Job ID = 5791244 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,615,799 reads read : 9,231,598 reads written : 9,231,598 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: 00:01:32 4615799 reads; of these: 4615799 (100.00%) were paired; of these: 337017 (7.30%) aligned concordantly 0 times 3677674 (79.68%) aligned concordantly exactly 1 time 601108 (13.02%) aligned concordantly >1 times ---- 337017 pairs aligned concordantly 0 times; of these: 75330 (22.35%) aligned discordantly 1 time ---- 261687 pairs aligned 0 times concordantly or discordantly; of these: 523374 mates make up the pairs; of these: 404700 (77.33%) aligned 0 times 76695 (14.65%) aligned exactly 1 time 41979 (8.02%) aligned >1 times 95.62% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 1555851 / 4294850 = 0.3623 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 09:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.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 09:15:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:15:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:15:09: 1000000 INFO @ Wed, 22 Apr 2020 09:15:14: 2000000 INFO @ Wed, 22 Apr 2020 09:15:18: 3000000 INFO @ Wed, 22 Apr 2020 09:15:23: 4000000 INFO @ Wed, 22 Apr 2020 09:15:27: 5000000 INFO @ Wed, 22 Apr 2020 09:15:30: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:15:30: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:15:30: #1 total tags in treatment: 2725109 INFO @ Wed, 22 Apr 2020 09:15:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:15:30: #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 09:15:30: #1 tags after filtering in treatment: 1550860 INFO @ Wed, 22 Apr 2020 09:15:30: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:15:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:15:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:15:30: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 09:15:30: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 09:15:30: start model_add_line... INFO @ Wed, 22 Apr 2020 09:15:30: start X-correlation... INFO @ Wed, 22 Apr 2020 09:15:30: end of X-cor INFO @ Wed, 22 Apr 2020 09:15:30: #2 finished! INFO @ Wed, 22 Apr 2020 09:15:30: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 09:15:30: #2 alternative fragment length(s) may be 2,64,80,115,138 bps INFO @ Wed, 22 Apr 2020 09:15:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05_model.r INFO @ Wed, 22 Apr 2020 09:15:30: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:15:30: #3 Pre-compute pvalue-qvalue table... 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 09:15:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.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 09:15:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:15:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.05_summits.bed INFO @ Wed, 22 Apr 2020 09:15:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2852 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:15:39: 1000000 INFO @ Wed, 22 Apr 2020 09:15:44: 2000000 INFO @ Wed, 22 Apr 2020 09:15:48: 3000000 INFO @ Wed, 22 Apr 2020 09:15:53: 4000000 INFO @ Wed, 22 Apr 2020 09:15:57: 5000000 INFO @ Wed, 22 Apr 2020 09:16:00: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:16:00: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:16:00: #1 total tags in treatment: 2725109 INFO @ Wed, 22 Apr 2020 09:16:00: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:00: #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 09:16:00: #1 tags after filtering in treatment: 1550860 INFO @ Wed, 22 Apr 2020 09:16:00: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:16:00: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:00: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 09:16:00: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 09:16:00: start model_add_line... INFO @ Wed, 22 Apr 2020 09:16:00: start X-correlation... INFO @ Wed, 22 Apr 2020 09:16:00: end of X-cor INFO @ Wed, 22 Apr 2020 09:16:00: #2 finished! INFO @ Wed, 22 Apr 2020 09:16:00: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 09:16:00: #2 alternative fragment length(s) may be 2,64,80,115,138 bps INFO @ Wed, 22 Apr 2020 09:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10_model.r INFO @ Wed, 22 Apr 2020 09:16:00: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:16:00: #3 Pre-compute pvalue-qvalue table... 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 09:16:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.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 09:16:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:16:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.10_summits.bed INFO @ Wed, 22 Apr 2020 09:16:05: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1950 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:16:09: 1000000 INFO @ Wed, 22 Apr 2020 09:16:14: 2000000 INFO @ Wed, 22 Apr 2020 09:16:19: 3000000 INFO @ Wed, 22 Apr 2020 09:16:24: 4000000 INFO @ Wed, 22 Apr 2020 09:16:29: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:16:33: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:16:33: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:16:33: #1 total tags in treatment: 2725109 INFO @ Wed, 22 Apr 2020 09:16:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:16:33: #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 09:16:33: #1 tags after filtering in treatment: 1550860 INFO @ Wed, 22 Apr 2020 09:16:33: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 09:16:33: #1 finished! INFO @ Wed, 22 Apr 2020 09:16:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:16:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:16:33: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 09:16:33: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 09:16:33: start model_add_line... INFO @ Wed, 22 Apr 2020 09:16:33: start X-correlation... INFO @ Wed, 22 Apr 2020 09:16:33: end of X-cor INFO @ Wed, 22 Apr 2020 09:16:33: #2 finished! INFO @ Wed, 22 Apr 2020 09:16:33: #2 predicted fragment length is 138 bps INFO @ Wed, 22 Apr 2020 09:16:33: #2 alternative fragment length(s) may be 2,64,80,115,138 bps INFO @ Wed, 22 Apr 2020 09:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20_model.r INFO @ Wed, 22 Apr 2020 09:16:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:16:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:16:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:16:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:16:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388387/SRX7388387.20_summits.bed INFO @ Wed, 22 Apr 2020 09:16:38: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (929 records, 4 fields): 3 millis CompletedMACS2peakCalling