Job ID = 6529149 SRX = SRX013071 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: 00:00:31 2924397 reads; of these: 2924397 (100.00%) were unpaired; of these: 632150 (21.62%) aligned 0 times 1906893 (65.21%) aligned exactly 1 time 385354 (13.18%) aligned >1 times 78.38% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 79066 / 2292247 = 0.0345 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 01:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.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 01:29:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:18: 1000000 INFO @ Tue, 30 Jun 2020 01:29:24: 2000000 INFO @ Tue, 30 Jun 2020 01:29:25: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:29:25: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:29:25: #1 total tags in treatment: 2213181 INFO @ Tue, 30 Jun 2020 01:29:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:25: #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 01:29:25: #1 tags after filtering in treatment: 2212931 INFO @ Tue, 30 Jun 2020 01:29:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:25: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:26: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 01:29:26: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:26: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:26: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:26: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:26: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:26: #2 predicted fragment length is 121 bps INFO @ Tue, 30 Jun 2020 01:29:26: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 30 Jun 2020 01:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05_model.r INFO @ Tue, 30 Jun 2020 01:29:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.05_summits.bed INFO @ Tue, 30 Jun 2020 01:29:33: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 01:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.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 01:29:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:48: 1000000 INFO @ Tue, 30 Jun 2020 01:29:54: 2000000 INFO @ Tue, 30 Jun 2020 01:29:55: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:29:55: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:29:55: #1 total tags in treatment: 2213181 INFO @ Tue, 30 Jun 2020 01:29:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:55: #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 01:29:55: #1 tags after filtering in treatment: 2212931 INFO @ Tue, 30 Jun 2020 01:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:56: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 01:29:56: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:56: #2 predicted fragment length is 121 bps INFO @ Tue, 30 Jun 2020 01:29:56: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 30 Jun 2020 01:29:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10_model.r INFO @ Tue, 30 Jun 2020 01:29:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.10_summits.bed INFO @ Tue, 30 Jun 2020 01:30:03: Done! pass1 - making usageList (63 chroms): 0 millis pass2 - checking and writing primary data (114 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 01:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.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 01:30:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:30:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:30:18: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:24: 2000000 INFO @ Tue, 30 Jun 2020 01:30:26: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:30:26: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:30:26: #1 total tags in treatment: 2213181 INFO @ Tue, 30 Jun 2020 01:30:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:30:26: #1 tags after filtering in treatment: 2212931 INFO @ Tue, 30 Jun 2020 01:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:26: #2 number of paired peaks: 227 WARNING @ Tue, 30 Jun 2020 01:30:26: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:26: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:26: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:26: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:26: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:26: #2 predicted fragment length is 121 bps INFO @ Tue, 30 Jun 2020 01:30:26: #2 alternative fragment length(s) may be 121 bps INFO @ Tue, 30 Jun 2020 01:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20_model.r INFO @ Tue, 30 Jun 2020 01:30:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013071/SRX013071.20_summits.bed INFO @ Tue, 30 Jun 2020 01:30:34: Done! pass1 - making usageList (46 chroms): 0 millis pass2 - checking and writing primary data (59 records, 4 fields): 3 millis CompletedMACS2peakCalling