Job ID = 5721131 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,070,771 reads read : 8,141,542 reads written : 8,141,542 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: 00:10:22 4070771 reads; of these: 4070771 (100.00%) were paired; of these: 1014116 (24.91%) aligned concordantly 0 times 2163558 (53.15%) aligned concordantly exactly 1 time 893097 (21.94%) aligned concordantly >1 times ---- 1014116 pairs aligned concordantly 0 times; of these: 513877 (50.67%) aligned discordantly 1 time ---- 500239 pairs aligned 0 times concordantly or discordantly; of these: 1000478 mates make up the pairs; of these: 385412 (38.52%) aligned 0 times 254486 (25.44%) aligned exactly 1 time 360580 (36.04%) aligned >1 times 95.27% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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_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] 220289 / 3551202 = 0.0620 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 05:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.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 05:25:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:25:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:25:35: 1000000 INFO @ Thu, 16 Apr 2020 05:25:40: 2000000 INFO @ Thu, 16 Apr 2020 05:25:45: 3000000 INFO @ Thu, 16 Apr 2020 05:25:51: 4000000 INFO @ Thu, 16 Apr 2020 05:25:56: 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 05:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.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 05:26:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:26:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:26:01: 6000000 INFO @ Thu, 16 Apr 2020 05:26:06: 1000000 INFO @ Thu, 16 Apr 2020 05:26:06: 7000000 INFO @ Thu, 16 Apr 2020 05:26:08: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:26:08: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:26:08: #1 total tags in treatment: 2849132 INFO @ Thu, 16 Apr 2020 05:26:08: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:26:08: #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 05:26:08: #1 tags after filtering in treatment: 2749189 INFO @ Thu, 16 Apr 2020 05:26:08: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:26:08: #1 finished! INFO @ Thu, 16 Apr 2020 05:26:08: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:26:08: #2 number of paired peaks: 657 WARNING @ Thu, 16 Apr 2020 05:26:08: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Thu, 16 Apr 2020 05:26:08: start model_add_line... INFO @ Thu, 16 Apr 2020 05:26:08: start X-correlation... INFO @ Thu, 16 Apr 2020 05:26:08: end of X-cor INFO @ Thu, 16 Apr 2020 05:26:08: #2 finished! INFO @ Thu, 16 Apr 2020 05:26:08: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:26:08: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05_model.r INFO @ Thu, 16 Apr 2020 05:26:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:26:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:26:11: 2000000 INFO @ Thu, 16 Apr 2020 05:26:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:26:17: 3000000 INFO @ Thu, 16 Apr 2020 05:26:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:26:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:26:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.05_summits.bed INFO @ Thu, 16 Apr 2020 05:26:17: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (967 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:26:22: 4000000 INFO @ Thu, 16 Apr 2020 05:26:27: 5000000 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 05:26:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.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 05:26:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:26:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:26:33: 6000000 INFO @ Thu, 16 Apr 2020 05:26:36: 1000000 INFO @ Thu, 16 Apr 2020 05:26:38: 7000000 INFO @ Thu, 16 Apr 2020 05:26:40: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:26:40: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:26:40: #1 total tags in treatment: 2849132 INFO @ Thu, 16 Apr 2020 05:26:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:26:40: #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 05:26:40: #1 tags after filtering in treatment: 2749189 INFO @ Thu, 16 Apr 2020 05:26:40: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:26:40: #1 finished! INFO @ Thu, 16 Apr 2020 05:26:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:26:40: #2 number of paired peaks: 657 WARNING @ Thu, 16 Apr 2020 05:26:40: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Thu, 16 Apr 2020 05:26:40: start model_add_line... INFO @ Thu, 16 Apr 2020 05:26:40: start X-correlation... INFO @ Thu, 16 Apr 2020 05:26:40: end of X-cor INFO @ Thu, 16 Apr 2020 05:26:40: #2 finished! INFO @ Thu, 16 Apr 2020 05:26:40: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:26:40: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10_model.r INFO @ Thu, 16 Apr 2020 05:26:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:26:41: 2000000 INFO @ Thu, 16 Apr 2020 05:26:46: 3000000 INFO @ Thu, 16 Apr 2020 05:26:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.10_summits.bed INFO @ Thu, 16 Apr 2020 05:26:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (497 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:26:52: 4000000 INFO @ Thu, 16 Apr 2020 05:26:57: 5000000 INFO @ Thu, 16 Apr 2020 05:27:03: 6000000 INFO @ Thu, 16 Apr 2020 05:27:08: 7000000 INFO @ Thu, 16 Apr 2020 05:27:10: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:27:10: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:27:10: #1 total tags in treatment: 2849132 INFO @ Thu, 16 Apr 2020 05:27:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:27:10: #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 05:27:10: #1 tags after filtering in treatment: 2749189 INFO @ Thu, 16 Apr 2020 05:27:10: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 05:27:10: #1 finished! INFO @ Thu, 16 Apr 2020 05:27:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:27:10: #2 number of paired peaks: 657 WARNING @ Thu, 16 Apr 2020 05:27:10: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Thu, 16 Apr 2020 05:27:10: start model_add_line... INFO @ Thu, 16 Apr 2020 05:27:10: start X-correlation... INFO @ Thu, 16 Apr 2020 05:27:10: end of X-cor INFO @ Thu, 16 Apr 2020 05:27:10: #2 finished! INFO @ Thu, 16 Apr 2020 05:27:10: #2 predicted fragment length is 179 bps INFO @ Thu, 16 Apr 2020 05:27:10: #2 alternative fragment length(s) may be 179 bps INFO @ Thu, 16 Apr 2020 05:27:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20_model.r INFO @ Thu, 16 Apr 2020 05:27:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:27:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:27:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708273/SRX6708273.20_summits.bed INFO @ Thu, 16 Apr 2020 05:27:19: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (259 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。