Job ID = 6529875 SRX = SRX5343139 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: 00:04:21 15155134 reads; of these: 15155134 (100.00%) were unpaired; of these: 654475 (4.32%) aligned 0 times 12382901 (81.71%) aligned exactly 1 time 2117758 (13.97%) aligned >1 times 95.68% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 2429933 / 14500659 = 0.1676 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 03:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.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 03:12:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:17: 1000000 INFO @ Tue, 30 Jun 2020 03:12:22: 2000000 INFO @ Tue, 30 Jun 2020 03:12:28: 3000000 INFO @ Tue, 30 Jun 2020 03:12:34: 4000000 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 03:12:40: 5000000 INFO @ Tue, 30 Jun 2020 03:12:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.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 03:12:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:46: 6000000 INFO @ Tue, 30 Jun 2020 03:12:47: 1000000 INFO @ Tue, 30 Jun 2020 03:12:52: 7000000 INFO @ Tue, 30 Jun 2020 03:12:54: 2000000 INFO @ Tue, 30 Jun 2020 03:12:58: 8000000 INFO @ Tue, 30 Jun 2020 03:13:00: 3000000 INFO @ Tue, 30 Jun 2020 03:13:04: 9000000 INFO @ Tue, 30 Jun 2020 03:13:07: 4000000 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 03:13:10: 10000000 INFO @ Tue, 30 Jun 2020 03:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.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 03:13:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:14: 5000000 INFO @ Tue, 30 Jun 2020 03:13:17: 1000000 INFO @ Tue, 30 Jun 2020 03:13:18: 11000000 INFO @ Tue, 30 Jun 2020 03:13:20: 6000000 INFO @ Tue, 30 Jun 2020 03:13:24: 2000000 INFO @ Tue, 30 Jun 2020 03:13:25: 12000000 INFO @ Tue, 30 Jun 2020 03:13:25: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:13:25: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:13:25: #1 total tags in treatment: 12070726 INFO @ Tue, 30 Jun 2020 03:13:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:13:25: #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 03:13:26: #1 tags after filtering in treatment: 12070719 INFO @ Tue, 30 Jun 2020 03:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:13:26: #1 finished! INFO @ Tue, 30 Jun 2020 03:13:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:13:27: 7000000 INFO @ Tue, 30 Jun 2020 03:13:27: #2 number of paired peaks: 165 WARNING @ Tue, 30 Jun 2020 03:13:27: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 30 Jun 2020 03:13:27: start model_add_line... INFO @ Tue, 30 Jun 2020 03:13:27: start X-correlation... INFO @ Tue, 30 Jun 2020 03:13:27: end of X-cor INFO @ Tue, 30 Jun 2020 03:13:27: #2 finished! INFO @ Tue, 30 Jun 2020 03:13:27: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:13:27: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 30 Jun 2020 03:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05_model.r WARNING @ Tue, 30 Jun 2020 03:13:27: #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 03:13:27: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 30 Jun 2020 03:13:27: #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 03:13:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:13:30: 3000000 INFO @ Tue, 30 Jun 2020 03:13:33: 8000000 INFO @ Tue, 30 Jun 2020 03:13:37: 4000000 INFO @ Tue, 30 Jun 2020 03:13:40: 9000000 INFO @ Tue, 30 Jun 2020 03:13:43: 5000000 INFO @ Tue, 30 Jun 2020 03:13:46: 10000000 INFO @ Tue, 30 Jun 2020 03:13:49: 6000000 INFO @ Tue, 30 Jun 2020 03:13:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:54: 11000000 INFO @ Tue, 30 Jun 2020 03:13:55: 7000000 INFO @ Tue, 30 Jun 2020 03:14:01: 12000000 INFO @ Tue, 30 Jun 2020 03:14:01: 8000000 INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:01: Done! INFO @ Tue, 30 Jun 2020 03:14:01: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:14:01: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:14:01: #1 total tags in treatment: 12070726 INFO @ Tue, 30 Jun 2020 03:14:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (315 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:02: #1 tags after filtering in treatment: 12070719 INFO @ Tue, 30 Jun 2020 03:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:02: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:03: #2 number of paired peaks: 165 WARNING @ Tue, 30 Jun 2020 03:14:03: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:03: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:03: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:03: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:03: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:03: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:14:03: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 30 Jun 2020 03:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10_model.r WARNING @ Tue, 30 Jun 2020 03:14:03: #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 03:14:03: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 30 Jun 2020 03:14:03: #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 03:14:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:07: 9000000 INFO @ Tue, 30 Jun 2020 03:14:13: 10000000 INFO @ Tue, 30 Jun 2020 03:14:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:14:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:25: 12000000 INFO @ Tue, 30 Jun 2020 03:14:26: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:14:26: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:14:26: #1 total tags in treatment: 12070726 INFO @ Tue, 30 Jun 2020 03:14:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:26: #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 03:14:27: #1 tags after filtering in treatment: 12070719 INFO @ Tue, 30 Jun 2020 03:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:27: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:28: #2 number of paired peaks: 165 WARNING @ Tue, 30 Jun 2020 03:14:28: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:28: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:28: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:28: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:28: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:28: #2 predicted fragment length is 66 bps INFO @ Tue, 30 Jun 2020 03:14:28: #2 alternative fragment length(s) may be 66 bps INFO @ Tue, 30 Jun 2020 03:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20_model.r WARNING @ Tue, 30 Jun 2020 03:14:28: #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 03:14:28: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Tue, 30 Jun 2020 03:14:28: #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 03:14:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.10_summits.bed INFO @ Tue, 30 Jun 2020 03:14:37: Done! pass1 - making usageList (175 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343139/SRX5343139.20_summits.bed INFO @ Tue, 30 Jun 2020 03:15:01: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 6 millis CompletedMACS2peakCalling