Job ID = 6454274 SRX = SRX193631 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:10:09 prefetch.2.10.7: 1) Downloading 'SRR586009'... 2020-06-21T09:10:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:14:45 prefetch.2.10.7: 1) 'SRR586009' was downloaded successfully Read 23293594 spots for SRR586009/SRR586009.sra Written 23293594 spots for SRR586009/SRR586009.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: 00:03:47 23293594 reads; of these: 23293594 (100.00%) were unpaired; of these: 14015299 (60.17%) aligned 0 times 7550566 (32.41%) aligned exactly 1 time 1727729 (7.42%) aligned >1 times 39.83% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 2119133 / 9278295 = 0.2284 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 18:22:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.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 18:22:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:22:33: 1000000 INFO @ Sun, 21 Jun 2020 18:22:40: 2000000 INFO @ Sun, 21 Jun 2020 18:22:47: 3000000 INFO @ Sun, 21 Jun 2020 18:22:53: 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 18:22:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.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 18:22:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:22:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:00: 5000000 INFO @ Sun, 21 Jun 2020 18:23:03: 1000000 INFO @ Sun, 21 Jun 2020 18:23:08: 6000000 INFO @ Sun, 21 Jun 2020 18:23:10: 2000000 INFO @ Sun, 21 Jun 2020 18:23:16: 7000000 INFO @ Sun, 21 Jun 2020 18:23:17: 3000000 INFO @ Sun, 21 Jun 2020 18:23:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:17: #1 total tags in treatment: 7159162 INFO @ Sun, 21 Jun 2020 18:23:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:17: #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 18:23:17: #1 tags after filtering in treatment: 7158995 INFO @ Sun, 21 Jun 2020 18:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:18: #2 number of paired peaks: 626 WARNING @ Sun, 21 Jun 2020 18:23:18: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:18: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:23:18: #2 alternative fragment length(s) may be 128,169,564 bps INFO @ Sun, 21 Jun 2020 18:23:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05_model.r INFO @ Sun, 21 Jun 2020 18:23:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:23: 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 18:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.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 18:23:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:29: 5000000 INFO @ Sun, 21 Jun 2020 18:23:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:23:34: 1000000 INFO @ Sun, 21 Jun 2020 18:23:36: 6000000 INFO @ Sun, 21 Jun 2020 18:23:41: 2000000 INFO @ Sun, 21 Jun 2020 18:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:23:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:23:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.05_summits.bed INFO @ Sun, 21 Jun 2020 18:23:42: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (883 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:23:43: 7000000 INFO @ Sun, 21 Jun 2020 18:23:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:23:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:23:44: #1 total tags in treatment: 7159162 INFO @ Sun, 21 Jun 2020 18:23:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:23:44: #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 18:23:45: #1 tags after filtering in treatment: 7158995 INFO @ Sun, 21 Jun 2020 18:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:23:45: #1 finished! INFO @ Sun, 21 Jun 2020 18:23:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:23:45: #2 number of paired peaks: 626 WARNING @ Sun, 21 Jun 2020 18:23:45: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sun, 21 Jun 2020 18:23:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:23:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:23:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:23:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:23:45: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:23:45: #2 alternative fragment length(s) may be 128,169,564 bps INFO @ Sun, 21 Jun 2020 18:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10_model.r INFO @ Sun, 21 Jun 2020 18:23:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:23:49: 3000000 INFO @ Sun, 21 Jun 2020 18:23:56: 4000000 INFO @ Sun, 21 Jun 2020 18:24:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:03: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:24:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.10_summits.bed INFO @ Sun, 21 Jun 2020 18:24:09: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:24:10: 6000000 INFO @ Sun, 21 Jun 2020 18:24:17: 7000000 INFO @ Sun, 21 Jun 2020 18:24:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:24:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:24:18: #1 total tags in treatment: 7159162 INFO @ Sun, 21 Jun 2020 18:24:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:18: #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 18:24:18: #1 tags after filtering in treatment: 7158995 INFO @ Sun, 21 Jun 2020 18:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:19: #2 number of paired peaks: 626 WARNING @ Sun, 21 Jun 2020 18:24:19: Fewer paired peaks (626) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 626 pairs to build model! INFO @ Sun, 21 Jun 2020 18:24:19: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:19: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:19: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 18:24:19: #2 alternative fragment length(s) may be 128,169,564 bps INFO @ Sun, 21 Jun 2020 18:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20_model.r INFO @ Sun, 21 Jun 2020 18:24:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:24:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193631/SRX193631.20_summits.bed INFO @ Sun, 21 Jun 2020 18:24:43: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling