Job ID = 6529144 SRX = SRX013012 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:03 5351406 reads; of these: 5351406 (100.00%) were unpaired; of these: 1003533 (18.75%) aligned 0 times 3465542 (64.76%) aligned exactly 1 time 882331 (16.49%) aligned >1 times 81.25% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 204062 / 4347873 = 0.0469 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 @ Tue, 30 Jun 2020 01:26:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.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 @ Tue, 30 Jun 2020 01:26:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:26:35: 1000000 INFO @ Tue, 30 Jun 2020 01:26:42: 2000000 INFO @ Tue, 30 Jun 2020 01:26:48: 3000000 INFO @ Tue, 30 Jun 2020 01:26:55: 4000000 INFO @ Tue, 30 Jun 2020 01:26:56: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:26:56: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:26:56: #1 total tags in treatment: 4143811 INFO @ Tue, 30 Jun 2020 01:26:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:26:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:26:57: #1 tags after filtering in treatment: 4143737 INFO @ Tue, 30 Jun 2020 01:26:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:26:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:26:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:26:57: #2 number of paired peaks: 307 WARNING @ Tue, 30 Jun 2020 01:26:57: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 30 Jun 2020 01:26:57: start model_add_line... INFO @ Tue, 30 Jun 2020 01:26:57: start X-correlation... 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 @ Tue, 30 Jun 2020 01:26:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:26:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:26:57: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 01:26:57: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 01:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05_model.r INFO @ Tue, 30 Jun 2020 01:26:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.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 @ Tue, 30 Jun 2020 01:26:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:26:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:06: 1000000 INFO @ Tue, 30 Jun 2020 01:27:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:27:12: 2000000 INFO @ Tue, 30 Jun 2020 01:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.05_summits.bed INFO @ Tue, 30 Jun 2020 01:27:14: Done! pass1 - making usageList (255 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:27:19: 3000000 INFO @ Tue, 30 Jun 2020 01:27:26: 4000000 INFO @ Tue, 30 Jun 2020 01:27:27: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:27:27: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:27:27: #1 total tags in treatment: 4143811 INFO @ Tue, 30 Jun 2020 01:27:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:27:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:27:27: #1 tags after filtering in treatment: 4143737 INFO @ Tue, 30 Jun 2020 01:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:27:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:27:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:27:27: #2 looking for paired plus/minus strand peaks... 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 @ Tue, 30 Jun 2020 01:27:27: #2 number of paired peaks: 307 WARNING @ Tue, 30 Jun 2020 01:27:27: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 30 Jun 2020 01:27:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:27:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:27:28: end of X-cor INFO @ Tue, 30 Jun 2020 01:27:28: #2 finished! INFO @ Tue, 30 Jun 2020 01:27:28: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 01:27:28: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 01:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10_model.r INFO @ Tue, 30 Jun 2020 01:27:28: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.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 @ Tue, 30 Jun 2020 01:27:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:27:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:27:36: 1000000 INFO @ Tue, 30 Jun 2020 01:27:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:27:43: 2000000 INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.10_summits.bed INFO @ Tue, 30 Jun 2020 01:27:44: Done! pass1 - making usageList (139 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:27:49: 3000000 INFO @ Tue, 30 Jun 2020 01:27:57: 4000000 INFO @ Tue, 30 Jun 2020 01:27:58: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:27:58: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:27:58: #1 total tags in treatment: 4143811 INFO @ Tue, 30 Jun 2020 01:27:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:27:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:27:58: #1 tags after filtering in treatment: 4143737 INFO @ Tue, 30 Jun 2020 01:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:27:58: #1 finished! INFO @ Tue, 30 Jun 2020 01:27:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:27:59: #2 number of paired peaks: 307 WARNING @ Tue, 30 Jun 2020 01:27:59: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Tue, 30 Jun 2020 01:27:59: start model_add_line... INFO @ Tue, 30 Jun 2020 01:27:59: start X-correlation... INFO @ Tue, 30 Jun 2020 01:27:59: end of X-cor INFO @ Tue, 30 Jun 2020 01:27:59: #2 finished! INFO @ Tue, 30 Jun 2020 01:27:59: #2 predicted fragment length is 94 bps INFO @ Tue, 30 Jun 2020 01:27:59: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 30 Jun 2020 01:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20_model.r INFO @ Tue, 30 Jun 2020 01:27:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:27:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:28:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:28:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013012/SRX013012.20_summits.bed INFO @ Tue, 30 Jun 2020 01:28:15: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 3 millis CompletedMACS2peakCalling