Job ID = 16434972 SRX = SRX9091661 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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 Warning: skipping mate #1 of read 'SRR12608198.10399737 10399737 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608198.10399737 10399737 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608198.10399737 10399737 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608198.10399737 10399737 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608198.22423271 22423271 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608198.22423271 22423271 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608198.22423271 22423271 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608198.22423271 22423271 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 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: 7 sequences. [bam_sort_core] merging from 28 files... [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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 33056886 / 33219826 = 0.9951 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:04:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 02 Aug 2022 11:04:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:13: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:04:13: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:04:13: #1 total tags in treatment: 166246 INFO @ Tue, 02 Aug 2022 11:04:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:04:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:04:13: #1 tags after filtering in treatment: 140111 INFO @ Tue, 02 Aug 2022 11:04:13: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:04:13: #1 finished! INFO @ Tue, 02 Aug 2022 11:04:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:13: #2 number of paired peaks: 3343 INFO @ Tue, 02 Aug 2022 11:04:13: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:13: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:14: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:14: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:14: #2 predicted fragment length is 252 bps INFO @ Tue, 02 Aug 2022 11:04:14: #2 alternative fragment length(s) may be 229,252 bps INFO @ Tue, 02 Aug 2022 11:04:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05_model.r INFO @ Tue, 02 Aug 2022 11:04:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.05_summits.bed INFO @ Tue, 02 Aug 2022 11:04:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 29 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:04:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 02 Aug 2022 11:04:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:44: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:04:44: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:04:44: #1 total tags in treatment: 166246 INFO @ Tue, 02 Aug 2022 11:04:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:04:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:04:44: #1 tags after filtering in treatment: 140111 INFO @ Tue, 02 Aug 2022 11:04:44: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:04:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:04:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:04:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:04:44: #2 number of paired peaks: 3343 INFO @ Tue, 02 Aug 2022 11:04:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:04:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:04:44: end of X-cor INFO @ Tue, 02 Aug 2022 11:04:44: #2 finished! INFO @ Tue, 02 Aug 2022 11:04:44: #2 predicted fragment length is 252 bps INFO @ Tue, 02 Aug 2022 11:04:44: #2 alternative fragment length(s) may be 229,252 bps INFO @ Tue, 02 Aug 2022 11:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10_model.r INFO @ Tue, 02 Aug 2022 11:04:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:04:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.10_summits.bed INFO @ Tue, 02 Aug 2022 11:04:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:05:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 02 Aug 2022 11:05:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:05:10: #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 @ Tue, 02 Aug 2022 11:05:13: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 11:05:13: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 11:05:13: #1 total tags in treatment: 166246 INFO @ Tue, 02 Aug 2022 11:05:13: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:05:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:05:13: #1 tags after filtering in treatment: 140111 INFO @ Tue, 02 Aug 2022 11:05:13: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 11:05:13: #1 finished! INFO @ Tue, 02 Aug 2022 11:05:13: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:05:13: #2 number of paired peaks: 3343 INFO @ Tue, 02 Aug 2022 11:05:13: start model_add_line... INFO @ Tue, 02 Aug 2022 11:05:13: start X-correlation... INFO @ Tue, 02 Aug 2022 11:05:13: end of X-cor INFO @ Tue, 02 Aug 2022 11:05:13: #2 finished! INFO @ Tue, 02 Aug 2022 11:05:13: #2 predicted fragment length is 252 bps INFO @ Tue, 02 Aug 2022 11:05:13: #2 alternative fragment length(s) may be 229,252 bps INFO @ Tue, 02 Aug 2022 11:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20_model.r INFO @ Tue, 02 Aug 2022 11:05:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:05:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:05:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:05:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:05:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091661/SRX9091661.20_summits.bed INFO @ Tue, 02 Aug 2022 11:05:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 15 millis CompletedMACS2peakCalling