Job ID = 6454305 SRX = SRX197576 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:08:39 prefetch.2.10.7: 1) Downloading 'SRR597004'... 2020-06-21T09:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:09:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:09:50 prefetch.2.10.7: 'SRR597004' is valid 2020-06-21T09:09:50 prefetch.2.10.7: 1) 'SRR597004' was downloaded successfully Read 13679068 spots for SRR597004/SRR597004.sra Written 13679068 spots for SRR597004/SRR597004.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: 00:04:16 13679068 reads; of these: 13679068 (100.00%) were unpaired; of these: 295207 (2.16%) aligned 0 times 6363064 (46.52%) aligned exactly 1 time 7020797 (51.33%) aligned >1 times 97.84% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 1324797 / 13383861 = 0.0990 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 18:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.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 18:18:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:21: 1000000 INFO @ Sun, 21 Jun 2020 18:18:27: 2000000 INFO @ Sun, 21 Jun 2020 18:18:34: 3000000 INFO @ Sun, 21 Jun 2020 18:18:40: 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 18:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.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 18:18:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:46: 5000000 INFO @ Sun, 21 Jun 2020 18:18:52: 1000000 INFO @ Sun, 21 Jun 2020 18:18:53: 6000000 INFO @ Sun, 21 Jun 2020 18:18:58: 2000000 INFO @ Sun, 21 Jun 2020 18:19:00: 7000000 INFO @ Sun, 21 Jun 2020 18:19:05: 3000000 INFO @ Sun, 21 Jun 2020 18:19:07: 8000000 INFO @ Sun, 21 Jun 2020 18:19:12: 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 18:19:13: 9000000 INFO @ Sun, 21 Jun 2020 18:19:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.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 18:19:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:19: 5000000 INFO @ Sun, 21 Jun 2020 18:19:21: 10000000 INFO @ Sun, 21 Jun 2020 18:19:22: 1000000 INFO @ Sun, 21 Jun 2020 18:19:26: 6000000 INFO @ Sun, 21 Jun 2020 18:19:28: 11000000 INFO @ Sun, 21 Jun 2020 18:19:29: 2000000 INFO @ Sun, 21 Jun 2020 18:19:32: 7000000 INFO @ Sun, 21 Jun 2020 18:19:35: 12000000 INFO @ Sun, 21 Jun 2020 18:19:35: 3000000 INFO @ Sun, 21 Jun 2020 18:19:35: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 18:19:35: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 18:19:35: #1 total tags in treatment: 12059064 INFO @ Sun, 21 Jun 2020 18:19:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:19:35: #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 18:19:36: #1 tags after filtering in treatment: 12059063 INFO @ Sun, 21 Jun 2020 18:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:19:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:19:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:19:37: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 18:19:37: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 18:19:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:19:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:19:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:19:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:19:37: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:19:37: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:19:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05_model.r INFO @ Sun, 21 Jun 2020 18:19:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:19:39: 8000000 INFO @ Sun, 21 Jun 2020 18:19:42: 4000000 INFO @ Sun, 21 Jun 2020 18:19:46: 9000000 INFO @ Sun, 21 Jun 2020 18:19:49: 5000000 INFO @ Sun, 21 Jun 2020 18:19:54: 10000000 INFO @ Sun, 21 Jun 2020 18:19:56: 6000000 INFO @ Sun, 21 Jun 2020 18:19:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:01: 11000000 INFO @ Sun, 21 Jun 2020 18:20:03: 7000000 INFO @ Sun, 21 Jun 2020 18:20:08: 12000000 INFO @ Sun, 21 Jun 2020 18:20:08: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 18:20:08: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 18:20:08: #1 total tags in treatment: 12059064 INFO @ Sun, 21 Jun 2020 18:20:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:08: #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 18:20:09: #1 tags after filtering in treatment: 12059063 INFO @ Sun, 21 Jun 2020 18:20:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:09: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:10: 8000000 INFO @ Sun, 21 Jun 2020 18:20:10: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 18:20:10: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:10: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:10: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:10: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:10: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:10: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:20:10: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:20:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10_model.r INFO @ Sun, 21 Jun 2020 18:20:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:11: Done! pass1 - making usageList (481 chroms): 1 millis pass2 - checking and writing primary data (1588 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:20:17: 9000000 INFO @ Sun, 21 Jun 2020 18:20:24: 10000000 INFO @ Sun, 21 Jun 2020 18:20:31: 11000000 INFO @ Sun, 21 Jun 2020 18:20:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:37: 12000000 INFO @ Sun, 21 Jun 2020 18:20:38: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 18:20:38: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 18:20:38: #1 total tags in treatment: 12059064 INFO @ Sun, 21 Jun 2020 18:20:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:38: #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 18:20:39: #1 tags after filtering in treatment: 12059063 INFO @ Sun, 21 Jun 2020 18:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:40: #2 number of paired peaks: 344 WARNING @ Sun, 21 Jun 2020 18:20:40: Fewer paired peaks (344) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 344 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:40: #2 predicted fragment length is 55 bps INFO @ Sun, 21 Jun 2020 18:20:40: #2 alternative fragment length(s) may be 4,55 bps INFO @ Sun, 21 Jun 2020 18:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20_model.r INFO @ Sun, 21 Jun 2020 18:20:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.10_summits.bed INFO @ Sun, 21 Jun 2020 18:20:44: Done! pass1 - making usageList (211 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197576/SRX197576.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:13: Done! pass1 - making usageList (105 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 8 millis CompletedMACS2peakCalling