Job ID = 14172513 SRX = SRX10089758 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: 00:04:45 26710604 reads; of these: 26710604 (100.00%) were unpaired; of these: 5021313 (18.80%) aligned 0 times 17329429 (64.88%) aligned exactly 1 time 4359862 (16.32%) aligned >1 times 81.20% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5274000 / 21689291 = 0.2432 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 15:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.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 15:54:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:54:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:08: 1000000 INFO @ Sat, 11 Dec 2021 15:54:14: 2000000 INFO @ Sat, 11 Dec 2021 15:54:20: 3000000 INFO @ Sat, 11 Dec 2021 15:54:26: 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 15:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.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 15:54:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:54:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:32: 5000000 INFO @ Sat, 11 Dec 2021 15:54:37: 1000000 INFO @ Sat, 11 Dec 2021 15:54:39: 6000000 INFO @ Sat, 11 Dec 2021 15:54:43: 2000000 INFO @ Sat, 11 Dec 2021 15:54:45: 7000000 INFO @ Sat, 11 Dec 2021 15:54:49: 3000000 INFO @ Sat, 11 Dec 2021 15:54:52: 8000000 INFO @ Sat, 11 Dec 2021 15:54:55: 4000000 INFO @ Sat, 11 Dec 2021 15:54:58: 9000000 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 15:55:01: 5000000 INFO @ Sat, 11 Dec 2021 15:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.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 15:55:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:55:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:55:05: 10000000 INFO @ Sat, 11 Dec 2021 15:55:07: 6000000 INFO @ Sat, 11 Dec 2021 15:55:07: 1000000 INFO @ Sat, 11 Dec 2021 15:55:12: 11000000 INFO @ Sat, 11 Dec 2021 15:55:13: 7000000 INFO @ Sat, 11 Dec 2021 15:55:13: 2000000 INFO @ Sat, 11 Dec 2021 15:55:18: 12000000 INFO @ Sat, 11 Dec 2021 15:55:19: 8000000 INFO @ Sat, 11 Dec 2021 15:55:19: 3000000 INFO @ Sat, 11 Dec 2021 15:55:25: 9000000 INFO @ Sat, 11 Dec 2021 15:55:25: 13000000 INFO @ Sat, 11 Dec 2021 15:55:25: 4000000 INFO @ Sat, 11 Dec 2021 15:55:31: 10000000 INFO @ Sat, 11 Dec 2021 15:55:31: 5000000 INFO @ Sat, 11 Dec 2021 15:55:32: 14000000 INFO @ Sat, 11 Dec 2021 15:55:37: 11000000 INFO @ Sat, 11 Dec 2021 15:55:37: 6000000 INFO @ Sat, 11 Dec 2021 15:55:39: 15000000 INFO @ Sat, 11 Dec 2021 15:55:43: 12000000 INFO @ Sat, 11 Dec 2021 15:55:43: 7000000 INFO @ Sat, 11 Dec 2021 15:55:45: 16000000 INFO @ Sat, 11 Dec 2021 15:55:48: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 15:55:48: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 15:55:48: #1 total tags in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:55:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:55:48: #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 15:55:49: 13000000 INFO @ Sat, 11 Dec 2021 15:55:49: #1 tags after filtering in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:55:49: #1 finished! INFO @ Sat, 11 Dec 2021 15:55:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:55:49: 8000000 INFO @ Sat, 11 Dec 2021 15:55:50: #2 number of paired peaks: 812 WARNING @ Sat, 11 Dec 2021 15:55:50: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Sat, 11 Dec 2021 15:55:50: start model_add_line... INFO @ Sat, 11 Dec 2021 15:55:50: start X-correlation... INFO @ Sat, 11 Dec 2021 15:55:50: end of X-cor INFO @ Sat, 11 Dec 2021 15:55:50: #2 finished! INFO @ Sat, 11 Dec 2021 15:55:50: #2 predicted fragment length is 200 bps INFO @ Sat, 11 Dec 2021 15:55:50: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 11 Dec 2021 15:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05_model.r INFO @ Sat, 11 Dec 2021 15:55:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:55:55: 9000000 INFO @ Sat, 11 Dec 2021 15:55:55: 14000000 INFO @ Sat, 11 Dec 2021 15:56:01: 10000000 INFO @ Sat, 11 Dec 2021 15:56:01: 15000000 INFO @ Sat, 11 Dec 2021 15:56:06: 11000000 INFO @ Sat, 11 Dec 2021 15:56:07: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:56:09: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 15:56:09: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 15:56:09: #1 total tags in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:56:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:56:09: #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 15:56:10: #1 tags after filtering in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:56:10: #1 finished! INFO @ Sat, 11 Dec 2021 15:56:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:56:11: #2 number of paired peaks: 812 WARNING @ Sat, 11 Dec 2021 15:56:11: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Sat, 11 Dec 2021 15:56:11: start model_add_line... INFO @ Sat, 11 Dec 2021 15:56:11: start X-correlation... INFO @ Sat, 11 Dec 2021 15:56:11: end of X-cor INFO @ Sat, 11 Dec 2021 15:56:11: #2 finished! INFO @ Sat, 11 Dec 2021 15:56:11: #2 predicted fragment length is 200 bps INFO @ Sat, 11 Dec 2021 15:56:11: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 11 Dec 2021 15:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10_model.r INFO @ Sat, 11 Dec 2021 15:56:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:56:12: 12000000 INFO @ Sat, 11 Dec 2021 15:56:17: 13000000 INFO @ Sat, 11 Dec 2021 15:56:23: 14000000 INFO @ Sat, 11 Dec 2021 15:56:25: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:56:29: 15000000 INFO @ Sat, 11 Dec 2021 15:56:34: 16000000 INFO @ Sat, 11 Dec 2021 15:56:36: #1 tag size is determined as 40 bps INFO @ Sat, 11 Dec 2021 15:56:36: #1 tag size = 40 INFO @ Sat, 11 Dec 2021 15:56:36: #1 total tags in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:56:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:56:36: #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 15:56:37: #1 tags after filtering in treatment: 16415291 INFO @ Sat, 11 Dec 2021 15:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:56:37: #1 finished! INFO @ Sat, 11 Dec 2021 15:56:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:56:38: #2 number of paired peaks: 812 WARNING @ Sat, 11 Dec 2021 15:56:38: Fewer paired peaks (812) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 812 pairs to build model! INFO @ Sat, 11 Dec 2021 15:56:38: start model_add_line... INFO @ Sat, 11 Dec 2021 15:56:38: start X-correlation... INFO @ Sat, 11 Dec 2021 15:56:38: end of X-cor INFO @ Sat, 11 Dec 2021 15:56:38: #2 finished! INFO @ Sat, 11 Dec 2021 15:56:38: #2 predicted fragment length is 200 bps INFO @ Sat, 11 Dec 2021 15:56:38: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 11 Dec 2021 15:56:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20_model.r INFO @ Sat, 11 Dec 2021 15:56:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:56:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:56:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:56:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.05_summits.bed INFO @ Sat, 11 Dec 2021 15:56:42: Done! BigWig に変換しました。 pass1 - making usageList (539 chroms): 2 millis pass2 - checking and writing primary data (6834 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:56:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:57:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:57:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:57:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.10_summits.bed INFO @ Sat, 11 Dec 2021 15:57:03: Done! pass1 - making usageList (480 chroms): 2 millis pass2 - checking and writing primary data (4643 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:57:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089758/SRX10089758.20_summits.bed INFO @ Sat, 11 Dec 2021 15:57:29: Done! pass1 - making usageList (386 chroms): 3 millis pass2 - checking and writing primary data (2898 records, 4 fields): 14 millis CompletedMACS2peakCalling