Job ID = 14167608 SRX = SRX4712959 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: 00:01:40 5866739 reads; of these: 5866739 (100.00%) were unpaired; of these: 132237 (2.25%) aligned 0 times 4633938 (78.99%) aligned exactly 1 time 1100564 (18.76%) aligned >1 times 97.75% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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] 270713 / 5734502 = 0.0472 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:51:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.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 @ Fri, 10 Dec 2021 12:51:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:51:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:51:56: 1000000 INFO @ Fri, 10 Dec 2021 12:52:05: 2000000 INFO @ Fri, 10 Dec 2021 12:52:13: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:52:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.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 @ Fri, 10 Dec 2021 12:52:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:52:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:52:20: 4000000 INFO @ Fri, 10 Dec 2021 12:52:26: 1000000 INFO @ Fri, 10 Dec 2021 12:52:29: 5000000 INFO @ Fri, 10 Dec 2021 12:52:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:52:33: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:52:33: #1 total tags in treatment: 5463789 INFO @ Fri, 10 Dec 2021 12:52:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:52:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:52:34: #1 tags after filtering in treatment: 5463623 INFO @ Fri, 10 Dec 2021 12:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:52:34: #1 finished! INFO @ Fri, 10 Dec 2021 12:52:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:52:34: #2 number of paired peaks: 751 WARNING @ Fri, 10 Dec 2021 12:52:34: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Fri, 10 Dec 2021 12:52:34: start model_add_line... INFO @ Fri, 10 Dec 2021 12:52:34: start X-correlation... INFO @ Fri, 10 Dec 2021 12:52:34: end of X-cor INFO @ Fri, 10 Dec 2021 12:52:34: #2 finished! INFO @ Fri, 10 Dec 2021 12:52:34: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 12:52:34: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 10 Dec 2021 12:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05_model.r INFO @ Fri, 10 Dec 2021 12:52:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:52:35: 2000000 INFO @ Fri, 10 Dec 2021 12:52:44: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:52:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.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 @ Fri, 10 Dec 2021 12:52:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:52:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.05_summits.bed INFO @ Fri, 10 Dec 2021 12:52:53: Done! INFO @ Fri, 10 Dec 2021 12:52:54: 4000000 pass1 - making usageList (333 chroms): 2 millis pass2 - checking and writing primary data (2156 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:52:57: 1000000 INFO @ Fri, 10 Dec 2021 12:53:03: 5000000 INFO @ Fri, 10 Dec 2021 12:53:04: 2000000 INFO @ Fri, 10 Dec 2021 12:53:07: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:53:07: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:53:07: #1 total tags in treatment: 5463789 INFO @ Fri, 10 Dec 2021 12:53:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:53:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:53:08: #1 tags after filtering in treatment: 5463623 INFO @ Fri, 10 Dec 2021 12:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:53:08: #1 finished! INFO @ Fri, 10 Dec 2021 12:53:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:53:08: #2 number of paired peaks: 751 WARNING @ Fri, 10 Dec 2021 12:53:08: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Fri, 10 Dec 2021 12:53:08: start model_add_line... INFO @ Fri, 10 Dec 2021 12:53:08: start X-correlation... INFO @ Fri, 10 Dec 2021 12:53:08: end of X-cor INFO @ Fri, 10 Dec 2021 12:53:08: #2 finished! INFO @ Fri, 10 Dec 2021 12:53:08: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 12:53:08: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 10 Dec 2021 12:53:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10_model.r INFO @ Fri, 10 Dec 2021 12:53:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:53:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:53:12: 3000000 INFO @ Fri, 10 Dec 2021 12:53:20: 4000000 INFO @ Fri, 10 Dec 2021 12:53:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.10_summits.bed INFO @ Fri, 10 Dec 2021 12:53:28: Done! pass1 - making usageList (244 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:53:29: 5000000 INFO @ Fri, 10 Dec 2021 12:53:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:53:33: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:53:33: #1 total tags in treatment: 5463789 INFO @ Fri, 10 Dec 2021 12:53:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:53:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:53:34: #1 tags after filtering in treatment: 5463623 INFO @ Fri, 10 Dec 2021 12:53:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:53:34: #1 finished! INFO @ Fri, 10 Dec 2021 12:53:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:53:34: #2 number of paired peaks: 751 WARNING @ Fri, 10 Dec 2021 12:53:34: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Fri, 10 Dec 2021 12:53:34: start model_add_line... INFO @ Fri, 10 Dec 2021 12:53:34: start X-correlation... INFO @ Fri, 10 Dec 2021 12:53:34: end of X-cor INFO @ Fri, 10 Dec 2021 12:53:34: #2 finished! INFO @ Fri, 10 Dec 2021 12:53:34: #2 predicted fragment length is 114 bps INFO @ Fri, 10 Dec 2021 12:53:34: #2 alternative fragment length(s) may be 114 bps INFO @ Fri, 10 Dec 2021 12:53:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20_model.r INFO @ Fri, 10 Dec 2021 12:53:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:53:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:53:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712959/SRX4712959.20_summits.bed INFO @ Fri, 10 Dec 2021 12:53:53: Done! pass1 - making usageList (166 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 12 millis CompletedMACS2peakCalling