Job ID = 6627537 SRX = SRX8521312 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: 00:17:43 94151587 reads; of these: 94151587 (100.00%) were unpaired; of these: 76021792 (80.74%) aligned 0 times 10917407 (11.60%) aligned exactly 1 time 7212388 (7.66%) aligned >1 times 19.26% overall alignment rate Time searching: 00:17:43 Overall time: 00:17:43 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] 6027649 / 18129795 = 0.3325 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, 14 Jul 2020 12:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.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, 14 Jul 2020 12:17:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:17:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:17:53: 1000000 INFO @ Tue, 14 Jul 2020 12:18:00: 2000000 INFO @ Tue, 14 Jul 2020 12:18:07: 3000000 INFO @ Tue, 14 Jul 2020 12:18:13: 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, 14 Jul 2020 12:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.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, 14 Jul 2020 12:18:15: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:18:15: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:18:20: 5000000 INFO @ Tue, 14 Jul 2020 12:18:22: 1000000 INFO @ Tue, 14 Jul 2020 12:18:27: 6000000 INFO @ Tue, 14 Jul 2020 12:18:29: 2000000 INFO @ Tue, 14 Jul 2020 12:18:34: 7000000 INFO @ Tue, 14 Jul 2020 12:18:36: 3000000 INFO @ Tue, 14 Jul 2020 12:18:42: 8000000 INFO @ Tue, 14 Jul 2020 12:18:43: 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, 14 Jul 2020 12:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.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, 14 Jul 2020 12:18:45: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:18:45: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:18:50: 5000000 INFO @ Tue, 14 Jul 2020 12:18:52: 9000000 INFO @ Tue, 14 Jul 2020 12:18:53: 1000000 INFO @ Tue, 14 Jul 2020 12:18:58: 6000000 INFO @ Tue, 14 Jul 2020 12:18:59: 10000000 INFO @ Tue, 14 Jul 2020 12:19:01: 2000000 INFO @ Tue, 14 Jul 2020 12:19:06: 7000000 INFO @ Tue, 14 Jul 2020 12:19:07: 11000000 INFO @ Tue, 14 Jul 2020 12:19:09: 3000000 INFO @ Tue, 14 Jul 2020 12:19:13: 8000000 INFO @ Tue, 14 Jul 2020 12:19:15: 12000000 INFO @ Tue, 14 Jul 2020 12:19:15: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 12:19:15: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 12:19:15: #1 total tags in treatment: 12102146 INFO @ Tue, 14 Jul 2020 12:19:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:19:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:19:16: #1 tags after filtering in treatment: 12102057 INFO @ Tue, 14 Jul 2020 12:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:19:16: #1 finished! INFO @ Tue, 14 Jul 2020 12:19:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:19:17: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 12:19:17: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 12:19:17: start model_add_line... INFO @ Tue, 14 Jul 2020 12:19:17: start X-correlation... INFO @ Tue, 14 Jul 2020 12:19:17: end of X-cor INFO @ Tue, 14 Jul 2020 12:19:17: #2 finished! INFO @ Tue, 14 Jul 2020 12:19:17: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:19:17: #2 alternative fragment length(s) may be 4,54,75,514,549 bps INFO @ Tue, 14 Jul 2020 12:19:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05_model.r WARNING @ Tue, 14 Jul 2020 12:19:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:19:17: #2 You may need to consider one of the other alternative d(s): 4,54,75,514,549 WARNING @ Tue, 14 Jul 2020 12:19:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:19:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:19:17: 4000000 INFO @ Tue, 14 Jul 2020 12:19:20: 9000000 INFO @ Tue, 14 Jul 2020 12:19:25: 5000000 INFO @ Tue, 14 Jul 2020 12:19:27: 10000000 INFO @ Tue, 14 Jul 2020 12:19:33: 6000000 INFO @ Tue, 14 Jul 2020 12:19:35: 11000000 INFO @ Tue, 14 Jul 2020 12:19:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:19:41: 7000000 INFO @ Tue, 14 Jul 2020 12:19:42: 12000000 INFO @ Tue, 14 Jul 2020 12:19:43: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 12:19:43: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 12:19:43: #1 total tags in treatment: 12102146 INFO @ Tue, 14 Jul 2020 12:19:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:19:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:19:43: #1 tags after filtering in treatment: 12102057 INFO @ Tue, 14 Jul 2020 12:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:19:43: #1 finished! INFO @ Tue, 14 Jul 2020 12:19:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:19:44: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 12:19:44: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 12:19:44: start model_add_line... INFO @ Tue, 14 Jul 2020 12:19:44: start X-correlation... INFO @ Tue, 14 Jul 2020 12:19:44: end of X-cor INFO @ Tue, 14 Jul 2020 12:19:44: #2 finished! INFO @ Tue, 14 Jul 2020 12:19:44: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:19:44: #2 alternative fragment length(s) may be 4,54,75,514,549 bps INFO @ Tue, 14 Jul 2020 12:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10_model.r WARNING @ Tue, 14 Jul 2020 12:19:44: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:19:44: #2 You may need to consider one of the other alternative d(s): 4,54,75,514,549 WARNING @ Tue, 14 Jul 2020 12:19:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:19:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:19:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:19:49: 8000000 INFO @ Tue, 14 Jul 2020 12:19:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:19:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:19:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.05_summits.bed INFO @ Tue, 14 Jul 2020 12:19:52: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (1298 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:19:56: 9000000 INFO @ Tue, 14 Jul 2020 12:20:03: 10000000 INFO @ Tue, 14 Jul 2020 12:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:20:11: 11000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:20:18: 12000000 INFO @ Tue, 14 Jul 2020 12:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.10_summits.bed INFO @ Tue, 14 Jul 2020 12:20:19: Done! pass1 - making usageList (202 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:20:19: #1 tag size is determined as 74 bps INFO @ Tue, 14 Jul 2020 12:20:19: #1 tag size = 74 INFO @ Tue, 14 Jul 2020 12:20:19: #1 total tags in treatment: 12102146 INFO @ Tue, 14 Jul 2020 12:20:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:20:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:20:20: #1 tags after filtering in treatment: 12102057 INFO @ Tue, 14 Jul 2020 12:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:20:20: #1 finished! INFO @ Tue, 14 Jul 2020 12:20:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:20:20: #2 number of paired peaks: 324 WARNING @ Tue, 14 Jul 2020 12:20:20: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 14 Jul 2020 12:20:20: start model_add_line... INFO @ Tue, 14 Jul 2020 12:20:20: start X-correlation... INFO @ Tue, 14 Jul 2020 12:20:20: end of X-cor INFO @ Tue, 14 Jul 2020 12:20:20: #2 finished! INFO @ Tue, 14 Jul 2020 12:20:20: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:20:20: #2 alternative fragment length(s) may be 4,54,75,514,549 bps INFO @ Tue, 14 Jul 2020 12:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20_model.r WARNING @ Tue, 14 Jul 2020 12:20:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:20:20: #2 You may need to consider one of the other alternative d(s): 4,54,75,514,549 WARNING @ Tue, 14 Jul 2020 12:20:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:20:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:20:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:20:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521312/SRX8521312.20_summits.bed INFO @ Tue, 14 Jul 2020 12:20:57: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 3 millis CompletedMACS2peakCalling