Job ID = 6455447 SRX = SRX287797 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:06 prefetch.2.10.7: 1) Downloading 'SRR869986'... 2020-06-21T10:09:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:11:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:11:12 prefetch.2.10.7: 'SRR869986' is valid 2020-06-21T10:11:12 prefetch.2.10.7: 1) 'SRR869986' was downloaded successfully Read 11363085 spots for SRR869986/SRR869986.sra Written 11363085 spots for SRR869986/SRR869986.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: 00:00:01 Multiseed full-index search: 00:03:14 11363085 reads; of these: 11363085 (100.00%) were unpaired; of these: 808737 (7.12%) aligned 0 times 7213500 (63.48%) aligned exactly 1 time 3340848 (29.40%) aligned >1 times 92.88% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 1790813 / 10554348 = 0.1697 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 19:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.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 19:18:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:23: 1000000 INFO @ Sun, 21 Jun 2020 19:18:29: 2000000 INFO @ Sun, 21 Jun 2020 19:18:36: 3000000 INFO @ Sun, 21 Jun 2020 19:18:42: 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 19:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.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 19:18:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:48: 5000000 INFO @ Sun, 21 Jun 2020 19:18:53: 1000000 INFO @ Sun, 21 Jun 2020 19:18:55: 6000000 INFO @ Sun, 21 Jun 2020 19:18:59: 2000000 INFO @ Sun, 21 Jun 2020 19:19:02: 7000000 INFO @ Sun, 21 Jun 2020 19:19:06: 3000000 INFO @ Sun, 21 Jun 2020 19:19:09: 8000000 INFO @ Sun, 21 Jun 2020 19:19:13: 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 @ Sun, 21 Jun 2020 19:19:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:14: #1 total tags in treatment: 8763535 INFO @ Sun, 21 Jun 2020 19:19:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:14: #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 19:19:14: #1 tags after filtering in treatment: 8763534 INFO @ Sun, 21 Jun 2020 19:19:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:15: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 19:19:15: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:15: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:19:15: #2 alternative fragment length(s) may be 4,47,575,579 bps INFO @ Sun, 21 Jun 2020 19:19:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05_model.r WARNING @ Sun, 21 Jun 2020 19:19:15: #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 19:19:15: #2 You may need to consider one of the other alternative d(s): 4,47,575,579 WARNING @ Sun, 21 Jun 2020 19:19:15: #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 19:19:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.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 19:19:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:19: 5000000 INFO @ Sun, 21 Jun 2020 19:19:23: 1000000 INFO @ Sun, 21 Jun 2020 19:19:26: 6000000 INFO @ Sun, 21 Jun 2020 19:19:29: 2000000 INFO @ Sun, 21 Jun 2020 19:19:33: 7000000 INFO @ Sun, 21 Jun 2020 19:19:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:19:36: 3000000 INFO @ Sun, 21 Jun 2020 19:19:40: 8000000 INFO @ Sun, 21 Jun 2020 19:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.05_summits.bed INFO @ Sun, 21 Jun 2020 19:19:42: Done! pass1 - making usageList (612 chroms): 2 millis pass2 - checking and writing primary data (2145 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:19:43: 4000000 INFO @ Sun, 21 Jun 2020 19:19:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:45: #1 total tags in treatment: 8763535 INFO @ Sun, 21 Jun 2020 19:19:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:45: #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 19:19:46: #1 tags after filtering in treatment: 8763534 INFO @ Sun, 21 Jun 2020 19:19:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:46: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 19:19:46: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 19:19:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:47: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:19:47: #2 alternative fragment length(s) may be 4,47,575,579 bps INFO @ Sun, 21 Jun 2020 19:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10_model.r WARNING @ Sun, 21 Jun 2020 19:19:47: #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 19:19:47: #2 You may need to consider one of the other alternative d(s): 4,47,575,579 WARNING @ Sun, 21 Jun 2020 19:19:47: #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 19:19:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:49: 5000000 INFO @ Sun, 21 Jun 2020 19:19:56: 6000000 INFO @ Sun, 21 Jun 2020 19:20:03: 7000000 INFO @ Sun, 21 Jun 2020 19:20:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:20:09: 8000000 INFO @ Sun, 21 Jun 2020 19:20:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:14: #1 total tags in treatment: 8763535 INFO @ Sun, 21 Jun 2020 19:20:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:14: #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 19:20:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.10_summits.bed INFO @ Sun, 21 Jun 2020 19:20:14: Done! INFO @ Sun, 21 Jun 2020 19:20:14: #1 tags after filtering in treatment: 8763534 INFO @ Sun, 21 Jun 2020 19:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:14: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (1700 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:15: #2 number of paired peaks: 832 WARNING @ Sun, 21 Jun 2020 19:20:15: Fewer paired peaks (832) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 832 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:15: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 19:20:15: #2 alternative fragment length(s) may be 4,47,575,579 bps INFO @ Sun, 21 Jun 2020 19:20:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20_model.r WARNING @ Sun, 21 Jun 2020 19:20:15: #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 19:20:15: #2 You may need to consider one of the other alternative d(s): 4,47,575,579 WARNING @ Sun, 21 Jun 2020 19:20:15: #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 19:20:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:20:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287797/SRX287797.20_summits.bed INFO @ Sun, 21 Jun 2020 19:20:41: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 11 millis CompletedMACS2peakCalling