering in treatment: 10529551 INFO @ Tue, 30 Jun 2020 02:24:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:45: #2 number of paired peaks: 474 WARNING @ Tue, 30 Jun 2020 02:24:45: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:45: #2 predicted fragment length is 88 bps INFO @ Tue, 30 Jun 2020 02:24:45: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 30 Jun 2020 02:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05_model.r WARNING @ Tue, 30 Jun 2020 02:24:45: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:45: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 30 Jun 2020 02:24:45: #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 02:24:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:48: 7000000 INFO @ Tue, 30 Jun 2020 02:24:49: 4000000 INFO @ Tue, 30 Jun 2020 02:24:56: 8000000 INFO @ Tue, 30 Jun 2020 02:24:57: 5000000 INFO @ Tue, 30 Jun 2020 02:25:05: 6000000 INFO @ Tue, 30 Jun 2020 02:25:05: 9000000 INFO @ Tue, 30 Jun 2020 02:25:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:25:12: 7000000 INFO @ Tue, 30 Jun 2020 02:25:13: 10000000 INFO @ Tue, 30 Jun 2020 02:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.05_summits.bed INFO @ Tue, 30 Jun 2020 02:25:17: Done! pass1 - making usageList (723 chroms): 1 millis pass2 - checking and writing primary data (2228 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:18: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:25:18: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:25:18: #1 total tags in treatment: 10529555 INFO @ Tue, 30 Jun 2020 02:25:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:18: #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 02:25:18: #1 tags after filtering in treatment: 10529551 INFO @ Tue, 30 Jun 2020 02:25:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:18: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:19: #2 number of paired peaks: 474 WARNING @ Tue, 30 Jun 2020 02:25:19: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:19: #2 predicted fragment length is 88 bps INFO @ Tue, 30 Jun 2020 02:25:19: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 30 Jun 2020 02:25:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10_model.r WARNING @ Tue, 30 Jun 2020 02:25:19: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:19: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 30 Jun 2020 02:25:19: #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 02:25:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:20: 8000000 INFO @ Tue, 30 Jun 2020 02:25:27: 9000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:25:34: 10000000 INFO @ Tue, 30 Jun 2020 02:25:38: #1 tag size is determined as 76 bps INFO @ Tue, 30 Jun 2020 02:25:38: #1 tag size = 76 INFO @ Tue, 30 Jun 2020 02:25:38: #1 total tags in treatment: 10529555 INFO @ Tue, 30 Jun 2020 02:25:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:38: #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 02:25:38: #1 tags after filtering in treatment: 10529551 INFO @ Tue, 30 Jun 2020 02:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:38: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:39: #2 number of paired peaks: 474 WARNING @ Tue, 30 Jun 2020 02:25:39: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:39: #2 predicted fragment length is 88 bps INFO @ Tue, 30 Jun 2020 02:25:39: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 30 Jun 2020 02:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20_model.r WARNING @ Tue, 30 Jun 2020 02:25:39: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:39: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 30 Jun 2020 02:25:39: #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 02:25:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.10_summits.bed INFO @ Tue, 30 Jun 2020 02:25:51: Done! pass1 - making usageList (543 chroms): 1 millis pass2 - checking and writing primary data (1222 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:26:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2325650/SRX2325650.20_summits.bed INFO @ Tue, 30 Jun 2020 02:26:10: Done! pass1 - making usageList (246 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 8 millis CompletedMACS2peakCalling