Job ID = 14171708 SRX = SRX9986129 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: 00:03:51 16295896 reads; of these: 16295896 (100.00%) were unpaired; of these: 1308467 (8.03%) aligned 0 times 12426475 (76.26%) aligned exactly 1 time 2560954 (15.72%) aligned >1 times 91.97% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 4455219 / 14987429 = 0.2973 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 12:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.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 12:40:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:24: 1000000 INFO @ Sat, 11 Dec 2021 12:40:30: 2000000 INFO @ Sat, 11 Dec 2021 12:40:36: 3000000 INFO @ Sat, 11 Dec 2021 12:40:43: 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 12:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.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 12:40:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:49: 5000000 INFO @ Sat, 11 Dec 2021 12:40:55: 1000000 INFO @ Sat, 11 Dec 2021 12:40:57: 6000000 INFO @ Sat, 11 Dec 2021 12:41:04: 2000000 INFO @ Sat, 11 Dec 2021 12:41:04: 7000000 INFO @ Sat, 11 Dec 2021 12:41:11: 8000000 INFO @ Sat, 11 Dec 2021 12:41:12: 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 @ Sat, 11 Dec 2021 12:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.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 12:41:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:18: 9000000 INFO @ Sat, 11 Dec 2021 12:41:20: 4000000 INFO @ Sat, 11 Dec 2021 12:41:26: 10000000 INFO @ Sat, 11 Dec 2021 12:41:26: 1000000 INFO @ Sat, 11 Dec 2021 12:41:28: 5000000 INFO @ Sat, 11 Dec 2021 12:41:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:41:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:41:30: #1 total tags in treatment: 10532210 INFO @ Sat, 11 Dec 2021 12:41:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:41:30: #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 12:41:30: #1 tags after filtering in treatment: 10532094 INFO @ Sat, 11 Dec 2021 12:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:41:30: #1 finished! INFO @ Sat, 11 Dec 2021 12:41:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:41:31: #2 number of paired peaks: 552 WARNING @ Sat, 11 Dec 2021 12:41:31: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 11 Dec 2021 12:41:31: start model_add_line... INFO @ Sat, 11 Dec 2021 12:41:31: start X-correlation... INFO @ Sat, 11 Dec 2021 12:41:31: end of X-cor INFO @ Sat, 11 Dec 2021 12:41:31: #2 finished! INFO @ Sat, 11 Dec 2021 12:41:31: #2 predicted fragment length is 234 bps INFO @ Sat, 11 Dec 2021 12:41:31: #2 alternative fragment length(s) may be 3,227,234 bps INFO @ Sat, 11 Dec 2021 12:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05_model.r INFO @ Sat, 11 Dec 2021 12:41:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:41:34: 2000000 INFO @ Sat, 11 Dec 2021 12:41:36: 6000000 INFO @ Sat, 11 Dec 2021 12:41:42: 3000000 INFO @ Sat, 11 Dec 2021 12:41:44: 7000000 INFO @ Sat, 11 Dec 2021 12:41:50: 4000000 INFO @ Sat, 11 Dec 2021 12:41:52: 8000000 INFO @ Sat, 11 Dec 2021 12:41:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:41:58: 5000000 INFO @ Sat, 11 Dec 2021 12:42:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:42:06: 6000000 INFO @ Sat, 11 Dec 2021 12:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.05_summits.bed INFO @ Sat, 11 Dec 2021 12:42:07: Done! INFO @ Sat, 11 Dec 2021 12:42:08: 10000000 pass1 - making usageList (95 chroms): 1 millis pass2 - checking and writing primary data (4842 records, 4 fields): 173 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:42:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:42:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:42:11: #1 total tags in treatment: 10532210 INFO @ Sat, 11 Dec 2021 12:42:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:42:11: #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 12:42:12: #1 tags after filtering in treatment: 10532094 INFO @ Sat, 11 Dec 2021 12:42:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:42:12: #1 finished! INFO @ Sat, 11 Dec 2021 12:42:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:42:13: #2 number of paired peaks: 552 WARNING @ Sat, 11 Dec 2021 12:42:13: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 11 Dec 2021 12:42:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:42:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:42:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:42:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:42:13: #2 predicted fragment length is 234 bps INFO @ Sat, 11 Dec 2021 12:42:13: #2 alternative fragment length(s) may be 3,227,234 bps INFO @ Sat, 11 Dec 2021 12:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10_model.r INFO @ Sat, 11 Dec 2021 12:42:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:42:14: 7000000 INFO @ Sat, 11 Dec 2021 12:42:21: 8000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:42:28: 9000000 INFO @ Sat, 11 Dec 2021 12:42:34: 10000000 INFO @ Sat, 11 Dec 2021 12:42:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:42:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 12:42:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 12:42:38: #1 total tags in treatment: 10532210 INFO @ Sat, 11 Dec 2021 12:42:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:42:38: #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 12:42:38: #1 tags after filtering in treatment: 10532094 INFO @ Sat, 11 Dec 2021 12:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:42:38: #1 finished! INFO @ Sat, 11 Dec 2021 12:42:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:42:39: #2 number of paired peaks: 552 WARNING @ Sat, 11 Dec 2021 12:42:39: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 11 Dec 2021 12:42:39: start model_add_line... INFO @ Sat, 11 Dec 2021 12:42:39: start X-correlation... INFO @ Sat, 11 Dec 2021 12:42:39: end of X-cor INFO @ Sat, 11 Dec 2021 12:42:39: #2 finished! INFO @ Sat, 11 Dec 2021 12:42:39: #2 predicted fragment length is 234 bps INFO @ Sat, 11 Dec 2021 12:42:39: #2 alternative fragment length(s) may be 3,227,234 bps INFO @ Sat, 11 Dec 2021 12:42:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20_model.r INFO @ Sat, 11 Dec 2021 12:42:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:42:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:42:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:42:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:42:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.10_summits.bed INFO @ Sat, 11 Dec 2021 12:42:46: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (1483 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:43:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:43:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:43:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:43:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9986129/SRX9986129.20_summits.bed INFO @ Sat, 11 Dec 2021 12:43:15: Done! pass1 - making usageList (42 chroms): 0 millis pass2 - checking and writing primary data (321 records, 4 fields): 3 millis CompletedMACS2peakCalling