Job ID = 6508475 SRX = SRX287897 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:45:52 prefetch.2.10.7: 1) Downloading 'SRR870086'... 2020-06-26T14:45:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:46:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:46:51 prefetch.2.10.7: 'SRR870086' is valid 2020-06-26T14:46:51 prefetch.2.10.7: 1) 'SRR870086' was downloaded successfully Read 11363085 spots for SRR870086/SRR870086.sra Written 11363085 spots for SRR870086/SRR870086.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: 00:04:14 11363085 reads; of these: 11363085 (100.00%) were unpaired; of these: 808740 (7.12%) aligned 0 times 7213528 (63.48%) aligned exactly 1 time 3340817 (29.40%) aligned >1 times 92.88% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 1790612 / 10554345 = 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 @ Fri, 26 Jun 2020 23:56:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.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 @ Fri, 26 Jun 2020 23:56:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:56:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:56:09: 1000000 INFO @ Fri, 26 Jun 2020 23:56:15: 2000000 INFO @ Fri, 26 Jun 2020 23:56:20: 3000000 INFO @ Fri, 26 Jun 2020 23:56:26: 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 @ Fri, 26 Jun 2020 23:56:32: 5000000 INFO @ Fri, 26 Jun 2020 23:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.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 @ Fri, 26 Jun 2020 23:56:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:56:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:56:38: 6000000 INFO @ Fri, 26 Jun 2020 23:56:40: 1000000 INFO @ Fri, 26 Jun 2020 23:56:45: 7000000 INFO @ Fri, 26 Jun 2020 23:56:46: 2000000 INFO @ Fri, 26 Jun 2020 23:56:51: 8000000 INFO @ Fri, 26 Jun 2020 23:56:53: 3000000 INFO @ Fri, 26 Jun 2020 23:56:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:56:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:56:57: #1 total tags in treatment: 8763733 INFO @ Fri, 26 Jun 2020 23:56:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:56:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:56:57: #1 tags after filtering in treatment: 8763732 INFO @ Fri, 26 Jun 2020 23:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:56:57: #1 finished! INFO @ Fri, 26 Jun 2020 23:56:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:56:58: #2 number of paired peaks: 825 WARNING @ Fri, 26 Jun 2020 23:56:58: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 26 Jun 2020 23:56:58: start model_add_line... INFO @ Fri, 26 Jun 2020 23:56:58: start X-correlation... INFO @ Fri, 26 Jun 2020 23:56:58: end of X-cor INFO @ Fri, 26 Jun 2020 23:56:58: #2 finished! INFO @ Fri, 26 Jun 2020 23:56:58: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:56:58: #2 alternative fragment length(s) may be 4,46 bps INFO @ Fri, 26 Jun 2020 23:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05_model.r WARNING @ Fri, 26 Jun 2020 23:56:58: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:56:58: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Fri, 26 Jun 2020 23:56:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:56:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:56:59: 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 @ Fri, 26 Jun 2020 23:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.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 @ Fri, 26 Jun 2020 23:57:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:57:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:57:05: 5000000 INFO @ Fri, 26 Jun 2020 23:57:10: 1000000 INFO @ Fri, 26 Jun 2020 23:57:11: 6000000 INFO @ Fri, 26 Jun 2020 23:57:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:57:15: 2000000 INFO @ Fri, 26 Jun 2020 23:57:17: 7000000 INFO @ Fri, 26 Jun 2020 23:57:21: 3000000 INFO @ Fri, 26 Jun 2020 23:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.05_summits.bed INFO @ Fri, 26 Jun 2020 23:57:23: Done! pass1 - making usageList (603 chroms): 1 millis pass2 - checking and writing primary data (2177 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:57:23: 8000000 INFO @ Fri, 26 Jun 2020 23:57:27: 4000000 INFO @ Fri, 26 Jun 2020 23:57:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:57:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:57:29: #1 total tags in treatment: 8763733 INFO @ Fri, 26 Jun 2020 23:57:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:57:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:57:29: #1 tags after filtering in treatment: 8763732 INFO @ Fri, 26 Jun 2020 23:57:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:57:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:57:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:57:30: #2 number of paired peaks: 825 WARNING @ Fri, 26 Jun 2020 23:57:30: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 26 Jun 2020 23:57:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:57:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:57:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:57:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:57:30: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:57:30: #2 alternative fragment length(s) may be 4,46 bps INFO @ Fri, 26 Jun 2020 23:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10_model.r WARNING @ Fri, 26 Jun 2020 23:57:30: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:57:30: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Fri, 26 Jun 2020 23:57:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:57:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:57:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:57:32: 5000000 INFO @ Fri, 26 Jun 2020 23:57:38: 6000000 INFO @ Fri, 26 Jun 2020 23:57:44: 7000000 INFO @ Fri, 26 Jun 2020 23:57:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:57:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:57:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:57:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:57:54: #1 total tags in treatment: 8763733 INFO @ Fri, 26 Jun 2020 23:57:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:57:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.10_summits.bed INFO @ Fri, 26 Jun 2020 23:57:55: Done! INFO @ Fri, 26 Jun 2020 23:57:55: #1 tags after filtering in treatment: 8763732 INFO @ Fri, 26 Jun 2020 23:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:57:55: #1 finished! INFO @ Fri, 26 Jun 2020 23:57:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:57:55: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (484 chroms): 1 millis pass2 - checking and writing primary data (1693 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:57:56: #2 number of paired peaks: 825 WARNING @ Fri, 26 Jun 2020 23:57:56: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 26 Jun 2020 23:57:56: start model_add_line... INFO @ Fri, 26 Jun 2020 23:57:56: start X-correlation... INFO @ Fri, 26 Jun 2020 23:57:56: end of X-cor INFO @ Fri, 26 Jun 2020 23:57:56: #2 finished! INFO @ Fri, 26 Jun 2020 23:57:56: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:57:56: #2 alternative fragment length(s) may be 4,46 bps INFO @ Fri, 26 Jun 2020 23:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20_model.r WARNING @ Fri, 26 Jun 2020 23:57:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:57:56: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Fri, 26 Jun 2020 23:57:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:57:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:58:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287897/SRX287897.20_summits.bed INFO @ Fri, 26 Jun 2020 23:58:20: Done! pass1 - making usageList (322 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 18 millis CompletedMACS2peakCalling