Job ID = 6459576 SRX = SRX706811 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:22:31 prefetch.2.10.7: 1) Downloading 'SRR1581492'... 2020-06-21T13:22:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:24:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:24:47 prefetch.2.10.7: 'SRR1581492' is valid 2020-06-21T13:24:47 prefetch.2.10.7: 1) 'SRR1581492' was downloaded successfully Read 10858467 spots for SRR1581492/SRR1581492.sra Written 10858467 spots for SRR1581492/SRR1581492.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: 00:00:46 10858467 reads; of these: 10858467 (100.00%) were unpaired; of these: 10137658 (93.36%) aligned 0 times 559834 (5.16%) aligned exactly 1 time 160975 (1.48%) aligned >1 times 6.64% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 375980 / 720809 = 0.5216 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 22:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.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 22:26:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:26:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:26:47: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:26:47: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:26:47: #1 total tags in treatment: 344829 INFO @ Sun, 21 Jun 2020 22:26:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:26:47: #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 22:26:47: #1 tags after filtering in treatment: 344079 INFO @ Sun, 21 Jun 2020 22:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:26:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:26:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:26:47: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:26:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:26:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:26:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:26:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:26:47: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 22:26:47: #2 alternative fragment length(s) may be 39,97,130,152,195,269,349,422,523,580 bps INFO @ Sun, 21 Jun 2020 22:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05_model.r WARNING @ Sun, 21 Jun 2020 22:26:47: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:26:47: #2 You may need to consider one of the other alternative d(s): 39,97,130,152,195,269,349,422,523,580 WARNING @ Sun, 21 Jun 2020 22:26:47: #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 22:26:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:26:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:26:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:26:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:26:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:26:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.05_summits.bed INFO @ Sun, 21 Jun 2020 22:26:49: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 3 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 22:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.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 22:27:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:27:17: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:27:17: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:27:17: #1 total tags in treatment: 344829 INFO @ Sun, 21 Jun 2020 22:27:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:17: #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 22:27:17: #1 tags after filtering in treatment: 344079 INFO @ Sun, 21 Jun 2020 22:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:17: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:17: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:27:17: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:17: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:17: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:17: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:17: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 22:27:17: #2 alternative fragment length(s) may be 39,97,130,152,195,269,349,422,523,580 bps INFO @ Sun, 21 Jun 2020 22:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10_model.r WARNING @ Sun, 21 Jun 2020 22:27:17: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:27:17: #2 You may need to consider one of the other alternative d(s): 39,97,130,152,195,269,349,422,523,580 WARNING @ Sun, 21 Jun 2020 22:27:17: #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 22:27:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.10_summits.bed INFO @ Sun, 21 Jun 2020 22:27:19: Done! pass1 - making usageList (19 chroms): 0 millis pass2 - checking and writing primary data (72 records, 4 fields): 2 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 22:27:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.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 22:27:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:27:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:27:47: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 22:27:47: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 22:27:47: #1 total tags in treatment: 344829 INFO @ Sun, 21 Jun 2020 22:27:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:27:47: #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 22:27:47: #1 tags after filtering in treatment: 344079 INFO @ Sun, 21 Jun 2020 22:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:27:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:27:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:27:47: #2 number of paired peaks: 1024 INFO @ Sun, 21 Jun 2020 22:27:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:27:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:27:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:27:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:27:47: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 22:27:47: #2 alternative fragment length(s) may be 39,97,130,152,195,269,349,422,523,580 bps INFO @ Sun, 21 Jun 2020 22:27:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20_model.r WARNING @ Sun, 21 Jun 2020 22:27:47: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:27:47: #2 You may need to consider one of the other alternative d(s): 39,97,130,152,195,269,349,422,523,580 WARNING @ Sun, 21 Jun 2020 22:27:47: #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 22:27:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:27:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:27:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706811/SRX706811.20_summits.bed INFO @ Sun, 21 Jun 2020 22:27:49: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 2 millis CompletedMACS2peakCalling