Job ID = 14167148 SRX = SRX10340457 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 705843 READS because READLEN < 1 Read 5534799 spots for SRR13962466/SRR13962466.sra Written 5534799 spots for SRR13962466/SRR13962466.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167653 ("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 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 1 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] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 1 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 709668 / 4453635 = 0.1593 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 10:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.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 10:46:08: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:46:08: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:46:14: 1000000 INFO @ Fri, 10 Dec 2021 10:46:20: 2000000 INFO @ Fri, 10 Dec 2021 10:46:26: 3000000 INFO @ Fri, 10 Dec 2021 10:46:32: 4000000 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 10:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.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 10:46:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:46:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:46:38: 5000000 INFO @ Fri, 10 Dec 2021 10:46:45: 6000000 INFO @ Fri, 10 Dec 2021 10:46:46: 1000000 INFO @ Fri, 10 Dec 2021 10:46:52: 7000000 INFO @ Fri, 10 Dec 2021 10:46:54: 2000000 INFO @ Fri, 10 Dec 2021 10:46:59: 8000000 INFO @ Fri, 10 Dec 2021 10:47:00: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:47:00: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:47:00: #1 total tags in treatment: 3695080 INFO @ Fri, 10 Dec 2021 10:47:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:47:00: #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 10:47:00: #1 tags after filtering in treatment: 3567215 INFO @ Fri, 10 Dec 2021 10:47:00: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 10:47:00: #1 finished! INFO @ Fri, 10 Dec 2021 10:47:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:47:01: #2 number of paired peaks: 5559 INFO @ Fri, 10 Dec 2021 10:47:01: start model_add_line... INFO @ Fri, 10 Dec 2021 10:47:01: start X-correlation... INFO @ Fri, 10 Dec 2021 10:47:01: end of X-cor INFO @ Fri, 10 Dec 2021 10:47:01: #2 finished! INFO @ Fri, 10 Dec 2021 10:47:01: #2 predicted fragment length is 312 bps INFO @ Fri, 10 Dec 2021 10:47:01: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 10 Dec 2021 10:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05_model.r INFO @ Fri, 10 Dec 2021 10:47:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:47:03: 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 10:47:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.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 10:47:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:47:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:47:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:47:11: 4000000 INFO @ Fri, 10 Dec 2021 10:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.05_summits.bed INFO @ Fri, 10 Dec 2021 10:47:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5944 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:47:15: 1000000 INFO @ Fri, 10 Dec 2021 10:47:19: 5000000 INFO @ Fri, 10 Dec 2021 10:47:22: 2000000 INFO @ Fri, 10 Dec 2021 10:47:28: 6000000 INFO @ Fri, 10 Dec 2021 10:47:29: 3000000 INFO @ Fri, 10 Dec 2021 10:47:36: 7000000 INFO @ Fri, 10 Dec 2021 10:47:36: 4000000 INFO @ Fri, 10 Dec 2021 10:47:43: 5000000 INFO @ Fri, 10 Dec 2021 10:47:44: 8000000 INFO @ Fri, 10 Dec 2021 10:47:46: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:47:46: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:47:46: #1 total tags in treatment: 3695080 INFO @ Fri, 10 Dec 2021 10:47:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:47:46: #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 10:47:46: #1 tags after filtering in treatment: 3567215 INFO @ Fri, 10 Dec 2021 10:47:46: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 10:47:46: #1 finished! INFO @ Fri, 10 Dec 2021 10:47:46: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:47:46: #2 number of paired peaks: 5559 INFO @ Fri, 10 Dec 2021 10:47:46: start model_add_line... INFO @ Fri, 10 Dec 2021 10:47:46: start X-correlation... INFO @ Fri, 10 Dec 2021 10:47:46: end of X-cor INFO @ Fri, 10 Dec 2021 10:47:46: #2 finished! INFO @ Fri, 10 Dec 2021 10:47:46: #2 predicted fragment length is 312 bps INFO @ Fri, 10 Dec 2021 10:47:46: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 10 Dec 2021 10:47:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10_model.r INFO @ Fri, 10 Dec 2021 10:47:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:47:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:47:50: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:47:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:47:57: 7000000 INFO @ Fri, 10 Dec 2021 10:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.10_summits.bed INFO @ Fri, 10 Dec 2021 10:47:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4529 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:48:04: 8000000 INFO @ Fri, 10 Dec 2021 10:48:04: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 10:48:04: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 10:48:04: #1 total tags in treatment: 3695080 INFO @ Fri, 10 Dec 2021 10:48:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:48:04: #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 10:48:05: #1 tags after filtering in treatment: 3567215 INFO @ Fri, 10 Dec 2021 10:48:05: #1 Redundant rate of treatment: 0.03 INFO @ Fri, 10 Dec 2021 10:48:05: #1 finished! INFO @ Fri, 10 Dec 2021 10:48:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:48:05: #2 number of paired peaks: 5559 INFO @ Fri, 10 Dec 2021 10:48:05: start model_add_line... INFO @ Fri, 10 Dec 2021 10:48:05: start X-correlation... INFO @ Fri, 10 Dec 2021 10:48:05: end of X-cor INFO @ Fri, 10 Dec 2021 10:48:05: #2 finished! INFO @ Fri, 10 Dec 2021 10:48:05: #2 predicted fragment length is 312 bps INFO @ Fri, 10 Dec 2021 10:48:05: #2 alternative fragment length(s) may be 312 bps INFO @ Fri, 10 Dec 2021 10:48:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20_model.r INFO @ Fri, 10 Dec 2021 10:48:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:48:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:48:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:48:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:48:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:48:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10340457/SRX10340457.20_summits.bed INFO @ Fri, 10 Dec 2021 10:48:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2631 records, 4 fields): 4 millis CompletedMACS2peakCalling