Job ID = 6458795 SRX = SRX5515081 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:10 prefetch.2.10.7: 1) Downloading 'SRR8721835'... 2020-06-21T12:51:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:51:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:51:40 prefetch.2.10.7: 'SRR8721835' is valid 2020-06-21T12:51:40 prefetch.2.10.7: 1) 'SRR8721835' was downloaded successfully 2020-06-21T12:51:40 prefetch.2.10.7: 'SRR8721835' has 0 unresolved dependencies Read 2293964 spots for SRR8721835/SRR8721835.sra Written 2293964 spots for SRR8721835/SRR8721835.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: 00:00:38 2293964 reads; of these: 2293964 (100.00%) were unpaired; of these: 603 (0.03%) aligned 0 times 1621075 (70.67%) aligned exactly 1 time 672286 (29.31%) aligned >1 times 99.97% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 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] 212976 / 2293361 = 0.0929 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 21:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.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 21:53:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:34: 1000000 INFO @ Sun, 21 Jun 2020 21:53:41: 2000000 INFO @ Sun, 21 Jun 2020 21:53:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:53:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:53:41: #1 total tags in treatment: 2080385 INFO @ Sun, 21 Jun 2020 21:53:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:41: #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 21:53:41: #1 tags after filtering in treatment: 2080126 INFO @ Sun, 21 Jun 2020 21:53:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:41: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:42: #2 number of paired peaks: 610 WARNING @ Sun, 21 Jun 2020 21:53:42: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sun, 21 Jun 2020 21:53:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:42: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:53:42: #2 alternative fragment length(s) may be 52,158,177,222,495,566 bps INFO @ Sun, 21 Jun 2020 21:53:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05_model.r WARNING @ Sun, 21 Jun 2020 21:53:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:53:42: #2 You may need to consider one of the other alternative d(s): 52,158,177,222,495,566 WARNING @ Sun, 21 Jun 2020 21:53:42: #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 21:53:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.05_summits.bed INFO @ Sun, 21 Jun 2020 21:53:49: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 9 millis CompletedMACS2peakCalling 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 21:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.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 21:53:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:04: 1000000 INFO @ Sun, 21 Jun 2020 21:54:10: 2000000 INFO @ Sun, 21 Jun 2020 21:54:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:54:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:54:11: #1 total tags in treatment: 2080385 INFO @ Sun, 21 Jun 2020 21:54:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:11: #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 21:54:11: #1 tags after filtering in treatment: 2080126 INFO @ Sun, 21 Jun 2020 21:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:11: #2 number of paired peaks: 610 WARNING @ Sun, 21 Jun 2020 21:54:11: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:11: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:54:11: #2 alternative fragment length(s) may be 52,158,177,222,495,566 bps INFO @ Sun, 21 Jun 2020 21:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:11: #2 You may need to consider one of the other alternative d(s): 52,158,177,222,495,566 WARNING @ Sun, 21 Jun 2020 21:54:11: #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 21:54:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:19: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 21:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.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 21:54:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:33: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:54:39: 2000000 INFO @ Sun, 21 Jun 2020 21:54:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:54:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:54:39: #1 total tags in treatment: 2080385 INFO @ Sun, 21 Jun 2020 21:54:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:39: #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 21:54:40: #1 tags after filtering in treatment: 2080126 INFO @ Sun, 21 Jun 2020 21:54:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:40: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:40: #2 number of paired peaks: 610 WARNING @ Sun, 21 Jun 2020 21:54:40: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:40: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 21:54:40: #2 alternative fragment length(s) may be 52,158,177,222,495,566 bps INFO @ Sun, 21 Jun 2020 21:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20_model.r WARNING @ Sun, 21 Jun 2020 21:54:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:40: #2 You may need to consider one of the other alternative d(s): 52,158,177,222,495,566 WARNING @ Sun, 21 Jun 2020 21:54:40: #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 21:54:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:54:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5515081/SRX5515081.20_summits.bed INFO @ Sun, 21 Jun 2020 21:54:47: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (49 records, 4 fields): 2 millis CompletedMACS2peakCalling