Job ID = 6459490 SRX = SRX6827672 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:22:19 prefetch.2.10.7: 1) Downloading 'SRR10095452'... 2020-06-21T13:22:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:26:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:26:53 prefetch.2.10.7: 1) 'SRR10095452' was downloaded successfully Read 24277298 spots for SRR10095452/SRR10095452.sra Written 24277298 spots for SRR10095452/SRR10095452.sra 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: 00:07:13 24277298 reads; of these: 24277298 (100.00%) were unpaired; of these: 1025865 (4.23%) aligned 0 times 16193294 (66.70%) aligned exactly 1 time 7058139 (29.07%) aligned >1 times 95.77% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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 12 files... [bam_rmdupse_core] 4015763 / 23251433 = 0.1727 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 @ Sun, 21 Jun 2020 22:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.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 @ Sun, 21 Jun 2020 22:39:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:39:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:04: 1000000 INFO @ Sun, 21 Jun 2020 22:40:11: 2000000 INFO @ Sun, 21 Jun 2020 22:40:18: 3000000 INFO @ Sun, 21 Jun 2020 22:40:25: 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 @ Sun, 21 Jun 2020 22:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.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 @ Sun, 21 Jun 2020 22:40:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:32: 5000000 INFO @ Sun, 21 Jun 2020 22:40:34: 1000000 INFO @ Sun, 21 Jun 2020 22:40:40: 6000000 INFO @ Sun, 21 Jun 2020 22:40:41: 2000000 INFO @ Sun, 21 Jun 2020 22:40:48: 7000000 INFO @ Sun, 21 Jun 2020 22:40:48: 3000000 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 @ Sun, 21 Jun 2020 22:40:56: 4000000 INFO @ Sun, 21 Jun 2020 22:40:56: 8000000 INFO @ Sun, 21 Jun 2020 22:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.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 @ Sun, 21 Jun 2020 22:40:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:03: 5000000 INFO @ Sun, 21 Jun 2020 22:41:04: 9000000 INFO @ Sun, 21 Jun 2020 22:41:04: 1000000 INFO @ Sun, 21 Jun 2020 22:41:10: 6000000 INFO @ Sun, 21 Jun 2020 22:41:12: 2000000 INFO @ Sun, 21 Jun 2020 22:41:12: 10000000 INFO @ Sun, 21 Jun 2020 22:41:17: 7000000 INFO @ Sun, 21 Jun 2020 22:41:20: 3000000 INFO @ Sun, 21 Jun 2020 22:41:21: 11000000 INFO @ Sun, 21 Jun 2020 22:41:24: 8000000 INFO @ Sun, 21 Jun 2020 22:41:28: 4000000 INFO @ Sun, 21 Jun 2020 22:41:29: 12000000 INFO @ Sun, 21 Jun 2020 22:41:32: 9000000 INFO @ Sun, 21 Jun 2020 22:41:35: 5000000 INFO @ Sun, 21 Jun 2020 22:41:37: 13000000 INFO @ Sun, 21 Jun 2020 22:41:39: 10000000 INFO @ Sun, 21 Jun 2020 22:41:43: 6000000 INFO @ Sun, 21 Jun 2020 22:41:45: 14000000 INFO @ Sun, 21 Jun 2020 22:41:46: 11000000 INFO @ Sun, 21 Jun 2020 22:41:50: 7000000 INFO @ Sun, 21 Jun 2020 22:41:53: 15000000 INFO @ Sun, 21 Jun 2020 22:41:53: 12000000 INFO @ Sun, 21 Jun 2020 22:41:57: 8000000 INFO @ Sun, 21 Jun 2020 22:42:01: 13000000 INFO @ Sun, 21 Jun 2020 22:42:01: 16000000 INFO @ Sun, 21 Jun 2020 22:42:04: 9000000 INFO @ Sun, 21 Jun 2020 22:42:08: 14000000 INFO @ Sun, 21 Jun 2020 22:42:10: 17000000 INFO @ Sun, 21 Jun 2020 22:42:11: 10000000 INFO @ Sun, 21 Jun 2020 22:42:15: 15000000 INFO @ Sun, 21 Jun 2020 22:42:18: 18000000 INFO @ Sun, 21 Jun 2020 22:42:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:42:22: 16000000 INFO @ Sun, 21 Jun 2020 22:42:26: 12000000 INFO @ Sun, 21 Jun 2020 22:42:26: 19000000 INFO @ Sun, 21 Jun 2020 22:42:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:28: #1 total tags in treatment: 19235670 INFO @ Sun, 21 Jun 2020 22:42:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:42:29: #1 tags after filtering in treatment: 19235605 INFO @ Sun, 21 Jun 2020 22:42:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:29: 17000000 INFO @ Sun, 21 Jun 2020 22:42:30: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 22:42:30: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 22:42:30: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:30: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:30: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:30: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:30: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:42:30: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 22:42:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05_model.r WARNING @ Sun, 21 Jun 2020 22:42:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:42:30: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 22:42:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:42:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:33: 13000000 INFO @ Sun, 21 Jun 2020 22:42:36: 18000000 INFO @ Sun, 21 Jun 2020 22:42:40: 14000000 INFO @ Sun, 21 Jun 2020 22:42:43: 19000000 INFO @ Sun, 21 Jun 2020 22:42:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:45: #1 total tags in treatment: 19235670 INFO @ Sun, 21 Jun 2020 22:42:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:42:45: #1 tags after filtering in treatment: 19235605 INFO @ Sun, 21 Jun 2020 22:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:46: 15000000 INFO @ Sun, 21 Jun 2020 22:42:47: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 22:42:47: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 22:42:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:47: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:42:47: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 22:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10_model.r WARNING @ Sun, 21 Jun 2020 22:42:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:42:47: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 22:42:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:42:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:52: 16000000 INFO @ Sun, 21 Jun 2020 22:42:59: 17000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:43:04: 18000000 INFO @ Sun, 21 Jun 2020 22:43:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:10: 19000000 INFO @ Sun, 21 Jun 2020 22:43:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:43:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:43:12: #1 total tags in treatment: 19235670 INFO @ Sun, 21 Jun 2020 22:43:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:43:12: #1 tags after filtering in treatment: 19235605 INFO @ Sun, 21 Jun 2020 22:43:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:13: #2 number of paired peaks: 870 WARNING @ Sun, 21 Jun 2020 22:43:13: Fewer paired peaks (870) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 870 pairs to build model! INFO @ Sun, 21 Jun 2020 22:43:13: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:14: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 22:43:14: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 22:43:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20_model.r WARNING @ Sun, 21 Jun 2020 22:43:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:43:14: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 22:43:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:43:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.05_summits.bed INFO @ Sun, 21 Jun 2020 22:43:21: Done! pass1 - making usageList (643 chroms): 1 millis pass2 - checking and writing primary data (3211 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.10_summits.bed INFO @ Sun, 21 Jun 2020 22:43:38: Done! pass1 - making usageList (511 chroms): 2 millis pass2 - checking and writing primary data (2183 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827672/SRX6827672.20_summits.bed INFO @ Sun, 21 Jun 2020 22:44:06: Done! pass1 - making usageList (336 chroms): 1 millis pass2 - checking and writing primary data (837 records, 4 fields): 12 millis CompletedMACS2peakCalling