Job ID = 6456322 SRX = SRX335520 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:38:30 prefetch.2.10.7: 1) Downloading 'SRR952862'... 2020-06-21T10:38:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:44:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:44:37 prefetch.2.10.7: 1) 'SRR952862' was downloaded successfully Read 25162813 spots for SRR952862/SRR952862.sra Written 25162813 spots for SRR952862/SRR952862.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: 00:07:05 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1448057 (5.75%) aligned 0 times 16797740 (66.76%) aligned exactly 1 time 6917016 (27.49%) aligned >1 times 94.25% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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] 6320212 / 23714756 = 0.2665 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 19:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.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 19:58:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:22: 1000000 INFO @ Sun, 21 Jun 2020 19:58:28: 2000000 INFO @ Sun, 21 Jun 2020 19:58:33: 3000000 INFO @ Sun, 21 Jun 2020 19:58:38: 4000000 INFO @ Sun, 21 Jun 2020 19:58:44: 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 19:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.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 19:58:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:58:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:58:49: 6000000 INFO @ Sun, 21 Jun 2020 19:58:52: 1000000 INFO @ Sun, 21 Jun 2020 19:58:55: 7000000 INFO @ Sun, 21 Jun 2020 19:58:57: 2000000 INFO @ Sun, 21 Jun 2020 19:59:01: 8000000 INFO @ Sun, 21 Jun 2020 19:59:01: 3000000 INFO @ Sun, 21 Jun 2020 19:59:06: 9000000 INFO @ Sun, 21 Jun 2020 19:59:06: 4000000 INFO @ Sun, 21 Jun 2020 19:59:11: 5000000 INFO @ Sun, 21 Jun 2020 19:59:12: 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 19:59:16: 6000000 INFO @ Sun, 21 Jun 2020 19:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.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 19:59:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:17: 11000000 INFO @ Sun, 21 Jun 2020 19:59:21: 7000000 INFO @ Sun, 21 Jun 2020 19:59:22: 1000000 INFO @ Sun, 21 Jun 2020 19:59:23: 12000000 INFO @ Sun, 21 Jun 2020 19:59:26: 8000000 INFO @ Sun, 21 Jun 2020 19:59:27: 2000000 INFO @ Sun, 21 Jun 2020 19:59:28: 13000000 INFO @ Sun, 21 Jun 2020 19:59:31: 9000000 INFO @ Sun, 21 Jun 2020 19:59:32: 3000000 INFO @ Sun, 21 Jun 2020 19:59:34: 14000000 INFO @ Sun, 21 Jun 2020 19:59:36: 10000000 INFO @ Sun, 21 Jun 2020 19:59:37: 4000000 INFO @ Sun, 21 Jun 2020 19:59:40: 15000000 INFO @ Sun, 21 Jun 2020 19:59:41: 11000000 INFO @ Sun, 21 Jun 2020 19:59:42: 5000000 INFO @ Sun, 21 Jun 2020 19:59:45: 16000000 INFO @ Sun, 21 Jun 2020 19:59:46: 12000000 INFO @ Sun, 21 Jun 2020 19:59:47: 6000000 INFO @ Sun, 21 Jun 2020 19:59:51: 17000000 INFO @ Sun, 21 Jun 2020 19:59:51: 13000000 INFO @ Sun, 21 Jun 2020 19:59:52: 7000000 INFO @ Sun, 21 Jun 2020 19:59:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:59:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:59:53: #1 total tags in treatment: 17394544 INFO @ Sun, 21 Jun 2020 19:59:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:59:53: #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 19:59:54: #1 tags after filtering in treatment: 17394464 INFO @ Sun, 21 Jun 2020 19:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:59:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:59:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:59:55: #2 number of paired peaks: 259 WARNING @ Sun, 21 Jun 2020 19:59:55: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sun, 21 Jun 2020 19:59:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:59:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:59:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:59:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:59:55: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 19:59:55: #2 alternative fragment length(s) may be 2,16,53,82,206,251,429,433,469,506,532,569 bps INFO @ Sun, 21 Jun 2020 19:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05_model.r WARNING @ Sun, 21 Jun 2020 19:59:55: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:59:55: #2 You may need to consider one of the other alternative d(s): 2,16,53,82,206,251,429,433,469,506,532,569 WARNING @ Sun, 21 Jun 2020 19:59:55: #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 19:59:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:59:56: 14000000 INFO @ Sun, 21 Jun 2020 19:59:57: 8000000 INFO @ Sun, 21 Jun 2020 20:00:01: 15000000 INFO @ Sun, 21 Jun 2020 20:00:02: 9000000 INFO @ Sun, 21 Jun 2020 20:00:06: 16000000 INFO @ Sun, 21 Jun 2020 20:00:07: 10000000 INFO @ Sun, 21 Jun 2020 20:00:11: 17000000 INFO @ Sun, 21 Jun 2020 20:00:11: 11000000 INFO @ Sun, 21 Jun 2020 20:00:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:13: #1 total tags in treatment: 17394544 INFO @ Sun, 21 Jun 2020 20:00:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:13: #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 20:00:14: #1 tags after filtering in treatment: 17394464 INFO @ Sun, 21 Jun 2020 20:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:15: #2 number of paired peaks: 259 WARNING @ Sun, 21 Jun 2020 20:00:15: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:15: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:15: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:15: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:15: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:00:15: #2 alternative fragment length(s) may be 2,16,53,82,206,251,429,433,469,506,532,569 bps INFO @ Sun, 21 Jun 2020 20:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10_model.r WARNING @ Sun, 21 Jun 2020 20:00:15: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:15: #2 You may need to consider one of the other alternative d(s): 2,16,53,82,206,251,429,433,469,506,532,569 WARNING @ Sun, 21 Jun 2020 20:00:15: #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 20:00:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:16: 12000000 INFO @ Sun, 21 Jun 2020 20:00:21: 13000000 INFO @ Sun, 21 Jun 2020 20:00:26: 14000000 INFO @ Sun, 21 Jun 2020 20:00:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:00:31: 15000000 INFO @ Sun, 21 Jun 2020 20:00:36: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:00:40: 17000000 INFO @ Sun, 21 Jun 2020 20:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:43: #1 total tags in treatment: 17394544 INFO @ Sun, 21 Jun 2020 20:00:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:43: #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 20:00:43: #1 tags after filtering in treatment: 17394464 INFO @ Sun, 21 Jun 2020 20:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:43: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:44: #2 number of paired peaks: 259 WARNING @ Sun, 21 Jun 2020 20:00:44: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:44: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:44: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:44: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:44: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:44: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 20:00:44: #2 alternative fragment length(s) may be 2,16,53,82,206,251,429,433,469,506,532,569 bps INFO @ Sun, 21 Jun 2020 20:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20_model.r WARNING @ Sun, 21 Jun 2020 20:00:44: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:44: #2 You may need to consider one of the other alternative d(s): 2,16,53,82,206,251,429,433,469,506,532,569 WARNING @ Sun, 21 Jun 2020 20:00:44: #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 20:00:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.05_summits.bed INFO @ Sun, 21 Jun 2020 20:00:45: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (1740 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:00:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.10_summits.bed INFO @ Sun, 21 Jun 2020 20:01:05: Done! pass1 - making usageList (190 chroms): 1 millis pass2 - checking and writing primary data (515 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:01:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335520/SRX335520.20_summits.bed INFO @ Sun, 21 Jun 2020 20:01:32: Done! pass1 - making usageList (92 chroms): 0 millis pass2 - checking and writing primary data (196 records, 4 fields): 4 millis CompletedMACS2peakCalling