Job ID = 6529370 SRX = SRX231873 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: 00:01:00 9320921 reads; of these: 9320921 (100.00%) were unpaired; of these: 5456563 (58.54%) aligned 0 times 3175620 (34.07%) aligned exactly 1 time 688738 (7.39%) aligned >1 times 41.46% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 147776 / 3864358 = 0.0382 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 01:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.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 01:45:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:47: 1000000 INFO @ Tue, 30 Jun 2020 01:45:52: 2000000 INFO @ Tue, 30 Jun 2020 01:45:57: 3000000 INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:46:02: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:46:02: #1 total tags in treatment: 3716582 INFO @ Tue, 30 Jun 2020 01:46:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:02: #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 01:46:03: #1 tags after filtering in treatment: 3716534 INFO @ Tue, 30 Jun 2020 01:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:03: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:46:03: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:03: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:03: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:03: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:03: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:03: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 01:46:03: #2 alternative fragment length(s) may be 73,529,537 bps INFO @ Tue, 30 Jun 2020 01:46:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05_model.r INFO @ Tue, 30 Jun 2020 01:46:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:03: #3 Pre-compute pvalue-qvalue table... 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 01:46:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.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 01:46:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:15: Done! pass1 - making usageList (184 chroms): 2 millis pass2 - checking and writing primary data (481 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:20: 1000000 INFO @ Tue, 30 Jun 2020 01:46:27: 2000000 INFO @ Tue, 30 Jun 2020 01:46:33: 3000000 INFO @ Tue, 30 Jun 2020 01:46:39: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:46:39: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:46:39: #1 total tags in treatment: 3716582 INFO @ Tue, 30 Jun 2020 01:46:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 01:46:40: #1 tags after filtering in treatment: 3716534 INFO @ Tue, 30 Jun 2020 01:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:40: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:46:40: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:40: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:40: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:40: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:40: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 01:46:40: #2 alternative fragment length(s) may be 73,529,537 bps INFO @ Tue, 30 Jun 2020 01:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10_model.r INFO @ Tue, 30 Jun 2020 01:46:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.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 01:46:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:47: 1000000 INFO @ Tue, 30 Jun 2020 01:46:48: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.10_summits.bed INFO @ Tue, 30 Jun 2020 01:46:52: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:53: 2000000 INFO @ Tue, 30 Jun 2020 01:46:58: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:47:03: #1 tag size is determined as 35 bps INFO @ Tue, 30 Jun 2020 01:47:03: #1 tag size = 35 INFO @ Tue, 30 Jun 2020 01:47:03: #1 total tags in treatment: 3716582 INFO @ Tue, 30 Jun 2020 01:47:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:03: #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 01:47:03: #1 tags after filtering in treatment: 3716534 INFO @ Tue, 30 Jun 2020 01:47:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:03: #2 number of paired peaks: 208 WARNING @ Tue, 30 Jun 2020 01:47:03: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:03: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:03: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:03: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:03: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:03: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 01:47:03: #2 alternative fragment length(s) may be 73,529,537 bps INFO @ Tue, 30 Jun 2020 01:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20_model.r INFO @ Tue, 30 Jun 2020 01:47:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX231873/SRX231873.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:15: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (78 records, 4 fields): 4 millis CompletedMACS2peakCalling