Job ID = 16438678 SRX = SRX14748157 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 3859 READS because READLEN < 1 Read 3931447 spots for SRR18645006/SRR18645006.sra Written 3931447 spots for SRR18645006/SRR18645006.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438934 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 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: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 196103 / 3127920 = 0.0627 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 14:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:12:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:12:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:12:59: 1000000 INFO @ Tue, 02 Aug 2022 14:13:04: 2000000 INFO @ Tue, 02 Aug 2022 14:13:10: 3000000 INFO @ Tue, 02 Aug 2022 14:13:15: 4000000 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 14:13:21: 5000000 INFO @ Tue, 02 Aug 2022 14:13:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:13:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:13:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:13:26: 6000000 INFO @ Tue, 02 Aug 2022 14:13:27: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 14:13:27: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 14:13:27: #1 total tags in treatment: 2911880 INFO @ Tue, 02 Aug 2022 14:13:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:27: #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 14:13:27: #1 tags after filtering in treatment: 2803727 INFO @ Tue, 02 Aug 2022 14:13:27: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:13:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:28: #2 number of paired peaks: 1744 INFO @ Tue, 02 Aug 2022 14:13:28: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:28: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:13:28: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05_model.r INFO @ Tue, 02 Aug 2022 14:13:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:29: 1000000 INFO @ Tue, 02 Aug 2022 14:13:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:13:34: 2000000 INFO @ Tue, 02 Aug 2022 14:13:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:13:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:13:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.05_summits.bed INFO @ Tue, 02 Aug 2022 14:13:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:13:40: 3000000 INFO @ Tue, 02 Aug 2022 14:13:45: 4000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 14:13:50: 5000000 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 14:13:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:13:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:13:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:13:56: 6000000 INFO @ Tue, 02 Aug 2022 14:13:57: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 14:13:57: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 14:13:57: #1 total tags in treatment: 2911880 INFO @ Tue, 02 Aug 2022 14:13:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:13:57: #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 14:13:57: #1 tags after filtering in treatment: 2803727 INFO @ Tue, 02 Aug 2022 14:13:57: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:13:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:13:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:13:57: #2 number of paired peaks: 1744 INFO @ Tue, 02 Aug 2022 14:13:57: start model_add_line... INFO @ Tue, 02 Aug 2022 14:13:57: start X-correlation... INFO @ Tue, 02 Aug 2022 14:13:57: end of X-cor INFO @ Tue, 02 Aug 2022 14:13:57: #2 finished! INFO @ Tue, 02 Aug 2022 14:13:57: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:13:57: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10_model.r INFO @ Tue, 02 Aug 2022 14:13:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:13:59: 1000000 INFO @ Tue, 02 Aug 2022 14:14:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:04: 2000000 INFO @ Tue, 02 Aug 2022 14:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.10_summits.bed INFO @ Tue, 02 Aug 2022 14:14:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (946 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:14:10: 3000000 INFO @ Tue, 02 Aug 2022 14:14:15: 4000000 INFO @ Tue, 02 Aug 2022 14:14:20: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:14:26: 6000000 INFO @ Tue, 02 Aug 2022 14:14:27: #1 tag size is determined as 70 bps INFO @ Tue, 02 Aug 2022 14:14:27: #1 tag size = 70 INFO @ Tue, 02 Aug 2022 14:14:27: #1 total tags in treatment: 2911880 INFO @ Tue, 02 Aug 2022 14:14:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:14:27: #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 14:14:27: #1 tags after filtering in treatment: 2803727 INFO @ Tue, 02 Aug 2022 14:14:27: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:14:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:14:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:14:27: #2 number of paired peaks: 1744 INFO @ Tue, 02 Aug 2022 14:14:27: start model_add_line... INFO @ Tue, 02 Aug 2022 14:14:27: start X-correlation... INFO @ Tue, 02 Aug 2022 14:14:27: end of X-cor INFO @ Tue, 02 Aug 2022 14:14:27: #2 finished! INFO @ Tue, 02 Aug 2022 14:14:27: #2 predicted fragment length is 227 bps INFO @ Tue, 02 Aug 2022 14:14:27: #2 alternative fragment length(s) may be 227 bps INFO @ Tue, 02 Aug 2022 14:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20_model.r INFO @ Tue, 02 Aug 2022 14:14:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:14:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748157/SRX14748157.20_summits.bed INFO @ Tue, 02 Aug 2022 14:14:37: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (445 records, 4 fields): 29 millis CompletedMACS2peakCalling BigWig に変換しました。