Job ID = 5721100 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,047,084 reads read : 20,094,168 reads written : 20,094,168 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:20:44 10047084 reads; of these: 10047084 (100.00%) were paired; of these: 800893 (7.97%) aligned concordantly 0 times 6721290 (66.90%) aligned concordantly exactly 1 time 2524901 (25.13%) aligned concordantly >1 times ---- 800893 pairs aligned concordantly 0 times; of these: 252368 (31.51%) aligned discordantly 1 time ---- 548525 pairs aligned 0 times concordantly or discordantly; of these: 1097050 mates make up the pairs; of these: 604016 (55.06%) aligned 0 times 264609 (24.12%) aligned exactly 1 time 228425 (20.82%) aligned >1 times 96.99% overall alignment rate Time searching: 00:20:44 Overall time: 00:20:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 709721 / 9447208 = 0.0751 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 @ Thu, 16 Apr 2020 05:08:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.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 @ Thu, 16 Apr 2020 05:08:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:05: 1000000 INFO @ Thu, 16 Apr 2020 05:09:10: 2000000 INFO @ Thu, 16 Apr 2020 05:09:16: 3000000 INFO @ Thu, 16 Apr 2020 05:09:21: 4000000 INFO @ Thu, 16 Apr 2020 05:09:26: 5000000 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 @ Thu, 16 Apr 2020 05:09:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.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 @ Thu, 16 Apr 2020 05:09:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:32: 6000000 INFO @ Thu, 16 Apr 2020 05:09:35: 1000000 INFO @ Thu, 16 Apr 2020 05:09:38: 7000000 INFO @ Thu, 16 Apr 2020 05:09:41: 2000000 INFO @ Thu, 16 Apr 2020 05:09:44: 8000000 INFO @ Thu, 16 Apr 2020 05:09:47: 3000000 INFO @ Thu, 16 Apr 2020 05:09:50: 9000000 INFO @ Thu, 16 Apr 2020 05:09:53: 4000000 INFO @ Thu, 16 Apr 2020 05:09:56: 10000000 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 @ Thu, 16 Apr 2020 05:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.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 @ Thu, 16 Apr 2020 05:09:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:59: 5000000 INFO @ Thu, 16 Apr 2020 05:10:02: 11000000 INFO @ Thu, 16 Apr 2020 05:10:06: 1000000 INFO @ Thu, 16 Apr 2020 05:10:06: 6000000 INFO @ Thu, 16 Apr 2020 05:10:08: 12000000 INFO @ Thu, 16 Apr 2020 05:10:12: 7000000 INFO @ Thu, 16 Apr 2020 05:10:12: 2000000 INFO @ Thu, 16 Apr 2020 05:10:15: 13000000 INFO @ Thu, 16 Apr 2020 05:10:18: 8000000 INFO @ Thu, 16 Apr 2020 05:10:18: 3000000 INFO @ Thu, 16 Apr 2020 05:10:21: 14000000 INFO @ Thu, 16 Apr 2020 05:10:24: 9000000 INFO @ Thu, 16 Apr 2020 05:10:24: 4000000 INFO @ Thu, 16 Apr 2020 05:10:27: 15000000 INFO @ Thu, 16 Apr 2020 05:10:30: 5000000 INFO @ Thu, 16 Apr 2020 05:10:30: 10000000 INFO @ Thu, 16 Apr 2020 05:10:33: 16000000 INFO @ Thu, 16 Apr 2020 05:10:36: 6000000 INFO @ Thu, 16 Apr 2020 05:10:37: 11000000 INFO @ Thu, 16 Apr 2020 05:10:39: 17000000 INFO @ Thu, 16 Apr 2020 05:10:42: 7000000 INFO @ Thu, 16 Apr 2020 05:10:43: 12000000 INFO @ Thu, 16 Apr 2020 05:10:45: 18000000 INFO @ Thu, 16 Apr 2020 05:10:45: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:45: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:45: #1 total tags in treatment: 8546297 INFO @ Thu, 16 Apr 2020 05:10:45: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:10:46: #1 tags after filtering in treatment: 8080664 INFO @ Thu, 16 Apr 2020 05:10:46: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:10:46: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:46: #2 number of paired peaks: 665 WARNING @ Thu, 16 Apr 2020 05:10:46: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:46: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:46: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:46: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:46: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:46: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:10:46: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05_model.r INFO @ Thu, 16 Apr 2020 05:10:46: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:48: 8000000 INFO @ Thu, 16 Apr 2020 05:10:49: 13000000 INFO @ Thu, 16 Apr 2020 05:10:54: 9000000 INFO @ Thu, 16 Apr 2020 05:10:55: 14000000 INFO @ Thu, 16 Apr 2020 05:11:00: 10000000 INFO @ Thu, 16 Apr 2020 05:11:01: 15000000 INFO @ Thu, 16 Apr 2020 05:11:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:05: 11000000 INFO @ Thu, 16 Apr 2020 05:11:07: 16000000 INFO @ Thu, 16 Apr 2020 05:11:11: 12000000 INFO @ Thu, 16 Apr 2020 05:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.05_summits.bed INFO @ Thu, 16 Apr 2020 05:11:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1864 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:11:12: 17000000 INFO @ Thu, 16 Apr 2020 05:11:17: 13000000 INFO @ Thu, 16 Apr 2020 05:11:18: 18000000 INFO @ Thu, 16 Apr 2020 05:11:19: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:19: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:19: #1 total tags in treatment: 8546297 INFO @ Thu, 16 Apr 2020 05:11:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:11:19: #1 tags after filtering in treatment: 8080664 INFO @ Thu, 16 Apr 2020 05:11:19: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:11:19: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:20: #2 number of paired peaks: 665 WARNING @ Thu, 16 Apr 2020 05:11:20: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Thu, 16 Apr 2020 05:11:20: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:20: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:20: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:20: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:20: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:11:20: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10_model.r INFO @ Thu, 16 Apr 2020 05:11:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:23: 14000000 INFO @ Thu, 16 Apr 2020 05:11:29: 15000000 INFO @ Thu, 16 Apr 2020 05:11:34: 16000000 INFO @ Thu, 16 Apr 2020 05:11:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:40: 17000000 INFO @ Thu, 16 Apr 2020 05:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.10_summits.bed INFO @ Thu, 16 Apr 2020 05:11:46: Done! INFO @ Thu, 16 Apr 2020 05:11:46: 18000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1025 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:11:46: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:46: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:46: #1 total tags in treatment: 8546297 INFO @ Thu, 16 Apr 2020 05:11:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 05:11:46: #1 tags after filtering in treatment: 8080664 INFO @ Thu, 16 Apr 2020 05:11:46: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 05:11:46: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:46: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:47: #2 number of paired peaks: 665 WARNING @ Thu, 16 Apr 2020 05:11:47: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Thu, 16 Apr 2020 05:11:47: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:47: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:47: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:47: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:47: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:11:47: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20_model.r INFO @ Thu, 16 Apr 2020 05:11:47: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:12:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708246/SRX6708246.20_summits.bed INFO @ Thu, 16 Apr 2020 05:12:13: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。