Job ID = 5791241 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,190,689 reads read : 6,381,378 reads written : 6,381,378 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: 00:01:05 3190689 reads; of these: 3190689 (100.00%) were paired; of these: 304431 (9.54%) aligned concordantly 0 times 2312679 (72.48%) aligned concordantly exactly 1 time 573579 (17.98%) aligned concordantly >1 times ---- 304431 pairs aligned concordantly 0 times; of these: 52256 (17.17%) aligned discordantly 1 time ---- 252175 pairs aligned 0 times concordantly or discordantly; of these: 504350 mates make up the pairs; of these: 415418 (82.37%) aligned 0 times 47316 (9.38%) aligned exactly 1 time 41616 (8.25%) aligned >1 times 93.49% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 751615 / 2918943 = 0.2575 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 09:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.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 09:12:52: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:12:52: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:12:57: 1000000 INFO @ Wed, 22 Apr 2020 09:13:01: 2000000 INFO @ Wed, 22 Apr 2020 09:13:06: 3000000 INFO @ Wed, 22 Apr 2020 09:13:10: 4000000 INFO @ Wed, 22 Apr 2020 09:13:12: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:13:12: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:13:12: #1 total tags in treatment: 2138666 INFO @ Wed, 22 Apr 2020 09:13:12: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:13:12: #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 09:13:13: #1 tags after filtering in treatment: 1415754 INFO @ Wed, 22 Apr 2020 09:13:13: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:13:13: #1 finished! INFO @ Wed, 22 Apr 2020 09:13:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:13:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:13:13: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:13:13: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:13:13: start model_add_line... INFO @ Wed, 22 Apr 2020 09:13:13: start X-correlation... INFO @ Wed, 22 Apr 2020 09:13:13: end of X-cor INFO @ Wed, 22 Apr 2020 09:13:13: #2 finished! INFO @ Wed, 22 Apr 2020 09:13:13: #2 predicted fragment length is 113 bps INFO @ Wed, 22 Apr 2020 09:13:13: #2 alternative fragment length(s) may be 88,113,154,192,199,213,242,298,332,410,420,469,475,536,550,563,594 bps INFO @ Wed, 22 Apr 2020 09:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05_model.r INFO @ Wed, 22 Apr 2020 09:13:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:13:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.05_summits.bed INFO @ Wed, 22 Apr 2020 09:13:17: Done! 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 pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 0 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.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 09:13:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:24: 1000000 INFO @ Wed, 22 Apr 2020 09:13:29: 2000000 INFO @ Wed, 22 Apr 2020 09:13:33: 3000000 INFO @ Wed, 22 Apr 2020 09:13:38: 4000000 INFO @ Wed, 22 Apr 2020 09:13:40: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:13:40: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:13:40: #1 total tags in treatment: 2138666 INFO @ Wed, 22 Apr 2020 09:13:40: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:13:40: #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 09:13:40: #1 tags after filtering in treatment: 1415754 INFO @ Wed, 22 Apr 2020 09:13:40: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:13:40: #1 finished! INFO @ Wed, 22 Apr 2020 09:13:40: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:13:40: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:13:40: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:13:40: start model_add_line... INFO @ Wed, 22 Apr 2020 09:13:40: start X-correlation... INFO @ Wed, 22 Apr 2020 09:13:40: end of X-cor INFO @ Wed, 22 Apr 2020 09:13:40: #2 finished! INFO @ Wed, 22 Apr 2020 09:13:40: #2 predicted fragment length is 113 bps INFO @ Wed, 22 Apr 2020 09:13:40: #2 alternative fragment length(s) may be 88,113,154,192,199,213,242,298,332,410,420,469,475,536,550,563,594 bps INFO @ Wed, 22 Apr 2020 09:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10_model.r INFO @ Wed, 22 Apr 2020 09:13:40: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:13:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:13:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:13:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:13:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.10_summits.bed INFO @ Wed, 22 Apr 2020 09:13:44: Done! 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 pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.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 09:13:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:13:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:13:55: 1000000 INFO @ Wed, 22 Apr 2020 09:14:00: 2000000 INFO @ Wed, 22 Apr 2020 09:14:04: 3000000 INFO @ Wed, 22 Apr 2020 09:14:09: 4000000 INFO @ Wed, 22 Apr 2020 09:14:11: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:14:11: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:14:11: #1 total tags in treatment: 2138666 INFO @ Wed, 22 Apr 2020 09:14:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:14:11: #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 09:14:11: #1 tags after filtering in treatment: 1415754 INFO @ Wed, 22 Apr 2020 09:14:11: #1 Redundant rate of treatment: 0.34 INFO @ Wed, 22 Apr 2020 09:14:11: #1 finished! INFO @ Wed, 22 Apr 2020 09:14:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:14:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:14:11: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 09:14:11: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 09:14:11: start model_add_line... INFO @ Wed, 22 Apr 2020 09:14:11: start X-correlation... INFO @ Wed, 22 Apr 2020 09:14:11: end of X-cor INFO @ Wed, 22 Apr 2020 09:14:11: #2 finished! INFO @ Wed, 22 Apr 2020 09:14:11: #2 predicted fragment length is 113 bps INFO @ Wed, 22 Apr 2020 09:14:11: #2 alternative fragment length(s) may be 88,113,154,192,199,213,242,298,332,410,420,469,475,536,550,563,594 bps INFO @ Wed, 22 Apr 2020 09:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20_model.r INFO @ Wed, 22 Apr 2020 09:14:11: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:14:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:14:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:14:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388384/SRX7388384.20_summits.bed INFO @ Wed, 22 Apr 2020 09:14:15: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 0 millis CompletedMACS2peakCalling BigWig に変換しました。