Job ID = 6529862 SRX = SRX5343096 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: 00:07:24 23398256 reads; of these: 23398256 (100.00%) were unpaired; of these: 925428 (3.96%) aligned 0 times 18814671 (80.41%) aligned exactly 1 time 3658157 (15.63%) aligned >1 times 96.04% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 2685870 / 22472828 = 0.1195 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 03:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.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 03:18:05: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:05: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:13: 1000000 INFO @ Tue, 30 Jun 2020 03:18:20: 2000000 INFO @ Tue, 30 Jun 2020 03:18:27: 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 03:18:34: 4000000 INFO @ Tue, 30 Jun 2020 03:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.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 03:18:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:42: 5000000 INFO @ Tue, 30 Jun 2020 03:18:44: 1000000 INFO @ Tue, 30 Jun 2020 03:18:49: 6000000 INFO @ Tue, 30 Jun 2020 03:18:51: 2000000 INFO @ Tue, 30 Jun 2020 03:18:57: 7000000 INFO @ Tue, 30 Jun 2020 03:18:59: 3000000 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 03:19:04: 8000000 INFO @ Tue, 30 Jun 2020 03:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.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 03:19:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:06: 4000000 INFO @ Tue, 30 Jun 2020 03:19:12: 9000000 INFO @ Tue, 30 Jun 2020 03:19:13: 1000000 INFO @ Tue, 30 Jun 2020 03:19:14: 5000000 INFO @ Tue, 30 Jun 2020 03:19:19: 10000000 INFO @ Tue, 30 Jun 2020 03:19:20: 2000000 INFO @ Tue, 30 Jun 2020 03:19:21: 6000000 INFO @ Tue, 30 Jun 2020 03:19:26: 3000000 INFO @ Tue, 30 Jun 2020 03:19:27: 11000000 INFO @ Tue, 30 Jun 2020 03:19:29: 7000000 INFO @ Tue, 30 Jun 2020 03:19:33: 4000000 INFO @ Tue, 30 Jun 2020 03:19:34: 12000000 INFO @ Tue, 30 Jun 2020 03:19:36: 8000000 INFO @ Tue, 30 Jun 2020 03:19:39: 5000000 INFO @ Tue, 30 Jun 2020 03:19:42: 13000000 INFO @ Tue, 30 Jun 2020 03:19:44: 9000000 INFO @ Tue, 30 Jun 2020 03:19:46: 6000000 INFO @ Tue, 30 Jun 2020 03:19:49: 14000000 INFO @ Tue, 30 Jun 2020 03:19:51: 10000000 INFO @ Tue, 30 Jun 2020 03:19:52: 7000000 INFO @ Tue, 30 Jun 2020 03:19:57: 15000000 INFO @ Tue, 30 Jun 2020 03:19:58: 11000000 INFO @ Tue, 30 Jun 2020 03:19:59: 8000000 INFO @ Tue, 30 Jun 2020 03:20:04: 16000000 INFO @ Tue, 30 Jun 2020 03:20:05: 9000000 INFO @ Tue, 30 Jun 2020 03:20:06: 12000000 INFO @ Tue, 30 Jun 2020 03:20:11: 10000000 INFO @ Tue, 30 Jun 2020 03:20:12: 17000000 INFO @ Tue, 30 Jun 2020 03:20:13: 13000000 INFO @ Tue, 30 Jun 2020 03:20:18: 11000000 INFO @ Tue, 30 Jun 2020 03:20:20: 18000000 INFO @ Tue, 30 Jun 2020 03:20:21: 14000000 INFO @ Tue, 30 Jun 2020 03:20:24: 12000000 INFO @ Tue, 30 Jun 2020 03:20:27: 19000000 INFO @ Tue, 30 Jun 2020 03:20:28: 15000000 INFO @ Tue, 30 Jun 2020 03:20:31: 13000000 INFO @ Tue, 30 Jun 2020 03:20:33: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:20:33: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:20:33: #1 total tags in treatment: 19786958 INFO @ Tue, 30 Jun 2020 03:20:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:20:33: #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 03:20:34: #1 tags after filtering in treatment: 19786956 INFO @ Tue, 30 Jun 2020 03:20:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:20:34: #1 finished! INFO @ Tue, 30 Jun 2020 03:20:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:20:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:20:35: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 03:20:35: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 03:20:35: start model_add_line... INFO @ Tue, 30 Jun 2020 03:20:35: start X-correlation... INFO @ Tue, 30 Jun 2020 03:20:35: end of X-cor INFO @ Tue, 30 Jun 2020 03:20:35: #2 finished! INFO @ Tue, 30 Jun 2020 03:20:35: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:20:35: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05_model.r WARNING @ Tue, 30 Jun 2020 03:20:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:20:35: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:20:35: #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 03:20:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:20:36: 16000000 INFO @ Tue, 30 Jun 2020 03:20:37: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:20:43: 17000000 INFO @ Tue, 30 Jun 2020 03:20:43: 15000000 INFO @ Tue, 30 Jun 2020 03:20:50: 16000000 INFO @ Tue, 30 Jun 2020 03:20:51: 18000000 INFO @ Tue, 30 Jun 2020 03:20:57: 17000000 INFO @ Tue, 30 Jun 2020 03:20:58: 19000000 INFO @ Tue, 30 Jun 2020 03:21:03: 18000000 INFO @ Tue, 30 Jun 2020 03:21:05: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:21:05: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:21:05: #1 total tags in treatment: 19786958 INFO @ Tue, 30 Jun 2020 03:21:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:05: #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 03:21:05: #1 tags after filtering in treatment: 19786956 INFO @ Tue, 30 Jun 2020 03:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:06: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 03:21:06: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:07: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:07: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:07: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:07: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:21:07: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10_model.r WARNING @ Tue, 30 Jun 2020 03:21:07: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:21:07: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:21:07: #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 03:21:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:21:09: 19000000 INFO @ Tue, 30 Jun 2020 03:21:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:15: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:21:15: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:21:15: #1 total tags in treatment: 19786958 INFO @ Tue, 30 Jun 2020 03:21:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:21:15: #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 03:21:15: #1 tags after filtering in treatment: 19786956 INFO @ Tue, 30 Jun 2020 03:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:21:15: #1 finished! INFO @ Tue, 30 Jun 2020 03:21:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:21:17: #2 number of paired peaks: 140 WARNING @ Tue, 30 Jun 2020 03:21:17: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 30 Jun 2020 03:21:17: start model_add_line... INFO @ Tue, 30 Jun 2020 03:21:17: start X-correlation... INFO @ Tue, 30 Jun 2020 03:21:17: end of X-cor INFO @ Tue, 30 Jun 2020 03:21:17: #2 finished! INFO @ Tue, 30 Jun 2020 03:21:17: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:21:17: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 30 Jun 2020 03:21:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20_model.r WARNING @ Tue, 30 Jun 2020 03:21:17: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:21:17: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 30 Jun 2020 03:21:17: #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 03:21:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:21:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.05_summits.bed INFO @ Tue, 30 Jun 2020 03:21:33: Done! pass1 - making usageList (375 chroms): 1 millis pass2 - checking and writing primary data (1106 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.10_summits.bed INFO @ Tue, 30 Jun 2020 03:22:06: Done! pass1 - making usageList (230 chroms): 0 millis pass2 - checking and writing primary data (537 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343096/SRX5343096.20_summits.bed INFO @ Tue, 30 Jun 2020 03:22:11: Done! pass1 - making usageList (116 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 5 millis CompletedMACS2peakCalling