Job ID = 6459409 SRX = SRX6747978 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:29:16 prefetch.2.10.7: 1) Downloading 'SRR10009753'... 2020-06-21T13:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:31:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:31:32 prefetch.2.10.7: 'SRR10009753' is valid 2020-06-21T13:31:32 prefetch.2.10.7: 1) 'SRR10009753' was downloaded successfully 2020-06-21T13:31:33 prefetch.2.10.7: 'SRR10009753' has 0 unresolved dependencies Read 13895577 spots for SRR10009753/SRR10009753.sra Written 13895577 spots for SRR10009753/SRR10009753.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:21 13895577 reads; of these: 13895577 (100.00%) were unpaired; of these: 8008747 (57.64%) aligned 0 times 4088945 (29.43%) aligned exactly 1 time 1797885 (12.94%) aligned >1 times 42.36% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 615224 / 5886830 = 0.1045 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 22:37:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.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 22:37:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:37:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:37:52: 1000000 INFO @ Sun, 21 Jun 2020 22:37:57: 2000000 INFO @ Sun, 21 Jun 2020 22:38:03: 3000000 INFO @ Sun, 21 Jun 2020 22:38:08: 4000000 INFO @ Sun, 21 Jun 2020 22:38:13: 5000000 INFO @ Sun, 21 Jun 2020 22:38:14: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:38:14: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:38:14: #1 total tags in treatment: 5271606 INFO @ Sun, 21 Jun 2020 22:38:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:14: #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 22:38:15: #1 tags after filtering in treatment: 5271444 INFO @ Sun, 21 Jun 2020 22:38:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:15: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:38:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:15: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2 alternative fragment length(s) may be 73,561,571,595,597 bps INFO @ Sun, 21 Jun 2020 22:38:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05_model.r WARNING @ Sun, 21 Jun 2020 22:38:15: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:15: #2 You may need to consider one of the other alternative d(s): 73,561,571,595,597 WARNING @ Sun, 21 Jun 2020 22:38:15: #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 22:38:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:15: #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 22:38:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.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 22:38:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:23: 1000000 INFO @ Sun, 21 Jun 2020 22:38:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:38:29: 2000000 INFO @ Sun, 21 Jun 2020 22:38:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:38:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:38:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.05_summits.bed INFO @ Sun, 21 Jun 2020 22:38:32: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (1711 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:38:35: 3000000 INFO @ Sun, 21 Jun 2020 22:38:41: 4000000 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 22:38:47: 5000000 INFO @ Sun, 21 Jun 2020 22:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.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 22:38:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:38:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:38:48: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:38:48: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:38:48: #1 total tags in treatment: 5271606 INFO @ Sun, 21 Jun 2020 22:38:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:38:48: #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 22:38:49: #1 tags after filtering in treatment: 5271444 INFO @ Sun, 21 Jun 2020 22:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:38:49: #1 finished! INFO @ Sun, 21 Jun 2020 22:38:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:38:49: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:38:49: start model_add_line... INFO @ Sun, 21 Jun 2020 22:38:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:38:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:38:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:38:49: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 22:38:49: #2 alternative fragment length(s) may be 73,561,571,595,597 bps INFO @ Sun, 21 Jun 2020 22:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10_model.r WARNING @ Sun, 21 Jun 2020 22:38:49: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:38:49: #2 You may need to consider one of the other alternative d(s): 73,561,571,595,597 WARNING @ Sun, 21 Jun 2020 22:38:49: #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 22:38:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:38:53: 1000000 INFO @ Sun, 21 Jun 2020 22:38:59: 2000000 INFO @ Sun, 21 Jun 2020 22:39:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:05: 3000000 INFO @ Sun, 21 Jun 2020 22:39:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.10_summits.bed INFO @ Sun, 21 Jun 2020 22:39:06: Done! pass1 - making usageList (440 chroms): 2 millis pass2 - checking and writing primary data (1143 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:39:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:39:18: 5000000 INFO @ Sun, 21 Jun 2020 22:39:19: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:39:19: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:39:19: #1 total tags in treatment: 5271606 INFO @ Sun, 21 Jun 2020 22:39:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:39:19: #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 22:39:20: #1 tags after filtering in treatment: 5271444 INFO @ Sun, 21 Jun 2020 22:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:39:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:39:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:39:20: #2 number of paired peaks: 1085 INFO @ Sun, 21 Jun 2020 22:39:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:39:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:39:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:39:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:39:20: #2 predicted fragment length is 73 bps INFO @ Sun, 21 Jun 2020 22:39:20: #2 alternative fragment length(s) may be 73,561,571,595,597 bps INFO @ Sun, 21 Jun 2020 22:39:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20_model.r WARNING @ Sun, 21 Jun 2020 22:39:20: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:39:20: #2 You may need to consider one of the other alternative d(s): 73,561,571,595,597 WARNING @ Sun, 21 Jun 2020 22:39:20: #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 22:39:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:39:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:39:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6747978/SRX6747978.20_summits.bed INFO @ Sun, 21 Jun 2020 22:39:37: Done! pass1 - making usageList (255 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 8 millis CompletedMACS2peakCalling