Job ID = 6529968 SRX = SRX5535381 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: 00:06:27 23714187 reads; of these: 23714187 (100.00%) were unpaired; of these: 664797 (2.80%) aligned 0 times 17667187 (74.50%) aligned exactly 1 time 5382203 (22.70%) aligned >1 times 97.20% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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 12 files... [bam_rmdupse_core] 7193206 / 23049390 = 0.3121 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 03:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.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 03:14:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:41: 1000000 INFO @ Tue, 30 Jun 2020 03:14:46: 2000000 INFO @ Tue, 30 Jun 2020 03:14:52: 3000000 INFO @ Tue, 30 Jun 2020 03:14:58: 4000000 INFO @ Tue, 30 Jun 2020 03:15:03: 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 03:15:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.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 03:15:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:09: 6000000 INFO @ Tue, 30 Jun 2020 03:15:11: 1000000 INFO @ Tue, 30 Jun 2020 03:15:15: 7000000 INFO @ Tue, 30 Jun 2020 03:15:17: 2000000 INFO @ Tue, 30 Jun 2020 03:15:21: 8000000 INFO @ Tue, 30 Jun 2020 03:15:23: 3000000 INFO @ Tue, 30 Jun 2020 03:15:27: 9000000 INFO @ Tue, 30 Jun 2020 03:15:29: 4000000 INFO @ Tue, 30 Jun 2020 03:15:33: 10000000 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 03:15:35: 5000000 INFO @ Tue, 30 Jun 2020 03:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.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 03:15:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:39: 11000000 INFO @ Tue, 30 Jun 2020 03:15:41: 6000000 INFO @ Tue, 30 Jun 2020 03:15:42: 1000000 INFO @ Tue, 30 Jun 2020 03:15:45: 12000000 INFO @ Tue, 30 Jun 2020 03:15:47: 7000000 INFO @ Tue, 30 Jun 2020 03:15:48: 2000000 INFO @ Tue, 30 Jun 2020 03:15:51: 13000000 INFO @ Tue, 30 Jun 2020 03:15:53: 8000000 INFO @ Tue, 30 Jun 2020 03:15:55: 3000000 INFO @ Tue, 30 Jun 2020 03:15:58: 14000000 INFO @ Tue, 30 Jun 2020 03:15:59: 9000000 INFO @ Tue, 30 Jun 2020 03:16:02: 4000000 INFO @ Tue, 30 Jun 2020 03:16:04: 15000000 INFO @ Tue, 30 Jun 2020 03:16:06: 10000000 INFO @ Tue, 30 Jun 2020 03:16:08: 5000000 INFO @ Tue, 30 Jun 2020 03:16:09: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:16:09: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:16:09: #1 total tags in treatment: 15856184 INFO @ Tue, 30 Jun 2020 03:16:09: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:09: #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 03:16:10: #1 tags after filtering in treatment: 15856089 INFO @ Tue, 30 Jun 2020 03:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:10: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:11: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 03:16:11: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:11: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:11: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:11: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:11: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:11: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:16:11: #2 alternative fragment length(s) may be 30,55,78,102,162,526,558,577 bps INFO @ Tue, 30 Jun 2020 03:16:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05_model.r WARNING @ Tue, 30 Jun 2020 03:16:11: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:11: #2 You may need to consider one of the other alternative d(s): 30,55,78,102,162,526,558,577 WARNING @ Tue, 30 Jun 2020 03:16:11: #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 03:16:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:12: 11000000 INFO @ Tue, 30 Jun 2020 03:16:14: 6000000 INFO @ Tue, 30 Jun 2020 03:16:18: 12000000 INFO @ Tue, 30 Jun 2020 03:16:21: 7000000 INFO @ Tue, 30 Jun 2020 03:16:24: 13000000 INFO @ Tue, 30 Jun 2020 03:16:28: 8000000 INFO @ Tue, 30 Jun 2020 03:16:30: 14000000 INFO @ Tue, 30 Jun 2020 03:16:34: 9000000 INFO @ Tue, 30 Jun 2020 03:16:36: 15000000 INFO @ Tue, 30 Jun 2020 03:16:41: 10000000 INFO @ Tue, 30 Jun 2020 03:16:41: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:16:41: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:16:41: #1 total tags in treatment: 15856184 INFO @ Tue, 30 Jun 2020 03:16:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:16:41: #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 03:16:42: #1 tags after filtering in treatment: 15856089 INFO @ Tue, 30 Jun 2020 03:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:16:42: #1 finished! INFO @ Tue, 30 Jun 2020 03:16:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:16:43: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 03:16:43: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 03:16:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:16:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:16:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:16:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:16:43: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:16:43: #2 alternative fragment length(s) may be 30,55,78,102,162,526,558,577 bps INFO @ Tue, 30 Jun 2020 03:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10_model.r WARNING @ Tue, 30 Jun 2020 03:16:43: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:16:43: #2 You may need to consider one of the other alternative d(s): 30,55,78,102,162,526,558,577 WARNING @ Tue, 30 Jun 2020 03:16:43: #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 03:16:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:16:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:16:47: 11000000 INFO @ Tue, 30 Jun 2020 03:16:54: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:17:00: 13000000 INFO @ Tue, 30 Jun 2020 03:17:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.05_summits.bed INFO @ Tue, 30 Jun 2020 03:17:05: Done! pass1 - making usageList (167 chroms): 1 millis pass2 - checking and writing primary data (1626 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:07: 14000000 INFO @ Tue, 30 Jun 2020 03:17:13: 15000000 INFO @ Tue, 30 Jun 2020 03:17:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:17:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:17:18: #1 total tags in treatment: 15856184 INFO @ Tue, 30 Jun 2020 03:17:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:18: #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 03:17:19: #1 tags after filtering in treatment: 15856089 INFO @ Tue, 30 Jun 2020 03:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:19: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:20: #2 number of paired peaks: 191 WARNING @ Tue, 30 Jun 2020 03:17:20: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:20: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:20: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:20: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:20: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:20: #2 predicted fragment length is 78 bps INFO @ Tue, 30 Jun 2020 03:17:20: #2 alternative fragment length(s) may be 30,55,78,102,162,526,558,577 bps INFO @ Tue, 30 Jun 2020 03:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20_model.r WARNING @ Tue, 30 Jun 2020 03:17:20: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:20: #2 You may need to consider one of the other alternative d(s): 30,55,78,102,162,526,558,577 WARNING @ Tue, 30 Jun 2020 03:17:20: #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 03:17:20: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:17:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:17:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:17:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.10_summits.bed INFO @ Tue, 30 Jun 2020 03:17:37: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:17:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5535381/SRX5535381.20_summits.bed INFO @ Tue, 30 Jun 2020 03:18:13: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 5 millis CompletedMACS2peakCalling