Job ID = 14172621 SRX = SRX9891437 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: 00:04:52 22641671 reads; of these: 22641671 (100.00%) were unpaired; of these: 3623373 (16.00%) aligned 0 times 16224761 (71.66%) aligned exactly 1 time 2793537 (12.34%) aligned >1 times 84.00% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 2592743 / 19018298 = 0.1363 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.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 @ Sat, 11 Dec 2021 16:22:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:22:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:22:46: 1000000 INFO @ Sat, 11 Dec 2021 16:22:51: 2000000 INFO @ Sat, 11 Dec 2021 16:22:56: 3000000 INFO @ Sat, 11 Dec 2021 16:23:01: 4000000 INFO @ Sat, 11 Dec 2021 16:23:07: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.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 @ Sat, 11 Dec 2021 16:23:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:23:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:23:12: 6000000 INFO @ Sat, 11 Dec 2021 16:23:17: 1000000 INFO @ Sat, 11 Dec 2021 16:23:18: 7000000 INFO @ Sat, 11 Dec 2021 16:23:24: 2000000 INFO @ Sat, 11 Dec 2021 16:23:24: 8000000 INFO @ Sat, 11 Dec 2021 16:23:30: 3000000 INFO @ Sat, 11 Dec 2021 16:23:30: 9000000 INFO @ Sat, 11 Dec 2021 16:23:36: 10000000 INFO @ Sat, 11 Dec 2021 16:23:37: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 16:23:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.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 @ Sat, 11 Dec 2021 16:23:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:23:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:23:42: 11000000 INFO @ Sat, 11 Dec 2021 16:23:43: 5000000 INFO @ Sat, 11 Dec 2021 16:23:46: 1000000 INFO @ Sat, 11 Dec 2021 16:23:49: 12000000 INFO @ Sat, 11 Dec 2021 16:23:50: 6000000 INFO @ Sat, 11 Dec 2021 16:23:53: 2000000 INFO @ Sat, 11 Dec 2021 16:23:55: 13000000 INFO @ Sat, 11 Dec 2021 16:23:57: 7000000 INFO @ Sat, 11 Dec 2021 16:23:59: 3000000 INFO @ Sat, 11 Dec 2021 16:24:01: 14000000 INFO @ Sat, 11 Dec 2021 16:24:03: 8000000 INFO @ Sat, 11 Dec 2021 16:24:05: 4000000 INFO @ Sat, 11 Dec 2021 16:24:07: 15000000 INFO @ Sat, 11 Dec 2021 16:24:10: 9000000 INFO @ Sat, 11 Dec 2021 16:24:11: 5000000 INFO @ Sat, 11 Dec 2021 16:24:13: 16000000 INFO @ Sat, 11 Dec 2021 16:24:16: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:24:16: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:24:16: #1 total tags in treatment: 16425555 INFO @ Sat, 11 Dec 2021 16:24:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:24:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:24:17: 10000000 INFO @ Sat, 11 Dec 2021 16:24:17: #1 tags after filtering in treatment: 16425546 INFO @ Sat, 11 Dec 2021 16:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:24:17: #1 finished! INFO @ Sat, 11 Dec 2021 16:24:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:24:17: 6000000 INFO @ Sat, 11 Dec 2021 16:24:18: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 16:24:18: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 16:24:18: start model_add_line... INFO @ Sat, 11 Dec 2021 16:24:18: start X-correlation... INFO @ Sat, 11 Dec 2021 16:24:18: end of X-cor INFO @ Sat, 11 Dec 2021 16:24:18: #2 finished! INFO @ Sat, 11 Dec 2021 16:24:18: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 16:24:18: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 16:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05_model.r WARNING @ Sat, 11 Dec 2021 16:24:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:24:18: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 16:24:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:24:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:24:23: 7000000 INFO @ Sat, 11 Dec 2021 16:24:23: 11000000 INFO @ Sat, 11 Dec 2021 16:24:29: 8000000 INFO @ Sat, 11 Dec 2021 16:24:30: 12000000 INFO @ Sat, 11 Dec 2021 16:24:35: 9000000 INFO @ Sat, 11 Dec 2021 16:24:37: 13000000 INFO @ Sat, 11 Dec 2021 16:24:41: 10000000 INFO @ Sat, 11 Dec 2021 16:24:44: 14000000 INFO @ Sat, 11 Dec 2021 16:24:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:24:47: 11000000 INFO @ Sat, 11 Dec 2021 16:24:50: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:24:53: 12000000 INFO @ Sat, 11 Dec 2021 16:24:57: 16000000 INFO @ Sat, 11 Dec 2021 16:24:59: 13000000 INFO @ Sat, 11 Dec 2021 16:25:00: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:25:00: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:25:00: #1 total tags in treatment: 16425555 INFO @ Sat, 11 Dec 2021 16:25:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:25:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.05_summits.bed INFO @ Sat, 11 Dec 2021 16:25:00: Done! INFO @ Sat, 11 Dec 2021 16:25:00: #1 tags after filtering in treatment: 16425546 INFO @ Sat, 11 Dec 2021 16:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:25:00: #1 finished! INFO @ Sat, 11 Dec 2021 16:25:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:25:00: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (481 chroms): 1 millis pass2 - checking and writing primary data (1698 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:25:01: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 16:25:01: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 16:25:01: start model_add_line... INFO @ Sat, 11 Dec 2021 16:25:02: start X-correlation... INFO @ Sat, 11 Dec 2021 16:25:02: end of X-cor INFO @ Sat, 11 Dec 2021 16:25:02: #2 finished! INFO @ Sat, 11 Dec 2021 16:25:02: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 16:25:02: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 16:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10_model.r WARNING @ Sat, 11 Dec 2021 16:25:02: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:25:02: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 16:25:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:25:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:25:05: 14000000 INFO @ Sat, 11 Dec 2021 16:25:10: 15000000 INFO @ Sat, 11 Dec 2021 16:25:16: 16000000 INFO @ Sat, 11 Dec 2021 16:25:18: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 16:25:18: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 16:25:18: #1 total tags in treatment: 16425555 INFO @ Sat, 11 Dec 2021 16:25:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 16:25:19: #1 tags after filtering in treatment: 16425546 INFO @ Sat, 11 Dec 2021 16:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:25:19: #1 finished! INFO @ Sat, 11 Dec 2021 16:25:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:25:20: #2 number of paired peaks: 126 WARNING @ Sat, 11 Dec 2021 16:25:20: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sat, 11 Dec 2021 16:25:20: start model_add_line... INFO @ Sat, 11 Dec 2021 16:25:20: start X-correlation... INFO @ Sat, 11 Dec 2021 16:25:20: end of X-cor INFO @ Sat, 11 Dec 2021 16:25:20: #2 finished! INFO @ Sat, 11 Dec 2021 16:25:20: #2 predicted fragment length is 69 bps INFO @ Sat, 11 Dec 2021 16:25:20: #2 alternative fragment length(s) may be 69 bps INFO @ Sat, 11 Dec 2021 16:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20_model.r WARNING @ Sat, 11 Dec 2021 16:25:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:25:20: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sat, 11 Dec 2021 16:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:25:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:25:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:25:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.10_summits.bed INFO @ Sat, 11 Dec 2021 16:25:44: Done! pass1 - making usageList (268 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:25:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9891437/SRX9891437.20_summits.bed INFO @ Sat, 11 Dec 2021 16:26:02: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 5 millis CompletedMACS2peakCalling