Job ID = 5791259 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,735,531 reads read : 11,471,062 reads written : 11,471,062 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: 00:02:29 5735531 reads; of these: 5735531 (100.00%) were paired; of these: 502256 (8.76%) aligned concordantly 0 times 4494775 (78.37%) aligned concordantly exactly 1 time 738500 (12.88%) aligned concordantly >1 times ---- 502256 pairs aligned concordantly 0 times; of these: 150874 (30.04%) aligned discordantly 1 time ---- 351382 pairs aligned 0 times concordantly or discordantly; of these: 702764 mates make up the pairs; of these: 519624 (73.94%) aligned 0 times 111440 (15.86%) aligned exactly 1 time 71700 (10.20%) aligned >1 times 95.47% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 1783885 / 5249268 = 0.3398 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 09:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.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 09:19:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:39: 1000000 INFO @ Wed, 22 Apr 2020 09:19:43: 2000000 INFO @ Wed, 22 Apr 2020 09:19:48: 3000000 INFO @ Wed, 22 Apr 2020 09:19:53: 4000000 INFO @ Wed, 22 Apr 2020 09:19:58: 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 @ Wed, 22 Apr 2020 09:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.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 09:20:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:20:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:20:02: 6000000 INFO @ Wed, 22 Apr 2020 09:20:07: 1000000 INFO @ Wed, 22 Apr 2020 09:20:07: 7000000 INFO @ Wed, 22 Apr 2020 09:20:09: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:09: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:09: #1 total tags in treatment: 3450772 INFO @ Wed, 22 Apr 2020 09:20:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:09: #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 09:20:09: #1 tags after filtering in treatment: 1711613 INFO @ Wed, 22 Apr 2020 09:20:09: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:20:09: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:09: #2 number of paired peaks: 223 WARNING @ Wed, 22 Apr 2020 09:20:09: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:09: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:09: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:09: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:09: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:09: #2 predicted fragment length is 69 bps INFO @ Wed, 22 Apr 2020 09:20:09: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 22 Apr 2020 09:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05_model.r INFO @ Wed, 22 Apr 2020 09:20:10: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:12: 2000000 INFO @ Wed, 22 Apr 2020 09:20:13: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.05_summits.bed INFO @ Wed, 22 Apr 2020 09:20:15: Done! INFO @ Wed, 22 Apr 2020 09:20:17: 3000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (3781 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:20:22: 4000000 INFO @ Wed, 22 Apr 2020 09:20:26: 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 @ Wed, 22 Apr 2020 09:20:31: 6000000 INFO @ Wed, 22 Apr 2020 09:20:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.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 09:20:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:20:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:20:36: 7000000 INFO @ Wed, 22 Apr 2020 09:20:37: 1000000 INFO @ Wed, 22 Apr 2020 09:20:38: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:38: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:38: #1 total tags in treatment: 3450772 INFO @ Wed, 22 Apr 2020 09:20:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:38: #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 09:20:38: #1 tags after filtering in treatment: 1711613 INFO @ Wed, 22 Apr 2020 09:20:38: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:20:38: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:38: #2 number of paired peaks: 223 WARNING @ Wed, 22 Apr 2020 09:20:38: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:38: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:38: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:38: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:38: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:38: #2 predicted fragment length is 69 bps INFO @ Wed, 22 Apr 2020 09:20:38: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 22 Apr 2020 09:20:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10_model.r INFO @ Wed, 22 Apr 2020 09:20:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:42: 2000000 INFO @ Wed, 22 Apr 2020 09:20:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.10_summits.bed INFO @ Wed, 22 Apr 2020 09:20:44: Done! INFO @ Wed, 22 Apr 2020 09:20:46: 3000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2224 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:20:51: 4000000 INFO @ Wed, 22 Apr 2020 09:20:56: 5000000 INFO @ Wed, 22 Apr 2020 09:21:01: 6000000 INFO @ Wed, 22 Apr 2020 09:21:05: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:21:07: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:21:07: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:21:07: #1 total tags in treatment: 3450772 INFO @ Wed, 22 Apr 2020 09:21:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:21:07: #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 09:21:07: #1 tags after filtering in treatment: 1711613 INFO @ Wed, 22 Apr 2020 09:21:07: #1 Redundant rate of treatment: 0.50 INFO @ Wed, 22 Apr 2020 09:21:07: #1 finished! INFO @ Wed, 22 Apr 2020 09:21:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:21:07: #2 number of paired peaks: 223 WARNING @ Wed, 22 Apr 2020 09:21:07: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Wed, 22 Apr 2020 09:21:07: start model_add_line... INFO @ Wed, 22 Apr 2020 09:21:07: start X-correlation... INFO @ Wed, 22 Apr 2020 09:21:07: end of X-cor INFO @ Wed, 22 Apr 2020 09:21:07: #2 finished! INFO @ Wed, 22 Apr 2020 09:21:07: #2 predicted fragment length is 69 bps INFO @ Wed, 22 Apr 2020 09:21:07: #2 alternative fragment length(s) may be 3,69 bps INFO @ Wed, 22 Apr 2020 09:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20_model.r INFO @ Wed, 22 Apr 2020 09:21:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:21:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:21:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:21:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:21:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388400/SRX7388400.20_summits.bed INFO @ Wed, 22 Apr 2020 09:21:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 1 millis CompletedMACS2peakCalling