Job ID = 6454184 SRX = SRX1850481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:51:34 prefetch.2.10.7: 1) Downloading 'SRR3675038'... 2020-06-21T08:51:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:34 prefetch.2.10.7: 1) 'SRR3675038' was downloaded successfully Read 10298719 spots for SRR3675038/SRR3675038.sra Written 10298719 spots for SRR3675038/SRR3675038.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: 00:05:01 10298719 reads; of these: 10298719 (100.00%) were unpaired; of these: 1583625 (15.38%) aligned 0 times 7206376 (69.97%) aligned exactly 1 time 1508718 (14.65%) aligned >1 times 84.62% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 6971865 / 8715094 = 0.8000 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 18:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.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 18:01:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:41: 1000000 INFO @ Sun, 21 Jun 2020 18:01:47: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:01:47: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:01:47: #1 total tags in treatment: 1743229 INFO @ Sun, 21 Jun 2020 18:01:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:47: #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 18:01:47: #1 tags after filtering in treatment: 1742911 INFO @ Sun, 21 Jun 2020 18:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:48: #2 number of paired peaks: 1834 INFO @ Sun, 21 Jun 2020 18:01:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:48: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:01:48: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05_model.r WARNING @ Sun, 21 Jun 2020 18:01:48: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:48: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:01:48: #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 18:01:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:54: Done! pass1 - making usageList (443 chroms): 1 millis pass2 - checking and writing primary data (1157 records, 4 fields): 13 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 18:02:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.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 18:02:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:11: 1000000 INFO @ Sun, 21 Jun 2020 18:02:17: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:02:17: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:02:17: #1 total tags in treatment: 1743229 INFO @ Sun, 21 Jun 2020 18:02:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:17: #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 18:02:18: #1 tags after filtering in treatment: 1742911 INFO @ Sun, 21 Jun 2020 18:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:18: #2 number of paired peaks: 1834 INFO @ Sun, 21 Jun 2020 18:02:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:18: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:02:18: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10_model.r WARNING @ Sun, 21 Jun 2020 18:02:18: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:18: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:02:18: #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 18:02:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:24: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 11 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 18:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.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 18:02:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:02:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:02:41: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:02:47: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:02:47: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:02:47: #1 total tags in treatment: 1743229 INFO @ Sun, 21 Jun 2020 18:02:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:47: #1 tags after filtering in treatment: 1742911 INFO @ Sun, 21 Jun 2020 18:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:47: #2 number of paired peaks: 1834 INFO @ Sun, 21 Jun 2020 18:02:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:48: #2 predicted fragment length is 98 bps INFO @ Sun, 21 Jun 2020 18:02:48: #2 alternative fragment length(s) may be 98 bps INFO @ Sun, 21 Jun 2020 18:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20_model.r WARNING @ Sun, 21 Jun 2020 18:02:48: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:48: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sun, 21 Jun 2020 18:02:48: #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 18:02:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1850481/SRX1850481.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:54: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 9 millis CompletedMACS2peakCalling