Job ID = 6459018 SRX = SRX5931380 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:44:52 prefetch.2.10.7: 1) Downloading 'SRR9158302'... 2020-06-21T12:44:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:26 prefetch.2.10.7: 'SRR9158302' is valid 2020-06-21T12:46:26 prefetch.2.10.7: 1) 'SRR9158302' was downloaded successfully 2020-06-21T12:46:26 prefetch.2.10.7: 'SRR9158302' has 0 unresolved dependencies Read 3949613 spots for SRR9158302/SRR9158302.sra Written 3949613 spots for SRR9158302/SRR9158302.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: 00:05:26 3949613 reads; of these: 3949613 (100.00%) were unpaired; of these: 533240 (13.50%) aligned 0 times 979447 (24.80%) aligned exactly 1 time 2436926 (61.70%) aligned >1 times 86.50% overall alignment rate Time searching: 00:05:27 Overall time: 00:05:27 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] 593720 / 3416373 = 0.1738 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 21:54:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.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 21:54:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:10: 1000000 INFO @ Sun, 21 Jun 2020 21:54:18: 2000000 INFO @ Sun, 21 Jun 2020 21:54:24: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 21:54:24: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 21:54:25: #1 total tags in treatment: 2822653 INFO @ Sun, 21 Jun 2020 21:54:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:25: #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 21:54:25: #1 tags after filtering in treatment: 2822473 INFO @ Sun, 21 Jun 2020 21:54:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:25: #2 number of paired peaks: 5154 INFO @ Sun, 21 Jun 2020 21:54:25: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:25: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:25: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:25: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:25: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 21:54:25: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 21:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:25: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:25: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 21 Jun 2020 21:54:25: #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 21:54:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:25: #3 Pre-compute pvalue-qvalue table... 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 21:54:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.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 21:54:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:36: Done! pass1 - making usageList (820 chroms): 1 millis pass2 - checking and writing primary data (2533 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:41: 1000000 INFO @ Sun, 21 Jun 2020 21:54:49: 2000000 INFO @ Sun, 21 Jun 2020 21:54:55: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 21:54:55: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 21:54:55: #1 total tags in treatment: 2822653 INFO @ Sun, 21 Jun 2020 21:54:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:55: #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 21:54:55: #1 tags after filtering in treatment: 2822473 INFO @ Sun, 21 Jun 2020 21:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:55: #2 number of paired peaks: 5154 INFO @ Sun, 21 Jun 2020 21:54:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:55: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 21:54:55: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 21:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:55: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:55: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 21 Jun 2020 21:54:55: #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 21:54:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:55: #3 Pre-compute pvalue-qvalue table... 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 21:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.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 21:55:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:55:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:55:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.10_summits.bed INFO @ Sun, 21 Jun 2020 21:55:06: Done! pass1 - making usageList (713 chroms): 1 millis pass2 - checking and writing primary data (1784 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:11: 1000000 INFO @ Sun, 21 Jun 2020 21:55:18: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 21:55:25: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 21:55:25: #1 total tags in treatment: 2822653 INFO @ Sun, 21 Jun 2020 21:55:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:25: #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 21:55:25: #1 tags after filtering in treatment: 2822473 INFO @ Sun, 21 Jun 2020 21:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:25: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:55:26: #2 number of paired peaks: 5154 INFO @ Sun, 21 Jun 2020 21:55:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:26: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 21:55:26: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 21:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20_model.r WARNING @ Sun, 21 Jun 2020 21:55:26: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:26: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 21 Jun 2020 21:55:26: #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 21:55:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5931380/SRX5931380.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:37: Done! pass1 - making usageList (632 chroms): 1 millis pass2 - checking and writing primary data (1280 records, 4 fields): 17 millis CompletedMACS2peakCalling