Job ID = 6459619 SRX = SRX7299243 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:27:46 prefetch.2.10.7: 1) Downloading 'SRR10620143'... 2020-06-21T13:27:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:29:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:29:52 prefetch.2.10.7: 'SRR10620143' is valid 2020-06-21T13:29:52 prefetch.2.10.7: 1) 'SRR10620143' was downloaded successfully 2020-06-21T13:29:52 prefetch.2.10.7: 'SRR10620143' has 0 unresolved dependencies Read 19310459 spots for SRR10620143/SRR10620143.sra Written 19310459 spots for SRR10620143/SRR10620143.sra 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: 00:05:10 19310459 reads; of these: 19310459 (100.00%) were unpaired; of these: 770595 (3.99%) aligned 0 times 14852826 (76.92%) aligned exactly 1 time 3687038 (19.09%) aligned >1 times 96.01% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:11 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] 3147653 / 18539864 = 0.1698 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 @ Sun, 21 Jun 2020 22:40:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.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 @ Sun, 21 Jun 2020 22:40:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:09: 1000000 INFO @ Sun, 21 Jun 2020 22:40:15: 2000000 INFO @ Sun, 21 Jun 2020 22:40:21: 3000000 INFO @ Sun, 21 Jun 2020 22:40:27: 4000000 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 @ Sun, 21 Jun 2020 22:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.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 @ Sun, 21 Jun 2020 22:40:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:40:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:40:33: 5000000 INFO @ Sun, 21 Jun 2020 22:40:40: 1000000 INFO @ Sun, 21 Jun 2020 22:40:40: 6000000 INFO @ Sun, 21 Jun 2020 22:40:47: 7000000 INFO @ Sun, 21 Jun 2020 22:40:47: 2000000 INFO @ Sun, 21 Jun 2020 22:40:54: 8000000 INFO @ Sun, 21 Jun 2020 22:40:55: 3000000 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 @ Sun, 21 Jun 2020 22:41:01: 9000000 INFO @ Sun, 21 Jun 2020 22:41:02: 4000000 INFO @ Sun, 21 Jun 2020 22:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.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 @ Sun, 21 Jun 2020 22:41:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:41:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:41:08: 10000000 INFO @ Sun, 21 Jun 2020 22:41:10: 5000000 INFO @ Sun, 21 Jun 2020 22:41:11: 1000000 INFO @ Sun, 21 Jun 2020 22:41:16: 11000000 INFO @ Sun, 21 Jun 2020 22:41:18: 6000000 INFO @ Sun, 21 Jun 2020 22:41:19: 2000000 INFO @ Sun, 21 Jun 2020 22:41:24: 12000000 INFO @ Sun, 21 Jun 2020 22:41:26: 7000000 INFO @ Sun, 21 Jun 2020 22:41:28: 3000000 INFO @ Sun, 21 Jun 2020 22:41:32: 13000000 INFO @ Sun, 21 Jun 2020 22:41:34: 8000000 INFO @ Sun, 21 Jun 2020 22:41:36: 4000000 INFO @ Sun, 21 Jun 2020 22:41:40: 14000000 INFO @ Sun, 21 Jun 2020 22:41:42: 9000000 INFO @ Sun, 21 Jun 2020 22:41:45: 5000000 INFO @ Sun, 21 Jun 2020 22:41:48: 15000000 INFO @ Sun, 21 Jun 2020 22:41:50: 10000000 INFO @ Sun, 21 Jun 2020 22:41:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:41:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:41:52: #1 total tags in treatment: 15392211 INFO @ Sun, 21 Jun 2020 22:41:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:41:52: #1 tags after filtering in treatment: 15392205 INFO @ Sun, 21 Jun 2020 22:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:41:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:41:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:41:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:41:53: 6000000 INFO @ Sun, 21 Jun 2020 22:41:53: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 22:41:53: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 22:41:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:41:54: start X-correlation... INFO @ Sun, 21 Jun 2020 22:41:54: end of X-cor INFO @ Sun, 21 Jun 2020 22:41:54: #2 finished! INFO @ Sun, 21 Jun 2020 22:41:54: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:41:54: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05_model.r INFO @ Sun, 21 Jun 2020 22:41:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:41:58: 11000000 INFO @ Sun, 21 Jun 2020 22:42:02: 7000000 INFO @ Sun, 21 Jun 2020 22:42:05: 12000000 INFO @ Sun, 21 Jun 2020 22:42:10: 8000000 INFO @ Sun, 21 Jun 2020 22:42:14: 13000000 INFO @ Sun, 21 Jun 2020 22:42:19: 9000000 INFO @ Sun, 21 Jun 2020 22:42:21: 14000000 INFO @ Sun, 21 Jun 2020 22:42:27: 10000000 INFO @ Sun, 21 Jun 2020 22:42:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:42:29: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:42:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:42:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:42:33: #1 total tags in treatment: 15392211 INFO @ Sun, 21 Jun 2020 22:42:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:42:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:42:33: #1 tags after filtering in treatment: 15392205 INFO @ Sun, 21 Jun 2020 22:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:42:33: #1 finished! INFO @ Sun, 21 Jun 2020 22:42:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:42:34: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 22:42:34: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 22:42:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:42:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:42:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:42:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:42:35: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:42:35: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10_model.r INFO @ Sun, 21 Jun 2020 22:42:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:42:35: 11000000 INFO @ Sun, 21 Jun 2020 22:42:43: 12000000 INFO @ Sun, 21 Jun 2020 22:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.05_summits.bed INFO @ Sun, 21 Jun 2020 22:42:48: Done! pass1 - making usageList (623 chroms): 1 millis pass2 - checking and writing primary data (5884 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:42:51: 13000000 INFO @ Sun, 21 Jun 2020 22:42:59: 14000000 INFO @ Sun, 21 Jun 2020 22:43:06: 15000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:43:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:43:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:43:09: #1 total tags in treatment: 15392211 INFO @ Sun, 21 Jun 2020 22:43:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:43:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:43:10: #1 tags after filtering in treatment: 15392205 INFO @ Sun, 21 Jun 2020 22:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:43:10: #1 finished! INFO @ Sun, 21 Jun 2020 22:43:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:43:11: #2 number of paired peaks: 477 WARNING @ Sun, 21 Jun 2020 22:43:11: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Sun, 21 Jun 2020 22:43:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:43:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:43:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:43:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:43:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:43:11: #2 predicted fragment length is 151 bps INFO @ Sun, 21 Jun 2020 22:43:11: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 21 Jun 2020 22:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20_model.r INFO @ Sun, 21 Jun 2020 22:43:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:43:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:43:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:43:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.10_summits.bed INFO @ Sun, 21 Jun 2020 22:43:30: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (3547 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:43:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299243/SRX7299243.20_summits.bed INFO @ Sun, 21 Jun 2020 22:44:06: Done! pass1 - making usageList (263 chroms): 1 millis pass2 - checking and writing primary data (1699 records, 4 fields): 9 millis CompletedMACS2peakCalling