Job ID = 6455298 SRX = SRX287675 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:25 prefetch.2.10.7: 1) Downloading 'SRR869863'... 2020-06-21T10:05:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:09:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:09:16 prefetch.2.10.7: 1) 'SRR869863' was downloaded successfully Read 27279884 spots for SRR869863/SRR869863.sra Written 27279884 spots for SRR869863/SRR869863.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: 00:13:57 27279884 reads; of these: 27279884 (100.00%) were unpaired; of these: 1422418 (5.21%) aligned 0 times 5642919 (20.69%) aligned exactly 1 time 20214547 (74.10%) aligned >1 times 94.79% overall alignment rate Time searching: 00:13:57 Overall time: 00:13:57 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] 12012785 / 25857466 = 0.4646 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 19:29:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.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 19:29:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:54: 1000000 INFO @ Sun, 21 Jun 2020 19:30:00: 2000000 INFO @ Sun, 21 Jun 2020 19:30:05: 3000000 INFO @ Sun, 21 Jun 2020 19:30:11: 4000000 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 19:30:17: 5000000 INFO @ Sun, 21 Jun 2020 19:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.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 19:30:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:23: 6000000 INFO @ Sun, 21 Jun 2020 19:30:25: 1000000 INFO @ Sun, 21 Jun 2020 19:30:29: 7000000 INFO @ Sun, 21 Jun 2020 19:30:32: 2000000 INFO @ Sun, 21 Jun 2020 19:30:36: 8000000 INFO @ Sun, 21 Jun 2020 19:30:38: 3000000 INFO @ Sun, 21 Jun 2020 19:30:42: 9000000 INFO @ Sun, 21 Jun 2020 19:30:45: 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 19:30:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.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 19:30:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:30:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:30:49: 10000000 INFO @ Sun, 21 Jun 2020 19:30:52: 5000000 INFO @ Sun, 21 Jun 2020 19:30:56: 1000000 INFO @ Sun, 21 Jun 2020 19:30:56: 11000000 INFO @ Sun, 21 Jun 2020 19:30:59: 6000000 INFO @ Sun, 21 Jun 2020 19:31:04: 12000000 INFO @ Sun, 21 Jun 2020 19:31:04: 2000000 INFO @ Sun, 21 Jun 2020 19:31:06: 7000000 INFO @ Sun, 21 Jun 2020 19:31:11: 13000000 INFO @ Sun, 21 Jun 2020 19:31:12: 3000000 INFO @ Sun, 21 Jun 2020 19:31:14: 8000000 INFO @ Sun, 21 Jun 2020 19:31:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:17: #1 total tags in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:31:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:17: #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 19:31:18: #1 tags after filtering in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:18: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:19: 4000000 INFO @ Sun, 21 Jun 2020 19:31:19: #2 number of paired peaks: 4335 INFO @ Sun, 21 Jun 2020 19:31:19: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:19: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:19: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:19: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:19: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:31:19: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 19:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05_model.r WARNING @ Sun, 21 Jun 2020 19:31:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:19: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 19:31:19: #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 19:31:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:21: 9000000 INFO @ Sun, 21 Jun 2020 19:31:27: 5000000 INFO @ Sun, 21 Jun 2020 19:31:29: 10000000 INFO @ Sun, 21 Jun 2020 19:31:34: 6000000 INFO @ Sun, 21 Jun 2020 19:31:36: 11000000 INFO @ Sun, 21 Jun 2020 19:31:42: 7000000 INFO @ Sun, 21 Jun 2020 19:31:43: 12000000 INFO @ Sun, 21 Jun 2020 19:31:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:49: 8000000 INFO @ Sun, 21 Jun 2020 19:31:51: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:56: Done! pass1 - making usageList (1432 chroms): 2 millis pass2 - checking and writing primary data (6599 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:57: 9000000 INFO @ Sun, 21 Jun 2020 19:31:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:57: #1 total tags in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:31:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:57: #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 19:31:58: #1 tags after filtering in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:59: #2 number of paired peaks: 4335 INFO @ Sun, 21 Jun 2020 19:31:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:59: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:31:59: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 19:31:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10_model.r WARNING @ Sun, 21 Jun 2020 19:31:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:31:59: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 19:31:59: #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 19:31:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:04: 10000000 INFO @ Sun, 21 Jun 2020 19:32:11: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:32:18: 12000000 INFO @ Sun, 21 Jun 2020 19:32:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:25: 13000000 INFO @ Sun, 21 Jun 2020 19:32:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:32:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:32:31: #1 total tags in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:32:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:32:31: #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 19:32:32: #1 tags after filtering in treatment: 13844681 INFO @ Sun, 21 Jun 2020 19:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:32:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:32:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:32:33: #2 number of paired peaks: 4335 INFO @ Sun, 21 Jun 2020 19:32:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:32:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:32:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:32:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:32:33: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 19:32:33: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 19:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20_model.r WARNING @ Sun, 21 Jun 2020 19:32:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:32:33: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 19:32:33: #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 19:32:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:32:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.10_summits.bed INFO @ Sun, 21 Jun 2020 19:32:36: Done! pass1 - making usageList (1172 chroms): 2 millis pass2 - checking and writing primary data (3887 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:32:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287675/SRX287675.20_summits.bed INFO @ Sun, 21 Jun 2020 19:33:09: Done! pass1 - making usageList (846 chroms): 1 millis pass2 - checking and writing primary data (2563 records, 4 fields): 23 millis CompletedMACS2peakCalling