Job ID = 6459494 SRX = SRX6827675 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:23:35 prefetch.2.10.7: 1) Downloading 'SRR10095455'... 2020-06-21T13:23:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:27:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:27:11 prefetch.2.10.7: 1) 'SRR10095455' was downloaded successfully Read 23713990 spots for SRR10095455/SRR10095455.sra Written 23713990 spots for SRR10095455/SRR10095455.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: 00:07:14 23713990 reads; of these: 23713990 (100.00%) were unpaired; of these: 1171016 (4.94%) aligned 0 times 15393863 (64.91%) aligned exactly 1 time 7149111 (30.15%) aligned >1 times 95.06% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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 12 files... [bam_rmdupse_core] 4678507 / 22542974 = 0.2075 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 22:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.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 22:40:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:12: 1000000 INFO @ Sun, 21 Jun 2020 22:40:17: 2000000 INFO @ Sun, 21 Jun 2020 22:40:22: 3000000 INFO @ Sun, 21 Jun 2020 22:40:27: 4000000 INFO @ Sun, 21 Jun 2020 22:40:32: 5000000 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 22:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.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 22:40:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:37: 6000000 INFO @ Sun, 21 Jun 2020 22:40:43: 1000000 INFO @ Sun, 21 Jun 2020 22:40:43: 7000000 INFO @ Sun, 21 Jun 2020 22:40:48: 2000000 INFO @ Sun, 21 Jun 2020 22:40:49: 8000000 INFO @ Sun, 21 Jun 2020 22:40:54: 3000000 INFO @ Sun, 21 Jun 2020 22:40:55: 9000000 INFO @ Sun, 21 Jun 2020 22:41:00: 4000000 INFO @ Sun, 21 Jun 2020 22:41:00: 10000000 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 22:41:05: 5000000 INFO @ Sun, 21 Jun 2020 22:41:06: 11000000 INFO @ Sun, 21 Jun 2020 22:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.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 22:41:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:11: 6000000 INFO @ Sun, 21 Jun 2020 22:41:12: 12000000 INFO @ Sun, 21 Jun 2020 22:41:13: 1000000 INFO @ Sun, 21 Jun 2020 22:41:17: 7000000 INFO @ Sun, 21 Jun 2020 22:41:17: 13000000 INFO @ Sun, 21 Jun 2020 22:41:18: 2000000 INFO @ Sun, 21 Jun 2020 22:41:23: 8000000 INFO @ Sun, 21 Jun 2020 22:41:23: 14000000 INFO @ Sun, 21 Jun 2020 22:41:24: 3000000 INFO @ Sun, 21 Jun 2020 22:41:28: 9000000 INFO @ Sun, 21 Jun 2020 22:41:29: 15000000 INFO @ Sun, 21 Jun 2020 22:41:30: 4000000 INFO @ Sun, 21 Jun 2020 22:41:34: 10000000 INFO @ Sun, 21 Jun 2020 22:41:35: 16000000 INFO @ Sun, 21 Jun 2020 22:41:36: 5000000 INFO @ Sun, 21 Jun 2020 22:41:40: 11000000 INFO @ Sun, 21 Jun 2020 22:41:41: 17000000 INFO @ Sun, 21 Jun 2020 22:41:41: 6000000 INFO @ Sun, 21 Jun 2020 22:41:45: 12000000 INFO @ Sun, 21 Jun 2020 22:41:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:41:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:41:47: #1 total tags in treatment: 17864467 INFO @ Sun, 21 Jun 2020 22:41:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:41:47: #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 22:41:47: 7000000 INFO @ Sun, 21 Jun 2020 22:41:47: #1 tags after filtering in treatment: 17864407 INFO @ Sun, 21 Jun 2020 22:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:41:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:41:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:41:48: #2 number of paired peaks: 1115 INFO @ Sun, 21 Jun 2020 22:41:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:41:49: start X-correlation... INFO @ Sun, 21 Jun 2020 22:41:49: end of X-cor INFO @ Sun, 21 Jun 2020 22:41:49: #2 finished! INFO @ Sun, 21 Jun 2020 22:41:49: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:41:49: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sun, 21 Jun 2020 22:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05_model.r WARNING @ Sun, 21 Jun 2020 22:41:49: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:41:49: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sun, 21 Jun 2020 22:41:49: #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 22:41:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:41:51: 13000000 INFO @ Sun, 21 Jun 2020 22:41:53: 8000000 INFO @ Sun, 21 Jun 2020 22:41:58: 14000000 INFO @ Sun, 21 Jun 2020 22:41:59: 9000000 INFO @ Sun, 21 Jun 2020 22:42:04: 15000000 INFO @ Sun, 21 Jun 2020 22:42:05: 10000000 INFO @ Sun, 21 Jun 2020 22:42:10: 16000000 INFO @ Sun, 21 Jun 2020 22:42:11: 11000000 INFO @ Sun, 21 Jun 2020 22:42:16: 17000000 INFO @ Sun, 21 Jun 2020 22:42:17: 12000000 INFO @ Sun, 21 Jun 2020 22:42:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:22: #1 total tags in treatment: 17864467 INFO @ Sun, 21 Jun 2020 22:42:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:22: #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 22:42:22: #1 tags after filtering in treatment: 17864407 INFO @ Sun, 21 Jun 2020 22:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:23: 13000000 INFO @ Sun, 21 Jun 2020 22:42:23: #2 number of paired peaks: 1115 INFO @ Sun, 21 Jun 2020 22:42:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:24: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:42:24: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sun, 21 Jun 2020 22:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10_model.r WARNING @ Sun, 21 Jun 2020 22:42:24: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:42:24: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sun, 21 Jun 2020 22:42:24: #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 22:42:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:42:29: 14000000 INFO @ Sun, 21 Jun 2020 22:42:35: 15000000 INFO @ Sun, 21 Jun 2020 22:42:41: 16000000 INFO @ Sun, 21 Jun 2020 22:42:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:42:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:42:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.05_summits.bed INFO @ Sun, 21 Jun 2020 22:42:44: Done! pass1 - making usageList (689 chroms): 1 millis pass2 - checking and writing primary data (3638 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:42:46: 17000000 INFO @ Sun, 21 Jun 2020 22:42:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:52: #1 total tags in treatment: 17864467 INFO @ Sun, 21 Jun 2020 22:42:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:52: #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 22:42:52: #1 tags after filtering in treatment: 17864407 INFO @ Sun, 21 Jun 2020 22:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:54: #2 number of paired peaks: 1115 INFO @ Sun, 21 Jun 2020 22:42:54: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:54: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 22:42:54: #2 alternative fragment length(s) may be 3,66 bps INFO @ Sun, 21 Jun 2020 22:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20_model.r WARNING @ Sun, 21 Jun 2020 22:42:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:42:54: #2 You may need to consider one of the other alternative d(s): 3,66 WARNING @ Sun, 21 Jun 2020 22:42:54: #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 22:42:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.10_summits.bed INFO @ Sun, 21 Jun 2020 22:43:18: Done! pass1 - making usageList (539 chroms): 1 millis pass2 - checking and writing primary data (2329 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6827675/SRX6827675.20_summits.bed INFO @ Sun, 21 Jun 2020 22:43:50: Done! pass1 - making usageList (401 chroms): 1 millis pass2 - checking and writing primary data (1191 records, 4 fields): 13 millis CompletedMACS2peakCalling