Job ID = 6459047 SRX = SRX6386728 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:56:07 prefetch.2.10.7: 1) Downloading 'SRR9624460'... 2020-06-21T12:56:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:59:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:59:39 prefetch.2.10.7: 1) 'SRR9624460' was downloaded successfully Read 18925858 spots for SRR9624460/SRR9624460.sra Written 18925858 spots for SRR9624460/SRR9624460.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: 00:02:59 18925858 reads; of these: 18925858 (100.00%) were unpaired; of these: 13123817 (69.34%) aligned 0 times 4169139 (22.03%) aligned exactly 1 time 1632902 (8.63%) aligned >1 times 30.66% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 3146982 / 5802041 = 0.5424 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 22:05:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.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 22:05:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:26: 1000000 INFO @ Sun, 21 Jun 2020 22:05:32: 2000000 INFO @ Sun, 21 Jun 2020 22:05:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:05:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:05:36: #1 total tags in treatment: 2655059 INFO @ Sun, 21 Jun 2020 22:05:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:36: #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 22:05:36: #1 tags after filtering in treatment: 2655033 INFO @ Sun, 21 Jun 2020 22:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:37: #2 number of paired peaks: 1306 INFO @ Sun, 21 Jun 2020 22:05:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:37: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:05:37: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 21 Jun 2020 22:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05_model.r WARNING @ Sun, 21 Jun 2020 22:05:37: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:37: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 21 Jun 2020 22:05:37: #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 22:05:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:47: Done! pass1 - making usageList (555 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 18 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 22:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.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 22:05:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:57: 1000000 INFO @ Sun, 21 Jun 2020 22:06:04: 2000000 INFO @ Sun, 21 Jun 2020 22:06:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:06:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:06:09: #1 total tags in treatment: 2655059 INFO @ Sun, 21 Jun 2020 22:06:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:09: #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 22:06:09: #1 tags after filtering in treatment: 2655033 INFO @ Sun, 21 Jun 2020 22:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:09: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #2 number of paired peaks: 1306 INFO @ Sun, 21 Jun 2020 22:06:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:09: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:09: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:09: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 21 Jun 2020 22:06:09: #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 22:06:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:16: #3 Call peaks for each chromosome... 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 22:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:20: Done! pass1 - making usageList (294 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.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 22:06:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:26: 1000000 INFO @ Sun, 21 Jun 2020 22:06:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:06:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:06:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:06:36: #1 total tags in treatment: 2655059 INFO @ Sun, 21 Jun 2020 22:06:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:36: #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 22:06:36: #1 tags after filtering in treatment: 2655033 INFO @ Sun, 21 Jun 2020 22:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:36: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:36: #2 number of paired peaks: 1306 INFO @ Sun, 21 Jun 2020 22:06:36: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:36: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 22:06:36: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 21 Jun 2020 22:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20_model.r WARNING @ Sun, 21 Jun 2020 22:06:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:36: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 21 Jun 2020 22:06:36: #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 22:06:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:06:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386728/SRX6386728.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:46: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling