Job ID = 5721103 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,731,621 reads read : 19,463,242 reads written : 19,463,242 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: 00:21:08 9731621 reads; of these: 9731621 (100.00%) were paired; of these: 891838 (9.16%) aligned concordantly 0 times 6234070 (64.06%) aligned concordantly exactly 1 time 2605713 (26.78%) aligned concordantly >1 times ---- 891838 pairs aligned concordantly 0 times; of these: 294884 (33.06%) aligned discordantly 1 time ---- 596954 pairs aligned 0 times concordantly or discordantly; of these: 1193908 mates make up the pairs; of these: 688577 (57.67%) aligned 0 times 254495 (21.32%) aligned exactly 1 time 250836 (21.01%) aligned >1 times 96.46% overall alignment rate Time searching: 00:21:08 Overall time: 00:21:08 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] 696218 / 9075570 = 0.0767 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 05:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.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 05:08:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:08:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:03: 1000000 INFO @ Thu, 16 Apr 2020 05:09:08: 2000000 INFO @ Thu, 16 Apr 2020 05:09:14: 3000000 INFO @ Thu, 16 Apr 2020 05:09:19: 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 @ Thu, 16 Apr 2020 05:09:25: 5000000 INFO @ Thu, 16 Apr 2020 05:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.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 05:09:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:09:30: 6000000 INFO @ Thu, 16 Apr 2020 05:09:34: 1000000 INFO @ Thu, 16 Apr 2020 05:09:36: 7000000 INFO @ Thu, 16 Apr 2020 05:09:42: 2000000 INFO @ Thu, 16 Apr 2020 05:09:43: 8000000 INFO @ Thu, 16 Apr 2020 05:09:49: 9000000 INFO @ Thu, 16 Apr 2020 05:09:49: 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 @ Thu, 16 Apr 2020 05:09:55: 10000000 INFO @ Thu, 16 Apr 2020 05:09:57: 4000000 INFO @ Thu, 16 Apr 2020 05:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.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 05:09:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:09:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:10:01: 11000000 INFO @ Thu, 16 Apr 2020 05:10:04: 1000000 INFO @ Thu, 16 Apr 2020 05:10:04: 5000000 INFO @ Thu, 16 Apr 2020 05:10:07: 12000000 INFO @ Thu, 16 Apr 2020 05:10:11: 2000000 INFO @ Thu, 16 Apr 2020 05:10:12: 6000000 INFO @ Thu, 16 Apr 2020 05:10:14: 13000000 INFO @ Thu, 16 Apr 2020 05:10:18: 3000000 INFO @ Thu, 16 Apr 2020 05:10:19: 7000000 INFO @ Thu, 16 Apr 2020 05:10:20: 14000000 INFO @ Thu, 16 Apr 2020 05:10:24: 4000000 INFO @ Thu, 16 Apr 2020 05:10:26: 15000000 INFO @ Thu, 16 Apr 2020 05:10:27: 8000000 INFO @ Thu, 16 Apr 2020 05:10:31: 5000000 INFO @ Thu, 16 Apr 2020 05:10:32: 16000000 INFO @ Thu, 16 Apr 2020 05:10:34: 9000000 INFO @ Thu, 16 Apr 2020 05:10:38: 6000000 INFO @ Thu, 16 Apr 2020 05:10:38: 17000000 INFO @ Thu, 16 Apr 2020 05:10:41: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:10:41: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:10:41: #1 total tags in treatment: 8153165 INFO @ Thu, 16 Apr 2020 05:10:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:10:41: #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 05:10:41: #1 tags after filtering in treatment: 7697880 INFO @ Thu, 16 Apr 2020 05:10:41: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:10:41: #1 finished! INFO @ Thu, 16 Apr 2020 05:10:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:10:41: 10000000 INFO @ Thu, 16 Apr 2020 05:10:42: #2 number of paired peaks: 677 WARNING @ Thu, 16 Apr 2020 05:10:42: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Thu, 16 Apr 2020 05:10:42: start model_add_line... INFO @ Thu, 16 Apr 2020 05:10:42: start X-correlation... INFO @ Thu, 16 Apr 2020 05:10:42: end of X-cor INFO @ Thu, 16 Apr 2020 05:10:42: #2 finished! INFO @ Thu, 16 Apr 2020 05:10:42: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:10:42: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:10:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05_model.r INFO @ Thu, 16 Apr 2020 05:10:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:10:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:10:45: 7000000 INFO @ Thu, 16 Apr 2020 05:10:49: 11000000 INFO @ Thu, 16 Apr 2020 05:10:52: 8000000 INFO @ Thu, 16 Apr 2020 05:10:56: 12000000 INFO @ Thu, 16 Apr 2020 05:10:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:10:59: 9000000 INFO @ Thu, 16 Apr 2020 05:11:03: 13000000 INFO @ Thu, 16 Apr 2020 05:11:06: 10000000 INFO @ Thu, 16 Apr 2020 05:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.05_summits.bed INFO @ Thu, 16 Apr 2020 05:11:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1865 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:11:10: 14000000 INFO @ Thu, 16 Apr 2020 05:11:13: 11000000 INFO @ Thu, 16 Apr 2020 05:11:17: 15000000 INFO @ Thu, 16 Apr 2020 05:11:20: 12000000 INFO @ Thu, 16 Apr 2020 05:11:24: 16000000 INFO @ Thu, 16 Apr 2020 05:11:26: 13000000 INFO @ Thu, 16 Apr 2020 05:11:31: 17000000 INFO @ Thu, 16 Apr 2020 05:11:33: 14000000 INFO @ Thu, 16 Apr 2020 05:11:34: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:34: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:34: #1 total tags in treatment: 8153165 INFO @ Thu, 16 Apr 2020 05:11:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:34: #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 05:11:34: #1 tags after filtering in treatment: 7697880 INFO @ Thu, 16 Apr 2020 05:11:34: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:11:34: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:34: #2 number of paired peaks: 677 WARNING @ Thu, 16 Apr 2020 05:11:34: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Thu, 16 Apr 2020 05:11:34: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:34: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:34: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:34: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:34: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:11:34: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10_model.r INFO @ Thu, 16 Apr 2020 05:11:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:40: 15000000 INFO @ Thu, 16 Apr 2020 05:11:46: 16000000 INFO @ Thu, 16 Apr 2020 05:11:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:11:53: 17000000 INFO @ Thu, 16 Apr 2020 05:11:55: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:11:55: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:11:55: #1 total tags in treatment: 8153165 INFO @ Thu, 16 Apr 2020 05:11:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:11:55: #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 05:11:56: #1 tags after filtering in treatment: 7697880 INFO @ Thu, 16 Apr 2020 05:11:56: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:11:56: #1 finished! INFO @ Thu, 16 Apr 2020 05:11:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:11:56: #2 number of paired peaks: 677 WARNING @ Thu, 16 Apr 2020 05:11:56: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Thu, 16 Apr 2020 05:11:56: start model_add_line... INFO @ Thu, 16 Apr 2020 05:11:56: start X-correlation... INFO @ Thu, 16 Apr 2020 05:11:56: end of X-cor INFO @ Thu, 16 Apr 2020 05:11:56: #2 finished! INFO @ Thu, 16 Apr 2020 05:11:56: #2 predicted fragment length is 168 bps INFO @ Thu, 16 Apr 2020 05:11:56: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 16 Apr 2020 05:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20_model.r INFO @ Thu, 16 Apr 2020 05:11:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.10_summits.bed INFO @ Thu, 16 Apr 2020 05:11:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1065 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:12:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:12:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708247/SRX6708247.20_summits.bed INFO @ Thu, 16 Apr 2020 05:12:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。