Job ID = 6459038 SRX = SRX6370202 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:54:25 prefetch.2.10.7: 1) Downloading 'SRR9606651'... 2020-06-21T12:54:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:55:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:55:55 prefetch.2.10.7: 'SRR9606651' is valid 2020-06-21T12:55:55 prefetch.2.10.7: 1) 'SRR9606651' was downloaded successfully 2020-06-21T12:55:55 prefetch.2.10.7: 'SRR9606651' has 0 unresolved dependencies Read 10009728 spots for SRR9606651/SRR9606651.sra Written 10009728 spots for SRR9606651/SRR9606651.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: 00:01:19 10009728 reads; of these: 10009728 (100.00%) were unpaired; of these: 9578539 (95.69%) aligned 0 times 304378 (3.04%) aligned exactly 1 time 126811 (1.27%) aligned >1 times 4.31% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 16068 / 431189 = 0.0373 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 21:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.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 21:58:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:28: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:58:28: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:58:28: #1 total tags in treatment: 415121 INFO @ Sun, 21 Jun 2020 21:58:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:28: #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 21:58:28: #1 tags after filtering in treatment: 414586 INFO @ Sun, 21 Jun 2020 21:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:28: #2 number of paired peaks: 1570 INFO @ Sun, 21 Jun 2020 21:58:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:28: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:58:28: #2 alternative fragment length(s) may be 76,195,227 bps INFO @ Sun, 21 Jun 2020 21:58:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05_model.r WARNING @ Sun, 21 Jun 2020 21:58:28: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:28: #2 You may need to consider one of the other alternative d(s): 76,195,227 WARNING @ Sun, 21 Jun 2020 21:58:28: #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 21:58:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.05_summits.bed INFO @ Sun, 21 Jun 2020 21:58:30: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 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 21:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.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 21:58:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:58: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:58:58: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:58:58: #1 total tags in treatment: 415121 INFO @ Sun, 21 Jun 2020 21:58:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:58:58: #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 21:58:58: #1 tags after filtering in treatment: 414586 INFO @ Sun, 21 Jun 2020 21:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:58:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:58:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:58:58: #2 number of paired peaks: 1570 INFO @ Sun, 21 Jun 2020 21:58:58: start model_add_line... INFO @ Sun, 21 Jun 2020 21:58:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:58:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:58:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:58:58: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:58:58: #2 alternative fragment length(s) may be 76,195,227 bps INFO @ Sun, 21 Jun 2020 21:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10_model.r WARNING @ Sun, 21 Jun 2020 21:58:58: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:58:58: #2 You may need to consider one of the other alternative d(s): 76,195,227 WARNING @ Sun, 21 Jun 2020 21:58:58: #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 21:58:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:58:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.10_summits.bed INFO @ Sun, 21 Jun 2020 21:59:00: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (50 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 21:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.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 21:59:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:25: #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 21:59:28: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 21:59:28: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 21:59:28: #1 total tags in treatment: 415121 INFO @ Sun, 21 Jun 2020 21:59:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:28: #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 21:59:28: #1 tags after filtering in treatment: 414586 INFO @ Sun, 21 Jun 2020 21:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:28: #2 number of paired peaks: 1570 INFO @ Sun, 21 Jun 2020 21:59:28: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:28: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:28: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:28: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:28: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 21:59:28: #2 alternative fragment length(s) may be 76,195,227 bps INFO @ Sun, 21 Jun 2020 21:59:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20_model.r WARNING @ Sun, 21 Jun 2020 21:59:28: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:28: #2 You may need to consider one of the other alternative d(s): 76,195,227 WARNING @ Sun, 21 Jun 2020 21:59:28: #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 21:59:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6370202/SRX6370202.20_summits.bed INFO @ Sun, 21 Jun 2020 21:59:30: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 2 millis CompletedMACS2peakCalling