Job ID = 14171850 SRX = SRX9986163 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: 00:06:25 20790482 reads; of these: 20790482 (100.00%) were unpaired; of these: 2925325 (14.07%) aligned 0 times 12619335 (60.70%) aligned exactly 1 time 5245822 (25.23%) aligned >1 times 85.93% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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] 4046561 / 17865157 = 0.2265 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 13:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.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 13:20:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:20:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:20:59: 1000000 INFO @ Sat, 11 Dec 2021 13:21:07: 2000000 INFO @ Sat, 11 Dec 2021 13:21:15: 3000000 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 13:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.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 13:21:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:21:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:23: 4000000 INFO @ Sat, 11 Dec 2021 13:21:28: 1000000 INFO @ Sat, 11 Dec 2021 13:21:31: 5000000 INFO @ Sat, 11 Dec 2021 13:21:36: 2000000 INFO @ Sat, 11 Dec 2021 13:21:39: 6000000 INFO @ Sat, 11 Dec 2021 13:21:44: 3000000 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 13:21:47: 7000000 INFO @ Sat, 11 Dec 2021 13:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.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 13:21:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:21:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:21:51: 4000000 INFO @ Sat, 11 Dec 2021 13:21:55: 8000000 INFO @ Sat, 11 Dec 2021 13:21:58: 1000000 INFO @ Sat, 11 Dec 2021 13:21:59: 5000000 INFO @ Sat, 11 Dec 2021 13:22:03: 9000000 INFO @ Sat, 11 Dec 2021 13:22:06: 2000000 INFO @ Sat, 11 Dec 2021 13:22:07: 6000000 INFO @ Sat, 11 Dec 2021 13:22:11: 10000000 INFO @ Sat, 11 Dec 2021 13:22:14: 3000000 INFO @ Sat, 11 Dec 2021 13:22:15: 7000000 INFO @ Sat, 11 Dec 2021 13:22:19: 11000000 INFO @ Sat, 11 Dec 2021 13:22:22: 4000000 INFO @ Sat, 11 Dec 2021 13:22:23: 8000000 INFO @ Sat, 11 Dec 2021 13:22:28: 12000000 INFO @ Sat, 11 Dec 2021 13:22:30: 5000000 INFO @ Sat, 11 Dec 2021 13:22:31: 9000000 INFO @ Sat, 11 Dec 2021 13:22:36: 13000000 INFO @ Sat, 11 Dec 2021 13:22:38: 6000000 INFO @ Sat, 11 Dec 2021 13:22:39: 10000000 INFO @ Sat, 11 Dec 2021 13:22:43: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:22:43: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:22:43: #1 total tags in treatment: 13818596 INFO @ Sat, 11 Dec 2021 13:22:43: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:43: #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 13:22:44: #1 tags after filtering in treatment: 13818525 INFO @ Sat, 11 Dec 2021 13:22:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:22:44: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:45: #2 number of paired peaks: 162 WARNING @ Sat, 11 Dec 2021 13:22:45: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:45: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:45: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:45: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:45: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:45: #2 predicted fragment length is 23 bps INFO @ Sat, 11 Dec 2021 13:22:45: #2 alternative fragment length(s) may be 23,70,474,511,537,576 bps INFO @ Sat, 11 Dec 2021 13:22:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05_model.r WARNING @ Sat, 11 Dec 2021 13:22:45: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:22:45: #2 You may need to consider one of the other alternative d(s): 23,70,474,511,537,576 WARNING @ Sat, 11 Dec 2021 13:22:45: #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 13:22:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:46: 7000000 INFO @ Sat, 11 Dec 2021 13:22:48: 11000000 INFO @ Sat, 11 Dec 2021 13:22:54: 8000000 INFO @ Sat, 11 Dec 2021 13:22:56: 12000000 INFO @ Sat, 11 Dec 2021 13:23:02: 9000000 INFO @ Sat, 11 Dec 2021 13:23:04: 13000000 INFO @ Sat, 11 Dec 2021 13:23:10: 10000000 INFO @ Sat, 11 Dec 2021 13:23:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:23:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:23:11: #1 total tags in treatment: 13818596 INFO @ Sat, 11 Dec 2021 13:23:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:23:11: #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 13:23:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:11: #1 tags after filtering in treatment: 13818525 INFO @ Sat, 11 Dec 2021 13:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:23:11: #1 finished! INFO @ Sat, 11 Dec 2021 13:23:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:23:12: #2 number of paired peaks: 162 WARNING @ Sat, 11 Dec 2021 13:23:12: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 11 Dec 2021 13:23:12: start model_add_line... INFO @ Sat, 11 Dec 2021 13:23:12: start X-correlation... INFO @ Sat, 11 Dec 2021 13:23:12: end of X-cor INFO @ Sat, 11 Dec 2021 13:23:12: #2 finished! INFO @ Sat, 11 Dec 2021 13:23:12: #2 predicted fragment length is 23 bps INFO @ Sat, 11 Dec 2021 13:23:12: #2 alternative fragment length(s) may be 23,70,474,511,537,576 bps INFO @ Sat, 11 Dec 2021 13:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10_model.r WARNING @ Sat, 11 Dec 2021 13:23:12: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:23:12: #2 You may need to consider one of the other alternative d(s): 23,70,474,511,537,576 WARNING @ Sat, 11 Dec 2021 13:23:12: #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 13:23:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:23:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:23:18: 11000000 INFO @ Sat, 11 Dec 2021 13:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.05_summits.bed INFO @ Sat, 11 Dec 2021 13:23:26: Done! INFO @ Sat, 11 Dec 2021 13:23:26: 12000000 pass1 - making usageList (377 chroms): 4 millis pass2 - checking and writing primary data (1119 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:23:34: 13000000 INFO @ Sat, 11 Dec 2021 13:23:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:23:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:23:41: #1 total tags in treatment: 13818596 INFO @ Sat, 11 Dec 2021 13:23:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:23:41: #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 13:23:41: #1 tags after filtering in treatment: 13818525 INFO @ Sat, 11 Dec 2021 13:23:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:23:41: #1 finished! INFO @ Sat, 11 Dec 2021 13:23:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:23:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:23:42: #2 number of paired peaks: 162 WARNING @ Sat, 11 Dec 2021 13:23:42: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 11 Dec 2021 13:23:42: start model_add_line... INFO @ Sat, 11 Dec 2021 13:23:42: start X-correlation... INFO @ Sat, 11 Dec 2021 13:23:42: end of X-cor INFO @ Sat, 11 Dec 2021 13:23:42: #2 finished! INFO @ Sat, 11 Dec 2021 13:23:42: #2 predicted fragment length is 23 bps INFO @ Sat, 11 Dec 2021 13:23:42: #2 alternative fragment length(s) may be 23,70,474,511,537,576 bps INFO @ Sat, 11 Dec 2021 13:23:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20_model.r WARNING @ Sat, 11 Dec 2021 13:23:42: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:23:42: #2 You may need to consider one of the other alternative d(s): 23,70,474,511,537,576 WARNING @ Sat, 11 Dec 2021 13:23:42: #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 13:23:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:23:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:23:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.10_summits.bed INFO @ Sat, 11 Dec 2021 13:23:53: Done! pass1 - making usageList (85 chroms): 2 millis pass2 - checking and writing primary data (162 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:24:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986163/SRX9986163.20_summits.bed INFO @ Sat, 11 Dec 2021 13:24:22: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (23 records, 4 fields): 3 millis CompletedMACS2peakCalling