Job ID = 14170820 SRX = SRX8784754 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: 00:02:36 5885452 reads; of these: 5885452 (100.00%) were unpaired; of these: 377711 (6.42%) aligned 0 times 4946264 (84.04%) aligned exactly 1 time 561477 (9.54%) aligned >1 times 93.58% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 324614 / 5507741 = 0.0589 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 @ Sat, 11 Dec 2021 08:55:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 08:55:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:55:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:55:23: 1000000 INFO @ Sat, 11 Dec 2021 08:55:30: 2000000 INFO @ Sat, 11 Dec 2021 08:55:36: 3000000 INFO @ Sat, 11 Dec 2021 08:55:43: 4000000 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 @ Sat, 11 Dec 2021 08:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 08:55:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:55:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:55:50: 5000000 INFO @ Sat, 11 Dec 2021 08:55:52: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 08:55:52: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 08:55:52: #1 total tags in treatment: 5183127 INFO @ Sat, 11 Dec 2021 08:55:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:55:52: #1 tags after filtering in treatment: 5182790 INFO @ Sat, 11 Dec 2021 08:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:52: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:53: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:55:53: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:53: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:53: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:53: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:53: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:53: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 08:55:53: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 08:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05_model.r INFO @ Sat, 11 Dec 2021 08:55:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:55:53: 1000000 INFO @ Sat, 11 Dec 2021 08:56:00: 2000000 INFO @ Sat, 11 Dec 2021 08:56:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:56:07: 3000000 INFO @ Sat, 11 Dec 2021 08:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.05_summits.bed INFO @ Sat, 11 Dec 2021 08:56:11: Done! pass1 - making usageList (214 chroms): 3 millis pass2 - checking and writing primary data (7486 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:56:13: 4000000 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 @ Sat, 11 Dec 2021 08:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.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 @ Sat, 11 Dec 2021 08:56:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:56:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:56:21: 5000000 INFO @ Sat, 11 Dec 2021 08:56:23: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 08:56:23: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 08:56:23: #1 total tags in treatment: 5183127 INFO @ Sat, 11 Dec 2021 08:56:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:56:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:56:23: #1 tags after filtering in treatment: 5182790 INFO @ Sat, 11 Dec 2021 08:56:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:56:23: #1 finished! INFO @ Sat, 11 Dec 2021 08:56:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:56:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:56:23: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:56:23: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:56:23: start model_add_line... INFO @ Sat, 11 Dec 2021 08:56:23: start X-correlation... INFO @ Sat, 11 Dec 2021 08:56:24: end of X-cor INFO @ Sat, 11 Dec 2021 08:56:24: #2 finished! INFO @ Sat, 11 Dec 2021 08:56:24: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 08:56:24: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 08:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10_model.r INFO @ Sat, 11 Dec 2021 08:56:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:56:24: 1000000 INFO @ Sat, 11 Dec 2021 08:56:30: 2000000 INFO @ Sat, 11 Dec 2021 08:56:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:56:37: 3000000 INFO @ Sat, 11 Dec 2021 08:56:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:56:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:56:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.10_summits.bed INFO @ Sat, 11 Dec 2021 08:56:42: Done! pass1 - making usageList (104 chroms): 2 millis pass2 - checking and writing primary data (1941 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:56:44: 4000000 INFO @ Sat, 11 Dec 2021 08:56:52: 5000000 INFO @ Sat, 11 Dec 2021 08:56:53: #1 tag size is determined as 99 bps INFO @ Sat, 11 Dec 2021 08:56:53: #1 tag size = 99 INFO @ Sat, 11 Dec 2021 08:56:53: #1 total tags in treatment: 5183127 INFO @ Sat, 11 Dec 2021 08:56:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:56:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:56:54: #1 tags after filtering in treatment: 5182790 INFO @ Sat, 11 Dec 2021 08:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:56:54: #1 finished! INFO @ Sat, 11 Dec 2021 08:56:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:56:54: #2 number of paired peaks: 706 WARNING @ Sat, 11 Dec 2021 08:56:54: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sat, 11 Dec 2021 08:56:54: start model_add_line... INFO @ Sat, 11 Dec 2021 08:56:54: start X-correlation... INFO @ Sat, 11 Dec 2021 08:56:54: end of X-cor INFO @ Sat, 11 Dec 2021 08:56:54: #2 finished! INFO @ Sat, 11 Dec 2021 08:56:54: #2 predicted fragment length is 207 bps INFO @ Sat, 11 Dec 2021 08:56:54: #2 alternative fragment length(s) may be 207 bps INFO @ Sat, 11 Dec 2021 08:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20_model.r INFO @ Sat, 11 Dec 2021 08:56:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:56:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:57:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8784754/SRX8784754.20_summits.bed INFO @ Sat, 11 Dec 2021 08:57:12: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。