Job ID = 6458265 SRX = SRX5011026 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:25:19 prefetch.2.10.7: 1) Downloading 'SRR8191475'... 2020-06-21T12:25:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:27:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:27:01 prefetch.2.10.7: 'SRR8191475' is valid 2020-06-21T12:27:01 prefetch.2.10.7: 1) 'SRR8191475' was downloaded successfully 2020-06-21T12:27:01 prefetch.2.10.7: 'SRR8191475' has 0 unresolved dependencies Read 26843880 spots for SRR8191475/SRR8191475.sra Written 26843880 spots for SRR8191475/SRR8191475.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: 00:08:11 26843880 reads; of these: 26843880 (100.00%) were unpaired; of these: 646635 (2.41%) aligned 0 times 18585521 (69.24%) aligned exactly 1 time 7611724 (28.36%) aligned >1 times 97.59% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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] 14320683 / 26197245 = 0.5466 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 21:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.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 21:41:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:57: 1000000 INFO @ Sun, 21 Jun 2020 21:42:05: 2000000 INFO @ Sun, 21 Jun 2020 21:42:12: 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 21:42:19: 4000000 INFO @ Sun, 21 Jun 2020 21:42:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.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 21:42:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:27: 5000000 INFO @ Sun, 21 Jun 2020 21:42:28: 1000000 INFO @ Sun, 21 Jun 2020 21:42:34: 6000000 INFO @ Sun, 21 Jun 2020 21:42:36: 2000000 INFO @ Sun, 21 Jun 2020 21:42:42: 7000000 INFO @ Sun, 21 Jun 2020 21:42:43: 3000000 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 21:42:50: 8000000 INFO @ Sun, 21 Jun 2020 21:42:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.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 21:42:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:51: 4000000 INFO @ Sun, 21 Jun 2020 21:42:58: 9000000 INFO @ Sun, 21 Jun 2020 21:42:58: 1000000 INFO @ Sun, 21 Jun 2020 21:42:59: 5000000 INFO @ Sun, 21 Jun 2020 21:43:06: 2000000 INFO @ Sun, 21 Jun 2020 21:43:07: 10000000 INFO @ Sun, 21 Jun 2020 21:43:08: 6000000 INFO @ Sun, 21 Jun 2020 21:43:14: 3000000 INFO @ Sun, 21 Jun 2020 21:43:15: 11000000 INFO @ Sun, 21 Jun 2020 21:43:16: 7000000 INFO @ Sun, 21 Jun 2020 21:43:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:22: #1 total tags in treatment: 11876562 INFO @ Sun, 21 Jun 2020 21:43:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:22: #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 21:43:22: 4000000 INFO @ Sun, 21 Jun 2020 21:43:22: #1 tags after filtering in treatment: 11876487 INFO @ Sun, 21 Jun 2020 21:43:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:23: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 21:43:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:24: 8000000 INFO @ Sun, 21 Jun 2020 21:43:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:24: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:43:24: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sun, 21 Jun 2020 21:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05_model.r WARNING @ Sun, 21 Jun 2020 21:43:24: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:24: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sun, 21 Jun 2020 21:43:24: #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 21:43:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:30: 5000000 INFO @ Sun, 21 Jun 2020 21:43:32: 9000000 INFO @ Sun, 21 Jun 2020 21:43:37: 6000000 INFO @ Sun, 21 Jun 2020 21:43:40: 10000000 INFO @ Sun, 21 Jun 2020 21:43:45: 7000000 INFO @ Sun, 21 Jun 2020 21:43:48: 11000000 INFO @ Sun, 21 Jun 2020 21:43:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:53: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:43:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:55: #1 total tags in treatment: 11876562 INFO @ Sun, 21 Jun 2020 21:43:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:55: #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 21:43:55: #1 tags after filtering in treatment: 11876487 INFO @ Sun, 21 Jun 2020 21:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:56: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 21:43:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:57: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:43:57: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sun, 21 Jun 2020 21:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10_model.r WARNING @ Sun, 21 Jun 2020 21:43:57: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:57: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sun, 21 Jun 2020 21:43:57: #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 21:43:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:44:00: 9000000 INFO @ Sun, 21 Jun 2020 21:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.05_summits.bed INFO @ Sun, 21 Jun 2020 21:44:01: Done! pass1 - making usageList (801 chroms): 2 millis pass2 - checking and writing primary data (4212 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:44:08: 10000000 INFO @ Sun, 21 Jun 2020 21:44:15: 11000000 INFO @ Sun, 21 Jun 2020 21:44:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:44:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:44:22: #1 total tags in treatment: 11876562 INFO @ Sun, 21 Jun 2020 21:44:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:44:22: #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 21:44:23: #1 tags after filtering in treatment: 11876487 INFO @ Sun, 21 Jun 2020 21:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:44:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:44:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:44:24: #2 number of paired peaks: 2371 INFO @ Sun, 21 Jun 2020 21:44:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:44:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:44:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:44:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:44:24: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 21:44:24: #2 alternative fragment length(s) may be 3,63 bps INFO @ Sun, 21 Jun 2020 21:44:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20_model.r WARNING @ Sun, 21 Jun 2020 21:44:24: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:44:24: #2 You may need to consider one of the other alternative d(s): 3,63 WARNING @ Sun, 21 Jun 2020 21:44:24: #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 21:44:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:44:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.10_summits.bed INFO @ Sun, 21 Jun 2020 21:44:33: Done! pass1 - making usageList (693 chroms): 2 millis pass2 - checking and writing primary data (2750 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:44:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011026/SRX5011026.20_summits.bed INFO @ Sun, 21 Jun 2020 21:45:00: Done! pass1 - making usageList (473 chroms): 2 millis pass2 - checking and writing primary data (1175 records, 4 fields): 26 millis CompletedMACS2peakCalling