Job ID = 6452948 SRX = SRX054534 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:13:03 prefetch.2.10.7: 1) Downloading 'SRR167349'... 2020-06-21T08:13:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:52 prefetch.2.10.7: 'SRR167349' is valid 2020-06-21T08:16:52 prefetch.2.10.7: 1) 'SRR167349' was downloaded successfully Read 17747019 spots for SRR167349/SRR167349.sra Written 17747019 spots for SRR167349/SRR167349.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: 00:00:01 Multiseed full-index search: 00:03:10 17747019 reads; of these: 17747019 (100.00%) were unpaired; of these: 3962144 (22.33%) aligned 0 times 10027988 (56.51%) aligned exactly 1 time 3756887 (21.17%) aligned >1 times 77.67% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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_rmdupse_core] 5204434 / 13784875 = 0.3775 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 17:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.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 17:23:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:42: 1000000 INFO @ Sun, 21 Jun 2020 17:23:48: 2000000 INFO @ Sun, 21 Jun 2020 17:23:53: 3000000 INFO @ Sun, 21 Jun 2020 17:23:58: 4000000 INFO @ Sun, 21 Jun 2020 17:24:04: 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 17:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.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 17:24:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:09: 6000000 INFO @ Sun, 21 Jun 2020 17:24:13: 1000000 INFO @ Sun, 21 Jun 2020 17:24:15: 7000000 INFO @ Sun, 21 Jun 2020 17:24:19: 2000000 INFO @ Sun, 21 Jun 2020 17:24:22: 8000000 INFO @ Sun, 21 Jun 2020 17:24:25: 3000000 INFO @ Sun, 21 Jun 2020 17:24:26: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:24:26: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:24:26: #1 total tags in treatment: 8580441 INFO @ Sun, 21 Jun 2020 17:24:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:26: #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 17:24:26: #1 tags after filtering in treatment: 8580362 INFO @ Sun, 21 Jun 2020 17:24:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:27: #2 number of paired peaks: 515 WARNING @ Sun, 21 Jun 2020 17:24:27: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sun, 21 Jun 2020 17:24:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:27: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:24:27: #2 alternative fragment length(s) may be 4,81,102,566 bps INFO @ Sun, 21 Jun 2020 17:24:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05_model.r INFO @ Sun, 21 Jun 2020 17:24:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:24:31: 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 17:24:36: 5000000 INFO @ Sun, 21 Jun 2020 17:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.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 17:24:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:43: 6000000 INFO @ Sun, 21 Jun 2020 17:24:43: 1000000 INFO @ Sun, 21 Jun 2020 17:24:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:49: 7000000 INFO @ Sun, 21 Jun 2020 17:24:50: 2000000 INFO @ Sun, 21 Jun 2020 17:24:55: 8000000 INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.05_summits.bed INFO @ Sun, 21 Jun 2020 17:24:56: Done! pass1 - making usageList (617 chroms): 2 millis pass2 - checking and writing primary data (3074 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:24:56: 3000000 INFO @ Sun, 21 Jun 2020 17:24:59: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:24:59: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:24:59: #1 total tags in treatment: 8580441 INFO @ Sun, 21 Jun 2020 17:24:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:59: #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 17:25:00: #1 tags after filtering in treatment: 8580362 INFO @ Sun, 21 Jun 2020 17:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:00: #2 number of paired peaks: 515 WARNING @ Sun, 21 Jun 2020 17:25:00: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sun, 21 Jun 2020 17:25:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:00: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:25:00: #2 alternative fragment length(s) may be 4,81,102,566 bps INFO @ Sun, 21 Jun 2020 17:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10_model.r INFO @ Sun, 21 Jun 2020 17:25:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:25:02: 4000000 INFO @ Sun, 21 Jun 2020 17:25:07: 5000000 INFO @ Sun, 21 Jun 2020 17:25:13: 6000000 INFO @ Sun, 21 Jun 2020 17:25:18: 7000000 INFO @ Sun, 21 Jun 2020 17:25:18: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:25:24: 8000000 INFO @ Sun, 21 Jun 2020 17:25:27: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:25:27: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:25:27: #1 total tags in treatment: 8580441 INFO @ Sun, 21 Jun 2020 17:25:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:27: #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 17:25:28: #1 tags after filtering in treatment: 8580362 INFO @ Sun, 21 Jun 2020 17:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.10_summits.bed INFO @ Sun, 21 Jun 2020 17:25:28: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (888 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:25:28: #2 number of paired peaks: 515 WARNING @ Sun, 21 Jun 2020 17:25:28: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sun, 21 Jun 2020 17:25:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:28: #2 predicted fragment length is 81 bps INFO @ Sun, 21 Jun 2020 17:25:28: #2 alternative fragment length(s) may be 4,81,102,566 bps INFO @ Sun, 21 Jun 2020 17:25:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20_model.r INFO @ Sun, 21 Jun 2020 17:25:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:25:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:25:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:25:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:25:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX054534/SRX054534.20_summits.bed INFO @ Sun, 21 Jun 2020 17:25:56: Done! pass1 - making usageList (118 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 5 millis CompletedMACS2peakCalling