Job ID = 5791228 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 857,906 reads read : 1,715,812 reads written : 1,715,812 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: 00:00:41 857906 reads; of these: 857906 (100.00%) were paired; of these: 347067 (40.46%) aligned concordantly 0 times 455056 (53.04%) aligned concordantly exactly 1 time 55783 (6.50%) aligned concordantly >1 times ---- 347067 pairs aligned concordantly 0 times; of these: 15368 (4.43%) aligned discordantly 1 time ---- 331699 pairs aligned 0 times concordantly or discordantly; of these: 663398 mates make up the pairs; of these: 586863 (88.46%) aligned 0 times 71151 (10.73%) aligned exactly 1 time 5384 (0.81%) aligned >1 times 65.80% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 451411 / 525144 = 0.8596 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 09:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.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 09:08:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:08:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:08:54: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:08:54: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:08:54: #1 total tags in treatment: 70804 INFO @ Wed, 22 Apr 2020 09:08:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:08:54: #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 09:08:54: #1 tags after filtering in treatment: 66762 INFO @ Wed, 22 Apr 2020 09:08:54: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 09:08:54: #1 finished! INFO @ Wed, 22 Apr 2020 09:08:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:08:54: #2 number of paired peaks: 421 WARNING @ Wed, 22 Apr 2020 09:08:54: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 22 Apr 2020 09:08:54: start model_add_line... INFO @ Wed, 22 Apr 2020 09:08:54: start X-correlation... INFO @ Wed, 22 Apr 2020 09:08:54: end of X-cor INFO @ Wed, 22 Apr 2020 09:08:54: #2 finished! INFO @ Wed, 22 Apr 2020 09:08:54: #2 predicted fragment length is 265 bps INFO @ Wed, 22 Apr 2020 09:08:54: #2 alternative fragment length(s) may be 3,217,265,293,550,586 bps INFO @ Wed, 22 Apr 2020 09:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05_model.r INFO @ Wed, 22 Apr 2020 09:08:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:08:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.05_summits.bed INFO @ Wed, 22 Apr 2020 09:08:54: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 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 09:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.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 09:09:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:09:24: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:09:24: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:09:24: #1 total tags in treatment: 70804 INFO @ Wed, 22 Apr 2020 09:09:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:24: #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 09:09:24: #1 tags after filtering in treatment: 66762 INFO @ Wed, 22 Apr 2020 09:09:24: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 09:09:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:24: #2 number of paired peaks: 421 WARNING @ Wed, 22 Apr 2020 09:09:24: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 22 Apr 2020 09:09:24: start model_add_line... INFO @ Wed, 22 Apr 2020 09:09:24: start X-correlation... INFO @ Wed, 22 Apr 2020 09:09:24: end of X-cor INFO @ Wed, 22 Apr 2020 09:09:24: #2 finished! INFO @ Wed, 22 Apr 2020 09:09:24: #2 predicted fragment length is 265 bps INFO @ Wed, 22 Apr 2020 09:09:24: #2 alternative fragment length(s) may be 3,217,265,293,550,586 bps INFO @ Wed, 22 Apr 2020 09:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10_model.r INFO @ Wed, 22 Apr 2020 09:09:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:09:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.10_summits.bed INFO @ Wed, 22 Apr 2020 09:09:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 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 09:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.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 09:09:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:09:53: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:09:54: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:09:54: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:09:54: #1 total tags in treatment: 70804 INFO @ Wed, 22 Apr 2020 09:09:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:09:54: #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 09:09:54: #1 tags after filtering in treatment: 66762 INFO @ Wed, 22 Apr 2020 09:09:54: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 09:09:54: #1 finished! INFO @ Wed, 22 Apr 2020 09:09:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:09:54: #2 number of paired peaks: 421 WARNING @ Wed, 22 Apr 2020 09:09:54: Fewer paired peaks (421) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 421 pairs to build model! INFO @ Wed, 22 Apr 2020 09:09:54: start model_add_line... INFO @ Wed, 22 Apr 2020 09:09:54: start X-correlation... INFO @ Wed, 22 Apr 2020 09:09:54: end of X-cor INFO @ Wed, 22 Apr 2020 09:09:54: #2 finished! INFO @ Wed, 22 Apr 2020 09:09:54: #2 predicted fragment length is 265 bps INFO @ Wed, 22 Apr 2020 09:09:54: #2 alternative fragment length(s) may be 3,217,265,293,550,586 bps INFO @ Wed, 22 Apr 2020 09:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20_model.r INFO @ Wed, 22 Apr 2020 09:09:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:09:54: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7255994/SRX7255994.20_summits.bed INFO @ Wed, 22 Apr 2020 09:09:54: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling