Job ID = 6458619 SRX = SRX5343150 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:31:34 prefetch.2.10.7: 1) Downloading 'SRR8540850'... 2020-06-21T12:31:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:16 prefetch.2.10.7: 1) 'SRR8540850' was downloaded successfully 2020-06-21T12:35:16 prefetch.2.10.7: 'SRR8540850' has 0 unresolved dependencies Read 25037254 spots for SRR8540850/SRR8540850.sra Written 25037254 spots for SRR8540850/SRR8540850.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: 00:06:01 25037254 reads; of these: 25037254 (100.00%) were unpaired; of these: 9823918 (39.24%) aligned 0 times 10954632 (43.75%) aligned exactly 1 time 4258704 (17.01%) aligned >1 times 60.76% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7917429 / 15213336 = 0.5204 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 21:45:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.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 21:45:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:45:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:00: 1000000 INFO @ Sun, 21 Jun 2020 21:46:07: 2000000 INFO @ Sun, 21 Jun 2020 21:46:15: 3000000 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 21:46:22: 4000000 INFO @ Sun, 21 Jun 2020 21:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.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 21:46:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:30: 5000000 INFO @ Sun, 21 Jun 2020 21:46:30: 1000000 INFO @ Sun, 21 Jun 2020 21:46:38: 6000000 INFO @ Sun, 21 Jun 2020 21:46:38: 2000000 INFO @ Sun, 21 Jun 2020 21:46:45: 7000000 INFO @ Sun, 21 Jun 2020 21:46:45: 3000000 INFO @ Sun, 21 Jun 2020 21:46:47: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:46:47: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:46:47: #1 total tags in treatment: 7295907 INFO @ Sun, 21 Jun 2020 21:46:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:46:47: #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 21:46:47: #1 tags after filtering in treatment: 7295906 INFO @ Sun, 21 Jun 2020 21:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:46:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:46:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #2 number of paired peaks: 1198 INFO @ Sun, 21 Jun 2020 21:46:48: start model_add_line... INFO @ Sun, 21 Jun 2020 21:46:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:46:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:46:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:46:48: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 21:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05_model.r WARNING @ Sun, 21 Jun 2020 21:46:48: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:46:48: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 21:46:48: #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 21:46:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:46:48: #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 21:46:52: 4000000 INFO @ Sun, 21 Jun 2020 21:46:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.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 21:46:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:46:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:46:59: 5000000 INFO @ Sun, 21 Jun 2020 21:47:00: 1000000 INFO @ Sun, 21 Jun 2020 21:47:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:07: 6000000 INFO @ Sun, 21 Jun 2020 21:47:07: 2000000 INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.05_summits.bed INFO @ Sun, 21 Jun 2020 21:47:11: Done! pass1 - making usageList (717 chroms): 1 millis pass2 - checking and writing primary data (2009 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:14: 7000000 INFO @ Sun, 21 Jun 2020 21:47:15: 3000000 INFO @ Sun, 21 Jun 2020 21:47:16: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:16: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:16: #1 total tags in treatment: 7295907 INFO @ Sun, 21 Jun 2020 21:47:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:16: #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 21:47:17: #1 tags after filtering in treatment: 7295906 INFO @ Sun, 21 Jun 2020 21:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:17: #2 number of paired peaks: 1198 INFO @ Sun, 21 Jun 2020 21:47:17: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:17: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:17: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:17: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:17: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:47:17: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 21:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10_model.r WARNING @ Sun, 21 Jun 2020 21:47:17: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:17: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 21:47:17: #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 21:47:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:47:21: 4000000 INFO @ Sun, 21 Jun 2020 21:47:28: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:47:35: 6000000 INFO @ Sun, 21 Jun 2020 21:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.10_summits.bed INFO @ Sun, 21 Jun 2020 21:47:41: Done! pass1 - making usageList (368 chroms): 0 millis pass2 - checking and writing primary data (778 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:47:42: 7000000 INFO @ Sun, 21 Jun 2020 21:47:44: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:47:44: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:47:44: #1 total tags in treatment: 7295907 INFO @ Sun, 21 Jun 2020 21:47:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:47:44: #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 21:47:45: #1 tags after filtering in treatment: 7295906 INFO @ Sun, 21 Jun 2020 21:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:47:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:47:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:47:45: #2 number of paired peaks: 1198 INFO @ Sun, 21 Jun 2020 21:47:45: start model_add_line... INFO @ Sun, 21 Jun 2020 21:47:45: start X-correlation... INFO @ Sun, 21 Jun 2020 21:47:45: end of X-cor INFO @ Sun, 21 Jun 2020 21:47:45: #2 finished! INFO @ Sun, 21 Jun 2020 21:47:45: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:47:45: #2 alternative fragment length(s) may be 84 bps INFO @ Sun, 21 Jun 2020 21:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20_model.r WARNING @ Sun, 21 Jun 2020 21:47:45: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:47:45: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sun, 21 Jun 2020 21:47:45: #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 21:47:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:47:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:48:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:48:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343150/SRX5343150.20_summits.bed INFO @ Sun, 21 Jun 2020 21:48:10: Done! pass1 - making usageList (178 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 6 millis CompletedMACS2peakCalling