Job ID = 5791255 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,196,394 reads read : 10,392,788 reads written : 10,392,788 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: 00:01:59 5196394 reads; of these: 5196394 (100.00%) were paired; of these: 746236 (14.36%) aligned concordantly 0 times 3559371 (68.50%) aligned concordantly exactly 1 time 890787 (17.14%) aligned concordantly >1 times ---- 746236 pairs aligned concordantly 0 times; of these: 66713 (8.94%) aligned discordantly 1 time ---- 679523 pairs aligned 0 times concordantly or discordantly; of these: 1359046 mates make up the pairs; of these: 1219783 (89.75%) aligned 0 times 83447 (6.14%) aligned exactly 1 time 55816 (4.11%) aligned >1 times 88.26% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 1751021 / 4464261 = 0.3922 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 09:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.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 09:17:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:17:31: 1000000 INFO @ Wed, 22 Apr 2020 09:17:34: 2000000 INFO @ Wed, 22 Apr 2020 09:17:38: 3000000 INFO @ Wed, 22 Apr 2020 09:17:42: 4000000 INFO @ Wed, 22 Apr 2020 09:17:45: 5000000 INFO @ Wed, 22 Apr 2020 09:17:48: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:17:48: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:17:48: #1 total tags in treatment: 2700624 INFO @ Wed, 22 Apr 2020 09:17:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:17:48: #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 09:17:48: #1 tags after filtering in treatment: 1344088 INFO @ Wed, 22 Apr 2020 09:17:48: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:17:48: #1 finished! INFO @ Wed, 22 Apr 2020 09:17:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:17:48: #2 number of paired peaks: 522 WARNING @ Wed, 22 Apr 2020 09:17:48: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Wed, 22 Apr 2020 09:17:48: start model_add_line... INFO @ Wed, 22 Apr 2020 09:17:48: start X-correlation... INFO @ Wed, 22 Apr 2020 09:17:48: end of X-cor INFO @ Wed, 22 Apr 2020 09:17:48: #2 finished! INFO @ Wed, 22 Apr 2020 09:17:48: #2 predicted fragment length is 57 bps INFO @ Wed, 22 Apr 2020 09:17:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 22 Apr 2020 09:17:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05_model.r INFO @ Wed, 22 Apr 2020 09:17:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:17:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:17:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.05_summits.bed INFO @ Wed, 22 Apr 2020 09:17:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2606 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 09:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.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 09:17:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:01: 1000000 INFO @ Wed, 22 Apr 2020 09:18:04: 2000000 INFO @ Wed, 22 Apr 2020 09:18:08: 3000000 INFO @ Wed, 22 Apr 2020 09:18:12: 4000000 INFO @ Wed, 22 Apr 2020 09:18:15: 5000000 INFO @ Wed, 22 Apr 2020 09:18:18: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:18: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:18: #1 total tags in treatment: 2700624 INFO @ Wed, 22 Apr 2020 09:18:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:18: #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 09:18:18: #1 tags after filtering in treatment: 1344088 INFO @ Wed, 22 Apr 2020 09:18:18: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:18:18: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:18: #2 number of paired peaks: 522 WARNING @ Wed, 22 Apr 2020 09:18:18: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:18: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:18: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:18: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:18: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:18: #2 predicted fragment length is 57 bps INFO @ Wed, 22 Apr 2020 09:18:18: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 22 Apr 2020 09:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10_model.r INFO @ Wed, 22 Apr 2020 09:18:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.10_summits.bed INFO @ Wed, 22 Apr 2020 09:18:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1712 records, 4 fields): 3 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 09:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.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 09:18:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:31: 1000000 INFO @ Wed, 22 Apr 2020 09:18:35: 2000000 INFO @ Wed, 22 Apr 2020 09:18:38: 3000000 INFO @ Wed, 22 Apr 2020 09:18:42: 4000000 INFO @ Wed, 22 Apr 2020 09:18:45: 5000000 INFO @ Wed, 22 Apr 2020 09:18:48: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:48: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:48: #1 total tags in treatment: 2700624 INFO @ Wed, 22 Apr 2020 09:18:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:48: #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 09:18:48: #1 tags after filtering in treatment: 1344088 INFO @ Wed, 22 Apr 2020 09:18:48: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:18:48: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:48: #2 number of paired peaks: 522 WARNING @ Wed, 22 Apr 2020 09:18:48: Fewer paired peaks (522) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 522 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:48: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:48: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:48: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:48: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:48: #2 predicted fragment length is 57 bps INFO @ Wed, 22 Apr 2020 09:18:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Wed, 22 Apr 2020 09:18:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20_model.r INFO @ Wed, 22 Apr 2020 09:18:48: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388396/SRX7388396.20_summits.bed INFO @ Wed, 22 Apr 2020 09:18:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (759 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。