Job ID = 14521441 SRX = SRX11788624 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 249722 READS because READLEN < 1 Read 734727 spots for SRR15488916/SRR15488916.sra Written 734727 spots for SRR15488916/SRR15488916.sra 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 Error, fewer reads in file specified with -2 than in file specified with -1 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) 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] 1 unmatched pairs [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] 3 unmatched pairs [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] 65623 / 423092 = 0.1551 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:03:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.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 @ Sat, 15 Jan 2022 21:03:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:03:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:03:47: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:03:47: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:03:47: #1 total tags in treatment: 357145 INFO @ Sat, 15 Jan 2022 21:03:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:03:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:03:47: #1 tags after filtering in treatment: 289532 INFO @ Sat, 15 Jan 2022 21:03:47: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:03:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:03:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:03:47: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 21:03:47: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 21:03:47: start model_add_line... INFO @ Sat, 15 Jan 2022 21:03:47: start X-correlation... INFO @ Sat, 15 Jan 2022 21:03:47: end of X-cor INFO @ Sat, 15 Jan 2022 21:03:47: #2 finished! INFO @ Sat, 15 Jan 2022 21:03:47: #2 predicted fragment length is 77 bps INFO @ Sat, 15 Jan 2022 21:03:47: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 15 Jan 2022 21:03:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05_model.r INFO @ Sat, 15 Jan 2022 21:03:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:03:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:03:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:03:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:03:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:03:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.05_summits.bed INFO @ Sat, 15 Jan 2022 21:03:48: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (289 records, 4 fields): 6 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.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 @ Sat, 15 Jan 2022 21:04:10: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:10: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:18: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:04:18: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:04:18: #1 total tags in treatment: 357145 INFO @ Sat, 15 Jan 2022 21:04:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:04:18: #1 tags after filtering in treatment: 289532 INFO @ Sat, 15 Jan 2022 21:04:18: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:04:18: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:18: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 21:04:18: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:18: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:18: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:18: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:18: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:18: #2 predicted fragment length is 77 bps INFO @ Sat, 15 Jan 2022 21:04:18: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 15 Jan 2022 21:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10_model.r INFO @ Sat, 15 Jan 2022 21:04:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.10_summits.bed INFO @ Sat, 15 Jan 2022 21:04:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 21:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.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 @ Sat, 15 Jan 2022 21:04:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:40: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:04:48: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:04:48: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:04:48: #1 total tags in treatment: 357145 INFO @ Sat, 15 Jan 2022 21:04:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:04:48: #1 tags after filtering in treatment: 289532 INFO @ Sat, 15 Jan 2022 21:04:48: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 21:04:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:48: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 21:04:48: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:48: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:48: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:48: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:48: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:48: #2 predicted fragment length is 77 bps INFO @ Sat, 15 Jan 2022 21:04:48: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 15 Jan 2022 21:04:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20_model.r INFO @ Sat, 15 Jan 2022 21:04:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:04:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:04:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:04:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788624/SRX11788624.20_summits.bed INFO @ Sat, 15 Jan 2022 21:04:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 5 millis CompletedMACS2peakCalling