Job ID = 5791254 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,969,179 reads read : 9,938,358 reads written : 9,938,358 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: 00:03:58 4969179 reads; of these: 4969179 (100.00%) were paired; of these: 1376815 (27.71%) aligned concordantly 0 times 1849482 (37.22%) aligned concordantly exactly 1 time 1742882 (35.07%) aligned concordantly >1 times ---- 1376815 pairs aligned concordantly 0 times; of these: 308653 (22.42%) aligned discordantly 1 time ---- 1068162 pairs aligned 0 times concordantly or discordantly; of these: 2136324 mates make up the pairs; of these: 316673 (14.82%) aligned 0 times 647668 (30.32%) aligned exactly 1 time 1171983 (54.86%) aligned >1 times 96.81% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 2403783 / 3611616 = 0.6656 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 09:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.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 09:19:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:19:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:19:09: 1000000 INFO @ Wed, 22 Apr 2020 09:19:13: 2000000 INFO @ Wed, 22 Apr 2020 09:19:17: 3000000 INFO @ Wed, 22 Apr 2020 09:19:21: 4000000 INFO @ Wed, 22 Apr 2020 09:19:25: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:25: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:25: #1 total tags in treatment: 1193211 INFO @ Wed, 22 Apr 2020 09:19:25: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:25: #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 09:19:25: #1 tags after filtering in treatment: 559871 INFO @ Wed, 22 Apr 2020 09:19:25: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 22 Apr 2020 09:19:25: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:25: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:25: #2 number of paired peaks: 698 WARNING @ Wed, 22 Apr 2020 09:19:25: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:25: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:25: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:25: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:25: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:25: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:19:25: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 09:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05_model.r INFO @ Wed, 22 Apr 2020 09:19:25: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.05_summits.bed INFO @ Wed, 22 Apr 2020 09:19:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2197 records, 4 fields): 4 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 09:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.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 09:19:34: #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 09:19:47: 3000000 INFO @ Wed, 22 Apr 2020 09:19:51: 4000000 INFO @ Wed, 22 Apr 2020 09:19:54: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:54: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:54: #1 total tags in treatment: 1193211 INFO @ Wed, 22 Apr 2020 09:19:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:54: #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 09:19:54: #1 tags after filtering in treatment: 559871 INFO @ Wed, 22 Apr 2020 09:19:54: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 22 Apr 2020 09:19:54: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:55: #2 number of paired peaks: 698 WARNING @ Wed, 22 Apr 2020 09:19:55: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:55: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:55: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:55: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:55: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:55: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:19:55: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 09:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10_model.r INFO @ Wed, 22 Apr 2020 09:19:55: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.10_summits.bed INFO @ Wed, 22 Apr 2020 09:19:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1409 records, 4 fields): 4 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 09:20:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.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 09:20:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:20:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:20:09: 1000000 INFO @ Wed, 22 Apr 2020 09:20:14: 2000000 INFO @ Wed, 22 Apr 2020 09:20:19: 3000000 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 09:20:24: 4000000 INFO @ Wed, 22 Apr 2020 09:20:28: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:20:28: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:20:28: #1 total tags in treatment: 1193211 INFO @ Wed, 22 Apr 2020 09:20:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:20:28: #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 09:20:28: #1 tags after filtering in treatment: 559871 INFO @ Wed, 22 Apr 2020 09:20:28: #1 Redundant rate of treatment: 0.53 INFO @ Wed, 22 Apr 2020 09:20:28: #1 finished! INFO @ Wed, 22 Apr 2020 09:20:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:20:28: #2 number of paired peaks: 698 WARNING @ Wed, 22 Apr 2020 09:20:28: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Wed, 22 Apr 2020 09:20:28: start model_add_line... INFO @ Wed, 22 Apr 2020 09:20:28: start X-correlation... INFO @ Wed, 22 Apr 2020 09:20:28: end of X-cor INFO @ Wed, 22 Apr 2020 09:20:28: #2 finished! INFO @ Wed, 22 Apr 2020 09:20:28: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:20:28: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 09:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20_model.r INFO @ Wed, 22 Apr 2020 09:20:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:20:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:20:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:20:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:20:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388395/SRX7388395.20_summits.bed INFO @ Wed, 22 Apr 2020 09:20:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 1 millis CompletedMACS2peakCalling