Job ID = 6459439 SRX = SRX6780072 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:07:49 prefetch.2.10.7: 1) Downloading 'SRR10045473'... 2020-06-21T13:07:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:21 prefetch.2.10.7: 'SRR10045473' is valid 2020-06-21T13:09:21 prefetch.2.10.7: 1) 'SRR10045473' was downloaded successfully Read 10843975 spots for SRR10045473/SRR10045473.sra Written 10843975 spots for SRR10045473/SRR10045473.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:35 10843975 reads; of these: 10843975 (100.00%) were unpaired; of these: 2811075 (25.92%) aligned 0 times 5559341 (51.27%) aligned exactly 1 time 2473559 (22.81%) aligned >1 times 74.08% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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_rmdupse_core] 1370011 / 8032900 = 0.1705 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 22:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.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 22:14:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:56: 1000000 INFO @ Sun, 21 Jun 2020 22:15:01: 2000000 INFO @ Sun, 21 Jun 2020 22:15:06: 3000000 INFO @ Sun, 21 Jun 2020 22:15:11: 4000000 INFO @ Sun, 21 Jun 2020 22:15:17: 5000000 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 22:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.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 22:15:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:15:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:15:22: 6000000 INFO @ Sun, 21 Jun 2020 22:15:26: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:15:26: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:15:26: #1 total tags in treatment: 6662889 INFO @ Sun, 21 Jun 2020 22:15:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:26: #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 22:15:26: 1000000 INFO @ Sun, 21 Jun 2020 22:15:27: #1 tags after filtering in treatment: 6662886 INFO @ Sun, 21 Jun 2020 22:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:27: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:27: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 22:15:27: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 22:15:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:27: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:15:27: #2 alternative fragment length(s) may be 57,66 bps INFO @ Sun, 21 Jun 2020 22:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05_model.r WARNING @ Sun, 21 Jun 2020 22:15:27: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:15:27: #2 You may need to consider one of the other alternative d(s): 57,66 WARNING @ Sun, 21 Jun 2020 22:15:27: #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 22:15:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:31: 2000000 INFO @ Sun, 21 Jun 2020 22:15:36: 3000000 INFO @ Sun, 21 Jun 2020 22:15:41: 4000000 INFO @ Sun, 21 Jun 2020 22:15:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:46: 5000000 INFO @ Sun, 21 Jun 2020 22:15:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:15:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:15:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.05_summits.bed INFO @ Sun, 21 Jun 2020 22:15:49: Done! 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 pass1 - making usageList (586 chroms): 1 millis pass2 - checking and writing primary data (1939 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.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 22:15:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:15:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:15:52: 6000000 INFO @ Sun, 21 Jun 2020 22:15:56: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:15:56: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:15:56: #1 total tags in treatment: 6662889 INFO @ Sun, 21 Jun 2020 22:15:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:56: #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 22:15:56: #1 tags after filtering in treatment: 6662886 INFO @ Sun, 21 Jun 2020 22:15:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:56: 1000000 INFO @ Sun, 21 Jun 2020 22:15:57: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 22:15:57: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 22:15:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:57: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:15:57: #2 alternative fragment length(s) may be 57,66 bps INFO @ Sun, 21 Jun 2020 22:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10_model.r WARNING @ Sun, 21 Jun 2020 22:15:57: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:15:57: #2 You may need to consider one of the other alternative d(s): 57,66 WARNING @ Sun, 21 Jun 2020 22:15:57: #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 22:15:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:16:02: 2000000 INFO @ Sun, 21 Jun 2020 22:16:07: 3000000 INFO @ Sun, 21 Jun 2020 22:16:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:12: 4000000 INFO @ Sun, 21 Jun 2020 22:16:17: 5000000 INFO @ Sun, 21 Jun 2020 22:16:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.10_summits.bed INFO @ Sun, 21 Jun 2020 22:16:18: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1406 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:16:22: 6000000 INFO @ Sun, 21 Jun 2020 22:16:26: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:16:26: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:16:26: #1 total tags in treatment: 6662889 INFO @ Sun, 21 Jun 2020 22:16:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:26: #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 22:16:26: #1 tags after filtering in treatment: 6662886 INFO @ Sun, 21 Jun 2020 22:16:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:26: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:27: #2 number of paired peaks: 867 WARNING @ Sun, 21 Jun 2020 22:16:27: Fewer paired peaks (867) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 867 pairs to build model! INFO @ Sun, 21 Jun 2020 22:16:27: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:27: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:27: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:27: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:27: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:16:27: #2 alternative fragment length(s) may be 57,66 bps INFO @ Sun, 21 Jun 2020 22:16:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20_model.r WARNING @ Sun, 21 Jun 2020 22:16:27: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:16:27: #2 You may need to consider one of the other alternative d(s): 57,66 WARNING @ Sun, 21 Jun 2020 22:16:27: #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 22:16:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:27: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:16:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6780072/SRX6780072.20_summits.bed INFO @ Sun, 21 Jun 2020 22:16:48: Done! pass1 - making usageList (246 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 8 millis CompletedMACS2peakCalling