Job ID = 6530059 SRX = SRX6962949 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: 00:10:56 48135049 reads; of these: 48135049 (100.00%) were unpaired; of these: 30353284 (63.06%) aligned 0 times 13238554 (27.50%) aligned exactly 1 time 4543211 (9.44%) aligned >1 times 36.94% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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] 6139093 / 17781765 = 0.3452 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 03:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.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 03:27:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:27:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:00: 1000000 INFO @ Tue, 30 Jun 2020 03:28:08: 2000000 INFO @ Tue, 30 Jun 2020 03:28:16: 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 03:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.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 03:28:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:25: 4000000 INFO @ Tue, 30 Jun 2020 03:28:32: 1000000 INFO @ Tue, 30 Jun 2020 03:28:35: 5000000 INFO @ Tue, 30 Jun 2020 03:28:41: 2000000 INFO @ Tue, 30 Jun 2020 03:28:44: 6000000 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 03:28:51: 3000000 INFO @ Tue, 30 Jun 2020 03:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.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 03:28:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:54: 7000000 INFO @ Tue, 30 Jun 2020 03:29:00: 1000000 INFO @ Tue, 30 Jun 2020 03:29:01: 4000000 INFO @ Tue, 30 Jun 2020 03:29:04: 8000000 INFO @ Tue, 30 Jun 2020 03:29:07: 2000000 INFO @ Tue, 30 Jun 2020 03:29:11: 5000000 INFO @ Tue, 30 Jun 2020 03:29:14: 9000000 INFO @ Tue, 30 Jun 2020 03:29:15: 3000000 INFO @ Tue, 30 Jun 2020 03:29:21: 6000000 INFO @ Tue, 30 Jun 2020 03:29:23: 4000000 INFO @ Tue, 30 Jun 2020 03:29:25: 10000000 INFO @ Tue, 30 Jun 2020 03:29:30: 5000000 INFO @ Tue, 30 Jun 2020 03:29:32: 7000000 INFO @ Tue, 30 Jun 2020 03:29:36: 11000000 INFO @ Tue, 30 Jun 2020 03:29:38: 6000000 INFO @ Tue, 30 Jun 2020 03:29:42: 8000000 INFO @ Tue, 30 Jun 2020 03:29:43: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:29:43: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:29:43: #1 total tags in treatment: 11642672 INFO @ Tue, 30 Jun 2020 03:29:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:29:43: #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 03:29:43: #1 tags after filtering in treatment: 11642670 INFO @ Tue, 30 Jun 2020 03:29:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:29:43: #1 finished! INFO @ Tue, 30 Jun 2020 03:29:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:29:44: #2 number of paired peaks: 786 WARNING @ Tue, 30 Jun 2020 03:29:44: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 30 Jun 2020 03:29:44: start model_add_line... INFO @ Tue, 30 Jun 2020 03:29:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:29:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:29:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:29:44: #2 predicted fragment length is 87 bps INFO @ Tue, 30 Jun 2020 03:29:44: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 30 Jun 2020 03:29:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05_model.r WARNING @ Tue, 30 Jun 2020 03:29:44: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:29:44: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 30 Jun 2020 03:29:44: #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 03:29:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:29:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:29:46: 7000000 INFO @ Tue, 30 Jun 2020 03:29:51: 9000000 INFO @ Tue, 30 Jun 2020 03:29:54: 8000000 INFO @ Tue, 30 Jun 2020 03:30:01: 9000000 INFO @ Tue, 30 Jun 2020 03:30:01: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:30:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:10: 10000000 INFO @ Tue, 30 Jun 2020 03:30:11: 11000000 INFO @ Tue, 30 Jun 2020 03:30:17: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:30:17: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:30:17: #1 total tags in treatment: 11642672 INFO @ Tue, 30 Jun 2020 03:30:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:17: #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 03:30:17: 11000000 INFO @ Tue, 30 Jun 2020 03:30:18: #1 tags after filtering in treatment: 11642670 INFO @ Tue, 30 Jun 2020 03:30:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:18: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:18: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:19: #2 number of paired peaks: 786 WARNING @ Tue, 30 Jun 2020 03:30:19: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 30 Jun 2020 03:30:19: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:19: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:19: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:19: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:19: #2 predicted fragment length is 87 bps INFO @ Tue, 30 Jun 2020 03:30:19: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 30 Jun 2020 03:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10_model.r WARNING @ Tue, 30 Jun 2020 03:30:19: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:19: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 30 Jun 2020 03:30:19: #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 03:30:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:30:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.05_summits.bed INFO @ Tue, 30 Jun 2020 03:30:19: Done! pass1 - making usageList (790 chroms): 2 millis pass2 - checking and writing primary data (2756 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:30:23: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:30:23: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:30:23: #1 total tags in treatment: 11642672 INFO @ Tue, 30 Jun 2020 03:30:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:23: #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 03:30:23: #1 tags after filtering in treatment: 11642670 INFO @ Tue, 30 Jun 2020 03:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:23: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:24: #2 number of paired peaks: 786 WARNING @ Tue, 30 Jun 2020 03:30:24: Fewer paired peaks (786) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 786 pairs to build model! INFO @ Tue, 30 Jun 2020 03:30:24: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:24: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:24: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:24: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:24: #2 predicted fragment length is 87 bps INFO @ Tue, 30 Jun 2020 03:30:24: #2 alternative fragment length(s) may be 87 bps INFO @ Tue, 30 Jun 2020 03:30:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20_model.r WARNING @ Tue, 30 Jun 2020 03:30:24: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:24: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Tue, 30 Jun 2020 03:30:24: #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 03:30:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:30:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.10_summits.bed INFO @ Tue, 30 Jun 2020 03:30:54: Done! pass1 - making usageList (626 chroms): 2 millis pass2 - checking and writing primary data (1819 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6962949/SRX6962949.20_summits.bed INFO @ Tue, 30 Jun 2020 03:31:01: Done! pass1 - making usageList (458 chroms): 1 millis pass2 - checking and writing primary data (946 records, 4 fields): 26 millis CompletedMACS2peakCalling