Job ID = 5790905 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,867,659 reads read : 3,735,318 reads written : 3,735,318 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: 00:03:12 1867659 reads; of these: 1867659 (100.00%) were paired; of these: 30149 (1.61%) aligned concordantly 0 times 891550 (47.74%) aligned concordantly exactly 1 time 945960 (50.65%) aligned concordantly >1 times ---- 30149 pairs aligned concordantly 0 times; of these: 1996 (6.62%) aligned discordantly 1 time ---- 28153 pairs aligned 0 times concordantly or discordantly; of these: 56306 mates make up the pairs; of these: 15969 (28.36%) aligned 0 times 9605 (17.06%) aligned exactly 1 time 30732 (54.58%) aligned >1 times 99.57% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:13 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] 756564 / 1803076 = 0.4196 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 08:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.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 08:08:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:08:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:08:47: 1000000 INFO @ Wed, 22 Apr 2020 08:08:53: 2000000 INFO @ Wed, 22 Apr 2020 08:08:54: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:08:54: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:08:54: #1 total tags in treatment: 1082073 INFO @ Wed, 22 Apr 2020 08:08:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:08:54: #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 08:08:55: #1 tags after filtering in treatment: 783420 INFO @ Wed, 22 Apr 2020 08:08:55: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 08:08:55: #1 finished! INFO @ Wed, 22 Apr 2020 08:08:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:08:55: #2 number of paired peaks: 176 WARNING @ Wed, 22 Apr 2020 08:08:55: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 22 Apr 2020 08:08:55: start model_add_line... INFO @ Wed, 22 Apr 2020 08:08:55: start X-correlation... INFO @ Wed, 22 Apr 2020 08:08:55: end of X-cor INFO @ Wed, 22 Apr 2020 08:08:55: #2 finished! INFO @ Wed, 22 Apr 2020 08:08:55: #2 predicted fragment length is 162 bps INFO @ Wed, 22 Apr 2020 08:08:55: #2 alternative fragment length(s) may be 162 bps INFO @ Wed, 22 Apr 2020 08:08:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05_model.r INFO @ Wed, 22 Apr 2020 08:08:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:08:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:08:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:08:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:08:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:08:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.05_summits.bed INFO @ Wed, 22 Apr 2020 08:08:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1354 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 08:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.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 08:09:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:09:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:09:15: 1000000 INFO @ Wed, 22 Apr 2020 08:09:20: 2000000 INFO @ Wed, 22 Apr 2020 08:09:21: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:09:21: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:09:21: #1 total tags in treatment: 1082073 INFO @ Wed, 22 Apr 2020 08:09:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:09:21: #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 08:09:21: #1 tags after filtering in treatment: 783420 INFO @ Wed, 22 Apr 2020 08:09:21: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 08:09:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:09:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:09:22: #2 number of paired peaks: 176 WARNING @ Wed, 22 Apr 2020 08:09:22: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 22 Apr 2020 08:09:22: start model_add_line... INFO @ Wed, 22 Apr 2020 08:09:22: start X-correlation... INFO @ Wed, 22 Apr 2020 08:09:22: end of X-cor INFO @ Wed, 22 Apr 2020 08:09:22: #2 finished! INFO @ Wed, 22 Apr 2020 08:09:22: #2 predicted fragment length is 162 bps INFO @ Wed, 22 Apr 2020 08:09:22: #2 alternative fragment length(s) may be 162 bps INFO @ Wed, 22 Apr 2020 08:09:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10_model.r INFO @ Wed, 22 Apr 2020 08:09:22: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:09:24: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.10_summits.bed INFO @ Wed, 22 Apr 2020 08:09:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (656 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 08:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.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 08:09:40: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:09:40: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:09:46: 1000000 INFO @ Wed, 22 Apr 2020 08:09:52: 2000000 INFO @ Wed, 22 Apr 2020 08:09:53: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 08:09:53: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 08:09:53: #1 total tags in treatment: 1082073 INFO @ Wed, 22 Apr 2020 08:09:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:09:53: #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 08:09:53: #1 tags after filtering in treatment: 783420 INFO @ Wed, 22 Apr 2020 08:09:53: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 08:09:53: #1 finished! INFO @ Wed, 22 Apr 2020 08:09:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:09:53: #2 number of paired peaks: 176 WARNING @ Wed, 22 Apr 2020 08:09:53: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Wed, 22 Apr 2020 08:09:53: start model_add_line... INFO @ Wed, 22 Apr 2020 08:09:53: start X-correlation... INFO @ Wed, 22 Apr 2020 08:09:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:09:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:09:53: #2 predicted fragment length is 162 bps INFO @ Wed, 22 Apr 2020 08:09:53: #2 alternative fragment length(s) may be 162 bps INFO @ Wed, 22 Apr 2020 08:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20_model.r INFO @ Wed, 22 Apr 2020 08:09:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:09:55: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5550832/SRX5550832.20_summits.bed INFO @ Wed, 22 Apr 2020 08:09:56: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (278 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。