Job ID = 6452447 SRX = SRX013067 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:25:17 prefetch.2.10.7: 1) Downloading 'SRR030333'... 2020-06-21T07:25:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:27:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:27:43 prefetch.2.10.7: 'SRR030333' is valid 2020-06-21T07:27:43 prefetch.2.10.7: 1) 'SRR030333' was downloaded successfully Read 10801724 spots for SRR030333/SRR030333.sra Written 10801724 spots for SRR030333/SRR030333.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: 00:00:59 10801724 reads; of these: 10801724 (100.00%) were unpaired; of these: 7321007 (67.78%) aligned 0 times 3287400 (30.43%) aligned exactly 1 time 193317 (1.79%) aligned >1 times 32.22% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 573156 / 3480717 = 0.1647 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 16:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.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 16:30:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:30:34: 1000000 INFO @ Sun, 21 Jun 2020 16:30:40: 2000000 INFO @ Sun, 21 Jun 2020 16:30:45: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:30:45: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:30:45: #1 total tags in treatment: 2907561 INFO @ Sun, 21 Jun 2020 16:30:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:30:45: #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 16:30:45: #1 tags after filtering in treatment: 2906965 INFO @ Sun, 21 Jun 2020 16:30:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:30:45: #1 finished! INFO @ Sun, 21 Jun 2020 16:30:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:30:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:30:46: #2 number of paired peaks: 2082 INFO @ Sun, 21 Jun 2020 16:30:46: start model_add_line... INFO @ Sun, 21 Jun 2020 16:30:46: start X-correlation... INFO @ Sun, 21 Jun 2020 16:30:46: end of X-cor INFO @ Sun, 21 Jun 2020 16:30:46: #2 finished! INFO @ Sun, 21 Jun 2020 16:30:46: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 16:30:46: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 16:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05_model.r WARNING @ Sun, 21 Jun 2020 16:30:46: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:30:46: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 16:30:46: #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 16:30:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:30:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.05_summits.bed INFO @ Sun, 21 Jun 2020 16:30:56: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (2486 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 16:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.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 16:30:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:31:04: 1000000 INFO @ Sun, 21 Jun 2020 16:31:10: 2000000 INFO @ Sun, 21 Jun 2020 16:31:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:31:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:31:16: #1 total tags in treatment: 2907561 INFO @ Sun, 21 Jun 2020 16:31:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:31:16: #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 16:31:16: #1 tags after filtering in treatment: 2906965 INFO @ Sun, 21 Jun 2020 16:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:31:16: #1 finished! INFO @ Sun, 21 Jun 2020 16:31:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:31:16: #2 number of paired peaks: 2082 INFO @ Sun, 21 Jun 2020 16:31:16: start model_add_line... INFO @ Sun, 21 Jun 2020 16:31:16: start X-correlation... INFO @ Sun, 21 Jun 2020 16:31:16: end of X-cor INFO @ Sun, 21 Jun 2020 16:31:16: #2 finished! INFO @ Sun, 21 Jun 2020 16:31:16: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 16:31:16: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 16:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10_model.r WARNING @ Sun, 21 Jun 2020 16:31:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:31:16: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 16:31:16: #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 16:31:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:31:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:31:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:31:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:31:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.10_summits.bed INFO @ Sun, 21 Jun 2020 16:31:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (378 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 16:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.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 16:31:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:31:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:31:34: 1000000 INFO @ Sun, 21 Jun 2020 16:31:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:31:45: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:31:45: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:31:45: #1 total tags in treatment: 2907561 INFO @ Sun, 21 Jun 2020 16:31:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:31:45: #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 16:31:46: #1 tags after filtering in treatment: 2906965 INFO @ Sun, 21 Jun 2020 16:31:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:31:46: #1 finished! INFO @ Sun, 21 Jun 2020 16:31:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:31:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:31:46: #2 number of paired peaks: 2082 INFO @ Sun, 21 Jun 2020 16:31:46: start model_add_line... INFO @ Sun, 21 Jun 2020 16:31:46: start X-correlation... INFO @ Sun, 21 Jun 2020 16:31:46: end of X-cor INFO @ Sun, 21 Jun 2020 16:31:46: #2 finished! INFO @ Sun, 21 Jun 2020 16:31:46: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 16:31:46: #2 alternative fragment length(s) may be 4,59 bps INFO @ Sun, 21 Jun 2020 16:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20_model.r WARNING @ Sun, 21 Jun 2020 16:31:46: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:31:46: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Sun, 21 Jun 2020 16:31:46: #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 16:31:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:31:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:31:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013067/SRX013067.20_summits.bed INFO @ Sun, 21 Jun 2020 16:31:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (30 records, 4 fields): 15 millis CompletedMACS2peakCalling