Job ID = 14521440 SRX = SRX11788623 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 349606 READS because READLEN < 1 Read 1249639 spots for SRR15488917/SRR15488917.sra Written 1249639 spots for SRR15488917/SRR15488917.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] 2 unmatched pairs [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] 1 unmatched pairs [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] 2 unmatched pairs [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] 135890 / 802398 = 0.1694 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 21:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.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 21:04:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:18: 1000000 INFO @ Sat, 15 Jan 2022 21:04:20: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:04:20: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:04:20: #1 total tags in treatment: 666198 INFO @ Sat, 15 Jan 2022 21:04:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:20: #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 21:04:20: #1 tags after filtering in treatment: 495075 INFO @ Sat, 15 Jan 2022 21:04:20: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:04:20: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:20: #2 number of paired peaks: 641 WARNING @ Sat, 15 Jan 2022 21:04:20: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:20: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:20: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:20: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:20: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:20: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 21:04:20: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 21:04:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05_model.r INFO @ Sat, 15 Jan 2022 21:04:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.05_summits.bed INFO @ Sat, 15 Jan 2022 21:04:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1176 records, 4 fields): 5 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 21:04:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.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 21:04:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:04:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:04:48: 1000000 INFO @ Sat, 15 Jan 2022 21:04:51: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:04:51: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:04:51: #1 total tags in treatment: 666198 INFO @ Sat, 15 Jan 2022 21:04:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:04:51: #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 21:04:51: #1 tags after filtering in treatment: 495075 INFO @ Sat, 15 Jan 2022 21:04:51: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:04:51: #1 finished! INFO @ Sat, 15 Jan 2022 21:04:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:04:51: #2 number of paired peaks: 641 WARNING @ Sat, 15 Jan 2022 21:04:51: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 15 Jan 2022 21:04:51: start model_add_line... INFO @ Sat, 15 Jan 2022 21:04:51: start X-correlation... INFO @ Sat, 15 Jan 2022 21:04:51: end of X-cor INFO @ Sat, 15 Jan 2022 21:04:51: #2 finished! INFO @ Sat, 15 Jan 2022 21:04:51: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 21:04:51: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 21:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10_model.r INFO @ Sat, 15 Jan 2022 21:04:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:04:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:04:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:04:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:04:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.10_summits.bed INFO @ Sat, 15 Jan 2022 21:04:53: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (650 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 21:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.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 21:05:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:13: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:05:18: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:05:20: #1 tag size is determined as 26 bps INFO @ Sat, 15 Jan 2022 21:05:20: #1 tag size = 26 INFO @ Sat, 15 Jan 2022 21:05:20: #1 total tags in treatment: 666198 INFO @ Sat, 15 Jan 2022 21:05:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:05:20: #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 21:05:20: #1 tags after filtering in treatment: 495075 INFO @ Sat, 15 Jan 2022 21:05:20: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 21:05:20: #1 finished! INFO @ Sat, 15 Jan 2022 21:05:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:05:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:05:21: #2 number of paired peaks: 641 WARNING @ Sat, 15 Jan 2022 21:05:21: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Sat, 15 Jan 2022 21:05:21: start model_add_line... INFO @ Sat, 15 Jan 2022 21:05:21: start X-correlation... INFO @ Sat, 15 Jan 2022 21:05:21: end of X-cor INFO @ Sat, 15 Jan 2022 21:05:21: #2 finished! INFO @ Sat, 15 Jan 2022 21:05:21: #2 predicted fragment length is 90 bps INFO @ Sat, 15 Jan 2022 21:05:21: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 15 Jan 2022 21:05:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20_model.r INFO @ Sat, 15 Jan 2022 21:05:21: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:05:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:05:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11788623/SRX11788623.20_summits.bed INFO @ Sat, 15 Jan 2022 21:05:22: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 2 millis CompletedMACS2peakCalling