Job ID = 5791242 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,568,529 reads read : 7,137,058 reads written : 7,137,058 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: 00:01:33 3568529 reads; of these: 3568529 (100.00%) were paired; of these: 307523 (8.62%) aligned concordantly 0 times 2610266 (73.15%) aligned concordantly exactly 1 time 650740 (18.24%) aligned concordantly >1 times ---- 307523 pairs aligned concordantly 0 times; of these: 56231 (18.29%) aligned discordantly 1 time ---- 251292 pairs aligned 0 times concordantly or discordantly; of these: 502584 mates make up the pairs; of these: 379560 (75.52%) aligned 0 times 70754 (14.08%) aligned exactly 1 time 52270 (10.40%) aligned >1 times 94.68% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1044800 / 3281218 = 0.3184 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 @ Wed, 22 Apr 2020 09:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:14:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:14:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:14:08: 1000000 INFO @ Wed, 22 Apr 2020 09:14:13: 2000000 INFO @ Wed, 22 Apr 2020 09:14:17: 3000000 INFO @ Wed, 22 Apr 2020 09:14:21: 4000000 INFO @ Wed, 22 Apr 2020 09:14:24: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:14:24: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:14:24: #1 total tags in treatment: 2218817 INFO @ Wed, 22 Apr 2020 09:14:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:14:24: #1 tags after filtering in treatment: 1368046 INFO @ Wed, 22 Apr 2020 09:14:24: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:14:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:24: #2 number of paired peaks: 315 WARNING @ Wed, 22 Apr 2020 09:14:24: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 22 Apr 2020 09:14:24: start model_add_line... INFO @ Wed, 22 Apr 2020 09:14:24: start X-correlation... INFO @ Wed, 22 Apr 2020 09:14:24: end of X-cor INFO @ Wed, 22 Apr 2020 09:14:24: #2 finished! INFO @ Wed, 22 Apr 2020 09:14:24: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:14:24: #2 alternative fragment length(s) may be 4,81,105 bps INFO @ Wed, 22 Apr 2020 09:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05_model.r INFO @ Wed, 22 Apr 2020 09:14:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:14:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.05_summits.bed INFO @ Wed, 22 Apr 2020 09:14:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1335 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 09:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:14:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:14:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:14:38: 1000000 INFO @ Wed, 22 Apr 2020 09:14:42: 2000000 INFO @ Wed, 22 Apr 2020 09:14:46: 3000000 INFO @ Wed, 22 Apr 2020 09:14:51: 4000000 INFO @ Wed, 22 Apr 2020 09:14:53: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:14:53: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:14:53: #1 total tags in treatment: 2218817 INFO @ Wed, 22 Apr 2020 09:14:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:14:53: #1 tags after filtering in treatment: 1368046 INFO @ Wed, 22 Apr 2020 09:14:53: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:14:53: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:53: #2 number of paired peaks: 315 WARNING @ Wed, 22 Apr 2020 09:14:53: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 22 Apr 2020 09:14:53: start model_add_line... INFO @ Wed, 22 Apr 2020 09:14:53: start X-correlation... INFO @ Wed, 22 Apr 2020 09:14:53: end of X-cor INFO @ Wed, 22 Apr 2020 09:14:53: #2 finished! INFO @ Wed, 22 Apr 2020 09:14:53: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:14:53: #2 alternative fragment length(s) may be 4,81,105 bps INFO @ Wed, 22 Apr 2020 09:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10_model.r INFO @ Wed, 22 Apr 2020 09:14:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:14:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:14:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:14:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:14:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.10_summits.bed INFO @ Wed, 22 Apr 2020 09:14:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (885 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 09:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:15:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:15:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:15:08: 1000000 INFO @ Wed, 22 Apr 2020 09:15:12: 2000000 INFO @ Wed, 22 Apr 2020 09:15:17: 3000000 INFO @ Wed, 22 Apr 2020 09:15:21: 4000000 INFO @ Wed, 22 Apr 2020 09:15:24: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:15:24: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:15:24: #1 total tags in treatment: 2218817 INFO @ Wed, 22 Apr 2020 09:15:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:15:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:15:24: #1 tags after filtering in treatment: 1368046 INFO @ Wed, 22 Apr 2020 09:15:24: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:15:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:15:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:15:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:15:24: #2 number of paired peaks: 315 WARNING @ Wed, 22 Apr 2020 09:15:24: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Wed, 22 Apr 2020 09:15:24: start model_add_line... INFO @ Wed, 22 Apr 2020 09:15:24: start X-correlation... INFO @ Wed, 22 Apr 2020 09:15:24: end of X-cor INFO @ Wed, 22 Apr 2020 09:15:24: #2 finished! INFO @ Wed, 22 Apr 2020 09:15:24: #2 predicted fragment length is 81 bps INFO @ Wed, 22 Apr 2020 09:15:24: #2 alternative fragment length(s) may be 4,81,105 bps INFO @ Wed, 22 Apr 2020 09:15:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20_model.r INFO @ Wed, 22 Apr 2020 09:15:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:15:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:15:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388385/SRX7388385.20_summits.bed INFO @ Wed, 22 Apr 2020 09:15:28: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (405 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。