Job ID = 6452813 SRX = SRX040615 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:57:59 prefetch.2.10.7: 1) Downloading 'SRR097984'... 2020-06-21T07:57:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:59:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:59:55 prefetch.2.10.7: 1) 'SRR097984' was downloaded successfully Read 25688390 spots for SRR097984/SRR097984.sra Written 25688390 spots for SRR097984/SRR097984.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: 00:03:46 25688390 reads; of these: 25688390 (100.00%) were unpaired; of these: 2416973 (9.41%) aligned 0 times 22351586 (87.01%) aligned exactly 1 time 919831 (3.58%) aligned >1 times 90.59% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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 8 files... [bam_rmdupse_core] 16077348 / 23271417 = 0.6909 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 17:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.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 17:08:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:50: 1000000 INFO @ Sun, 21 Jun 2020 17:08:57: 2000000 INFO @ Sun, 21 Jun 2020 17:09:03: 3000000 INFO @ Sun, 21 Jun 2020 17:09:10: 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 17:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.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 17:09:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:16: 5000000 INFO @ Sun, 21 Jun 2020 17:09:21: 1000000 INFO @ Sun, 21 Jun 2020 17:09:24: 6000000 INFO @ Sun, 21 Jun 2020 17:09:28: 2000000 INFO @ Sun, 21 Jun 2020 17:09:32: 7000000 INFO @ Sun, 21 Jun 2020 17:09:33: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:09:33: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:09:33: #1 total tags in treatment: 7194069 INFO @ Sun, 21 Jun 2020 17:09:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:33: #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 17:09:33: #1 tags after filtering in treatment: 7193576 INFO @ Sun, 21 Jun 2020 17:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:34: 3000000 INFO @ Sun, 21 Jun 2020 17:09:35: #2 number of paired peaks: 11130 INFO @ Sun, 21 Jun 2020 17:09:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:35: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 17:09:35: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 17:09:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05_model.r INFO @ Sun, 21 Jun 2020 17:09:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:40: 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 17:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.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 17:09:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:09:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:09:46: 5000000 INFO @ Sun, 21 Jun 2020 17:09:51: 1000000 INFO @ Sun, 21 Jun 2020 17:09:53: 6000000 INFO @ Sun, 21 Jun 2020 17:09:58: 2000000 INFO @ Sun, 21 Jun 2020 17:10:00: 7000000 INFO @ Sun, 21 Jun 2020 17:10:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:01: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:10:01: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:10:01: #1 total tags in treatment: 7194069 INFO @ Sun, 21 Jun 2020 17:10:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:01: #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 17:10:02: #1 tags after filtering in treatment: 7193576 INFO @ Sun, 21 Jun 2020 17:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:03: #2 number of paired peaks: 11130 INFO @ Sun, 21 Jun 2020 17:10:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:03: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 17:10:03: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 17:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10_model.r INFO @ Sun, 21 Jun 2020 17:10:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:05: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.05_summits.bed INFO @ Sun, 21 Jun 2020 17:10:10: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (9277 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:12: 4000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:18: 5000000 INFO @ Sun, 21 Jun 2020 17:10:25: 6000000 INFO @ Sun, 21 Jun 2020 17:10:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:31: 7000000 INFO @ Sun, 21 Jun 2020 17:10:32: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:10:32: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:10:32: #1 total tags in treatment: 7194069 INFO @ Sun, 21 Jun 2020 17:10:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:32: #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 17:10:33: #1 tags after filtering in treatment: 7193576 INFO @ Sun, 21 Jun 2020 17:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:33: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:34: #2 number of paired peaks: 11130 INFO @ Sun, 21 Jun 2020 17:10:34: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:34: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:34: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:34: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:34: #2 predicted fragment length is 172 bps INFO @ Sun, 21 Jun 2020 17:10:34: #2 alternative fragment length(s) may be 172 bps INFO @ Sun, 21 Jun 2020 17:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20_model.r INFO @ Sun, 21 Jun 2020 17:10:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:37: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (8291 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX040615/SRX040615.20_summits.bed INFO @ Sun, 21 Jun 2020 17:11:07: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (7009 records, 4 fields): 10 millis CompletedMACS2peakCalling