Job ID = 6458923 SRX = SRX5775928 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:38:59 prefetch.2.10.7: 1) Downloading 'SRR8997131'... 2020-06-21T12:38:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:03 prefetch.2.10.7: 1) 'SRR8997131' was downloaded successfully Read 24948107 spots for SRR8997131/SRR8997131.sra Written 24948107 spots for SRR8997131/SRR8997131.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: 00:03:52 24948107 reads; of these: 24948107 (100.00%) were unpaired; of these: 21344817 (85.56%) aligned 0 times 2603177 (10.43%) aligned exactly 1 time 1000113 (4.01%) aligned >1 times 14.44% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1710472 / 3603290 = 0.4747 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 21:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.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 21:51:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:42: 1000000 INFO @ Sun, 21 Jun 2020 21:51:48: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:51:48: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:51:48: #1 total tags in treatment: 1892818 INFO @ Sun, 21 Jun 2020 21:51:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:48: #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 21:51:48: #1 tags after filtering in treatment: 1892704 INFO @ Sun, 21 Jun 2020 21:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #2 number of paired peaks: 1136 INFO @ Sun, 21 Jun 2020 21:51:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:48: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:48: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:48: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:51:48: #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 21:51:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:55: Done! pass1 - making usageList (527 chroms): 1 millis pass2 - checking and writing primary data (1485 records, 4 fields): 15 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 21:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.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 21:52:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:12: 1000000 INFO @ Sun, 21 Jun 2020 21:52:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:52:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:52:17: #1 total tags in treatment: 1892818 INFO @ Sun, 21 Jun 2020 21:52:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:17: #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 21:52:18: #1 tags after filtering in treatment: 1892704 INFO @ Sun, 21 Jun 2020 21:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:18: #2 number of paired peaks: 1136 INFO @ Sun, 21 Jun 2020 21:52:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:18: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:52:18: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10_model.r WARNING @ Sun, 21 Jun 2020 21:52:18: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:18: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:52:18: #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 21:52:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:25: Done! pass1 - making usageList (382 chroms): 1 millis pass2 - checking and writing primary data (769 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 21:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.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 21:52:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:42: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:52:47: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:52:47: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:52:47: #1 total tags in treatment: 1892818 INFO @ Sun, 21 Jun 2020 21:52:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:47: #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 21:52:48: #1 tags after filtering in treatment: 1892704 INFO @ Sun, 21 Jun 2020 21:52:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:48: #2 number of paired peaks: 1136 INFO @ Sun, 21 Jun 2020 21:52:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:48: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 21:52:48: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 21:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:48: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:48: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Sun, 21 Jun 2020 21:52:48: #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 21:52:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775928/SRX5775928.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:55: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 5 millis CompletedMACS2peakCalling