Job ID = 6459107 SRX = SRX6386778 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:02:16 prefetch.2.10.7: 1) Downloading 'SRR9624510'... 2020-06-21T13:02:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:10:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:10:04 prefetch.2.10.7: 1) 'SRR9624510' was downloaded successfully Read 32807276 spots for SRR9624510/SRR9624510.sra Written 32807276 spots for SRR9624510/SRR9624510.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: 00:05:13 32807276 reads; of these: 32807276 (100.00%) were unpaired; of these: 26380770 (80.41%) aligned 0 times 4119990 (12.56%) aligned exactly 1 time 2306516 (7.03%) aligned >1 times 19.59% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 5006456 / 6426506 = 0.7790 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 22:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.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 22:18:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:39: 1000000 INFO @ Sun, 21 Jun 2020 22:18:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:18:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:18:42: #1 total tags in treatment: 1420050 INFO @ Sun, 21 Jun 2020 22:18:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:42: #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 22:18:42: #1 tags after filtering in treatment: 1419995 INFO @ Sun, 21 Jun 2020 22:18:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:42: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:42: #2 number of paired peaks: 1998 INFO @ Sun, 21 Jun 2020 22:18:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:42: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:18:42: #2 alternative fragment length(s) may be 48,199 bps INFO @ Sun, 21 Jun 2020 22:18:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05_model.r WARNING @ Sun, 21 Jun 2020 22:18:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:42: #2 You may need to consider one of the other alternative d(s): 48,199 WARNING @ Sun, 21 Jun 2020 22:18:42: #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 22:18:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:47: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (1773 records, 4 fields): 16 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 22:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.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 22:19:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:19:09: 1000000 INFO @ Sun, 21 Jun 2020 22:19:12: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:12: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:12: #1 total tags in treatment: 1420050 INFO @ Sun, 21 Jun 2020 22:19:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:12: #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 22:19:12: #1 tags after filtering in treatment: 1419995 INFO @ Sun, 21 Jun 2020 22:19:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:12: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:12: #2 number of paired peaks: 1998 INFO @ Sun, 21 Jun 2020 22:19:12: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:12: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:12: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:12: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:12: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:19:12: #2 alternative fragment length(s) may be 48,199 bps INFO @ Sun, 21 Jun 2020 22:19:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10_model.r WARNING @ Sun, 21 Jun 2020 22:19:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:12: #2 You may need to consider one of the other alternative d(s): 48,199 WARNING @ Sun, 21 Jun 2020 22:19:12: #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 22:19:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.10_summits.bed INFO @ Sun, 21 Jun 2020 22:19:18: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (607 records, 4 fields): 8 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 22:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.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 22:19:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:19:33: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:39: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:19:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:19:42: #1 total tags in treatment: 1420050 INFO @ Sun, 21 Jun 2020 22:19:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:42: #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 22:19:42: #1 tags after filtering in treatment: 1419995 INFO @ Sun, 21 Jun 2020 22:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:42: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:42: #2 number of paired peaks: 1998 INFO @ Sun, 21 Jun 2020 22:19:42: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:42: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:42: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:42: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:42: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 22:19:42: #2 alternative fragment length(s) may be 48,199 bps INFO @ Sun, 21 Jun 2020 22:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20_model.r WARNING @ Sun, 21 Jun 2020 22:19:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:42: #2 You may need to consider one of the other alternative d(s): 48,199 WARNING @ Sun, 21 Jun 2020 22:19:42: #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 22:19:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386778/SRX6386778.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:48: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 4 millis CompletedMACS2peakCalling