Job ID = 14167128 SRX = SRX10340447 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 886152 READS because READLEN < 1 Read 9407350 spots for SRR13962456/SRR13962456.sra Written 9407350 spots for SRR13962456/SRR13962456.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167622 ("srTdm6") has been submitted 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: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 2 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 5 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 2 unmatched pairs [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] 5 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4539870 / 6655262 = 0.6821 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 @ Fri, 10 Dec 2021 10:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.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 @ Fri, 10 Dec 2021 10:41:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:41:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:41:33: 1000000 INFO @ Fri, 10 Dec 2021 10:41:41: 2000000 INFO @ Fri, 10 Dec 2021 10:41:49: 3000000 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 @ Fri, 10 Dec 2021 10:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.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 @ Fri, 10 Dec 2021 10:41:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:41:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:41:56: 4000000 INFO @ Fri, 10 Dec 2021 10:42:04: 1000000 INFO @ Fri, 10 Dec 2021 10:42:05: 5000000 INFO @ Fri, 10 Dec 2021 10:42:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:42:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:42:07: #1 total tags in treatment: 1964511 INFO @ Fri, 10 Dec 2021 10:42:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:42:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:42:07: #1 tags after filtering in treatment: 1848920 INFO @ Fri, 10 Dec 2021 10:42:07: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:42:07: #1 finished! INFO @ Fri, 10 Dec 2021 10:42:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:42:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:42:07: #2 number of paired peaks: 4158 INFO @ Fri, 10 Dec 2021 10:42:07: start model_add_line... INFO @ Fri, 10 Dec 2021 10:42:07: start X-correlation... INFO @ Fri, 10 Dec 2021 10:42:07: end of X-cor INFO @ Fri, 10 Dec 2021 10:42:07: #2 finished! INFO @ Fri, 10 Dec 2021 10:42:07: #2 predicted fragment length is 284 bps INFO @ Fri, 10 Dec 2021 10:42:07: #2 alternative fragment length(s) may be 284 bps INFO @ Fri, 10 Dec 2021 10:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05_model.r INFO @ Fri, 10 Dec 2021 10:42:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:42:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:42:12: 2000000 INFO @ Fri, 10 Dec 2021 10:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.05_summits.bed INFO @ Fri, 10 Dec 2021 10:42:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5088 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:42:20: 3000000 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 @ Fri, 10 Dec 2021 10:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.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 @ Fri, 10 Dec 2021 10:42:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:42:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:42:28: 4000000 INFO @ Fri, 10 Dec 2021 10:42:33: 1000000 INFO @ Fri, 10 Dec 2021 10:42:37: 5000000 INFO @ Fri, 10 Dec 2021 10:42:39: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:42:39: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:42:39: #1 total tags in treatment: 1964511 INFO @ Fri, 10 Dec 2021 10:42:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:42:39: #1 tags after filtering in treatment: 1848920 INFO @ Fri, 10 Dec 2021 10:42:39: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:42:39: #1 finished! INFO @ Fri, 10 Dec 2021 10:42:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:42:40: #2 number of paired peaks: 4158 INFO @ Fri, 10 Dec 2021 10:42:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:42:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:42:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:42:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:42:40: #2 predicted fragment length is 284 bps INFO @ Fri, 10 Dec 2021 10:42:40: #2 alternative fragment length(s) may be 284 bps INFO @ Fri, 10 Dec 2021 10:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10_model.r INFO @ Fri, 10 Dec 2021 10:42:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:42:42: 2000000 INFO @ Fri, 10 Dec 2021 10:42:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.10_summits.bed INFO @ Fri, 10 Dec 2021 10:42:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3813 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:42:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:42:57: 4000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:43:05: 5000000 INFO @ Fri, 10 Dec 2021 10:43:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:43:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:43:07: #1 total tags in treatment: 1964511 INFO @ Fri, 10 Dec 2021 10:43:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:43:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 10:43:07: #1 tags after filtering in treatment: 1848920 INFO @ Fri, 10 Dec 2021 10:43:07: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 10:43:07: #1 finished! INFO @ Fri, 10 Dec 2021 10:43:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:43:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:43:07: #2 number of paired peaks: 4158 INFO @ Fri, 10 Dec 2021 10:43:07: start model_add_line... INFO @ Fri, 10 Dec 2021 10:43:07: start X-correlation... INFO @ Fri, 10 Dec 2021 10:43:07: end of X-cor INFO @ Fri, 10 Dec 2021 10:43:07: #2 finished! INFO @ Fri, 10 Dec 2021 10:43:07: #2 predicted fragment length is 284 bps INFO @ Fri, 10 Dec 2021 10:43:07: #2 alternative fragment length(s) may be 284 bps INFO @ Fri, 10 Dec 2021 10:43:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20_model.r INFO @ Fri, 10 Dec 2021 10:43:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:43:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340447/SRX10340447.20_summits.bed INFO @ Fri, 10 Dec 2021 10:43:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 4 millis CompletedMACS2peakCalling