Job ID = 6454746 SRX = SRX2564130 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:29 prefetch.2.10.7: 1) Downloading 'SRR5259250'... 2020-06-21T09:28:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:30:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:30:40 prefetch.2.10.7: 'SRR5259250' is valid 2020-06-21T09:30:40 prefetch.2.10.7: 1) 'SRR5259250' was downloaded successfully Read 18916953 spots for SRR5259250/SRR5259250.sra Written 18916953 spots for SRR5259250/SRR5259250.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: 00:02:04 18916953 reads; of these: 18916953 (100.00%) were unpaired; of these: 13765267 (72.77%) aligned 0 times 4037247 (21.34%) aligned exactly 1 time 1114439 (5.89%) aligned >1 times 27.23% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 2573418 / 5151686 = 0.4995 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 18:35:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.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 18:35:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:08: 1000000 INFO @ Sun, 21 Jun 2020 18:35:13: 2000000 INFO @ Sun, 21 Jun 2020 18:35:16: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:35:16: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:35:16: #1 total tags in treatment: 2578268 INFO @ Sun, 21 Jun 2020 18:35:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:16: #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 18:35:17: #1 tags after filtering in treatment: 2578045 INFO @ Sun, 21 Jun 2020 18:35:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:17: #2 number of paired peaks: 5357 INFO @ Sun, 21 Jun 2020 18:35:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:17: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:35:17: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 18:35:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05_model.r WARNING @ Sun, 21 Jun 2020 18:35:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:17: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 18:35:17: #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 18:35:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.05_summits.bed INFO @ Sun, 21 Jun 2020 18:35:26: Done! pass1 - making usageList (286 chroms): 1 millis pass2 - checking and writing primary data (5711 records, 4 fields): 13 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 18:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.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 18:35:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:35:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:35:38: 1000000 INFO @ Sun, 21 Jun 2020 18:35:44: 2000000 INFO @ Sun, 21 Jun 2020 18:35:47: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:35:47: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:35:47: #1 total tags in treatment: 2578268 INFO @ Sun, 21 Jun 2020 18:35:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:35:47: #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 18:35:47: #1 tags after filtering in treatment: 2578045 INFO @ Sun, 21 Jun 2020 18:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:35:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:35:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:35:48: #2 number of paired peaks: 5357 INFO @ Sun, 21 Jun 2020 18:35:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:35:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:35:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:35:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:35:48: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:35:48: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 18:35:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10_model.r WARNING @ Sun, 21 Jun 2020 18:35:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:35:48: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 18:35:48: #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 18:35:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:35:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:35:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.10_summits.bed INFO @ Sun, 21 Jun 2020 18:35:57: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (1462 records, 4 fields): 7 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 18:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.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 18:36:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:36:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:36:08: 1000000 INFO @ Sun, 21 Jun 2020 18:36:13: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:36:16: #1 tag size is determined as 42 bps INFO @ Sun, 21 Jun 2020 18:36:16: #1 tag size = 42 INFO @ Sun, 21 Jun 2020 18:36:16: #1 total tags in treatment: 2578268 INFO @ Sun, 21 Jun 2020 18:36:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:36:16: #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 18:36:16: #1 tags after filtering in treatment: 2578045 INFO @ Sun, 21 Jun 2020 18:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:36:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:36:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:36:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:36:17: #2 number of paired peaks: 5357 INFO @ Sun, 21 Jun 2020 18:36:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:36:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:36:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:36:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:36:17: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 18:36:17: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 18:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20_model.r WARNING @ Sun, 21 Jun 2020 18:36:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:36:17: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 18:36:17: #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 18:36:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:36:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:36:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:36:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:36:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:36:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564130/SRX2564130.20_summits.bed INFO @ Sun, 21 Jun 2020 18:36:25: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 6 millis CompletedMACS2peakCalling