Job ID = 16435141 SRX = SRX9091663 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 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 44 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] 49378933 / 52480808 = 0.9409 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 12:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.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 12:10:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:10:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:10:52: 1000000 INFO @ Tue, 02 Aug 2022 12:11:00: 2000000 INFO @ Tue, 02 Aug 2022 12:11:08: 3000000 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 12:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.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 12:11:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:11:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:11:16: 4000000 INFO @ Tue, 02 Aug 2022 12:11:23: 1000000 INFO @ Tue, 02 Aug 2022 12:11:24: 5000000 INFO @ Tue, 02 Aug 2022 12:11:32: 2000000 INFO @ Tue, 02 Aug 2022 12:11:33: 6000000 INFO @ Tue, 02 Aug 2022 12:11:40: 3000000 INFO @ Tue, 02 Aug 2022 12:11:41: 7000000 INFO @ Tue, 02 Aug 2022 12:11:41: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:11:41: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:11:41: #1 total tags in treatment: 3107425 INFO @ Tue, 02 Aug 2022 12:11:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:11:41: #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 12:11:41: #1 tags after filtering in treatment: 2614834 INFO @ Tue, 02 Aug 2022 12:11:41: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:11:41: #1 finished! INFO @ Tue, 02 Aug 2022 12:11:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:11:42: #2 number of paired peaks: 1310 INFO @ Tue, 02 Aug 2022 12:11:42: start model_add_line... INFO @ Tue, 02 Aug 2022 12:11:42: start X-correlation... INFO @ Tue, 02 Aug 2022 12:11:42: end of X-cor INFO @ Tue, 02 Aug 2022 12:11:42: #2 finished! INFO @ Tue, 02 Aug 2022 12:11:42: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 12:11:42: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 12:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05_model.r INFO @ Tue, 02 Aug 2022 12:11:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:11:42: #3 Pre-compute pvalue-qvalue table... 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 12:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.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 12:11:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:11:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:11:49: 4000000 INFO @ Tue, 02 Aug 2022 12:11:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:11:50: 1000000 INFO @ Tue, 02 Aug 2022 12:11:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:11:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:11:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.05_summits.bed INFO @ Tue, 02 Aug 2022 12:11:52: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (845 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:11:56: 2000000 INFO @ Tue, 02 Aug 2022 12:11:57: 5000000 INFO @ Tue, 02 Aug 2022 12:12:02: 3000000 INFO @ Tue, 02 Aug 2022 12:12:05: 6000000 INFO @ Tue, 02 Aug 2022 12:12:08: 4000000 INFO @ Tue, 02 Aug 2022 12:12:14: 7000000 INFO @ Tue, 02 Aug 2022 12:12:14: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:12:14: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:12:14: #1 total tags in treatment: 3107425 INFO @ Tue, 02 Aug 2022 12:12:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:12:14: #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 12:12:14: #1 tags after filtering in treatment: 2614834 INFO @ Tue, 02 Aug 2022 12:12:14: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:12:14: #1 finished! INFO @ Tue, 02 Aug 2022 12:12:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:12:14: #2 number of paired peaks: 1310 INFO @ Tue, 02 Aug 2022 12:12:14: start model_add_line... INFO @ Tue, 02 Aug 2022 12:12:14: start X-correlation... INFO @ Tue, 02 Aug 2022 12:12:14: end of X-cor INFO @ Tue, 02 Aug 2022 12:12:14: #2 finished! INFO @ Tue, 02 Aug 2022 12:12:14: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 12:12:14: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 12:12:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10_model.r INFO @ Tue, 02 Aug 2022 12:12:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:12:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:12:14: 5000000 INFO @ Tue, 02 Aug 2022 12:12:20: 6000000 INFO @ Tue, 02 Aug 2022 12:12:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.10_summits.bed INFO @ Tue, 02 Aug 2022 12:12:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:12:26: 7000000 INFO @ Tue, 02 Aug 2022 12:12:26: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:12:26: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:12:26: #1 total tags in treatment: 3107425 INFO @ Tue, 02 Aug 2022 12:12:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:12:26: #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 12:12:26: #1 tags after filtering in treatment: 2614834 INFO @ Tue, 02 Aug 2022 12:12:26: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:12:26: #1 finished! INFO @ Tue, 02 Aug 2022 12:12:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:12:26: #2 number of paired peaks: 1310 INFO @ Tue, 02 Aug 2022 12:12:26: start model_add_line... INFO @ Tue, 02 Aug 2022 12:12:26: start X-correlation... INFO @ Tue, 02 Aug 2022 12:12:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:12:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:12:26: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 12:12:26: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 12:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20_model.r INFO @ Tue, 02 Aug 2022 12:12:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:12:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:12:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:12:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091663/SRX9091663.20_summits.bed INFO @ Tue, 02 Aug 2022 12:12:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。