Job ID = 14171355 SRX = SRX9005689 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1030070 READS because READLEN < 1 Read 5012055 spots for SRR12515090/SRR12515090.sra Written 5012055 spots for SRR12515090/SRR12515090.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171819 ("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_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] 1 unmatched pairs [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] 24611 / 118031 = 0.2085 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 @ Sat, 11 Dec 2021 11:28:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.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 @ Sat, 11 Dec 2021 11:28:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:28:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:28:39: 1000000 INFO @ Sat, 11 Dec 2021 11:28:42: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:28:42: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:28:42: #1 total tags in treatment: 90294 INFO @ Sat, 11 Dec 2021 11:28:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:28:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:28:42: #1 tags after filtering in treatment: 86499 INFO @ Sat, 11 Dec 2021 11:28:42: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:28:42: #1 finished! INFO @ Sat, 11 Dec 2021 11:28:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:28:42: #2 number of paired peaks: 4741 INFO @ Sat, 11 Dec 2021 11:28:42: start model_add_line... INFO @ Sat, 11 Dec 2021 11:28:42: start X-correlation... INFO @ Sat, 11 Dec 2021 11:28:42: end of X-cor INFO @ Sat, 11 Dec 2021 11:28:42: #2 finished! INFO @ Sat, 11 Dec 2021 11:28:42: #2 predicted fragment length is 300 bps INFO @ Sat, 11 Dec 2021 11:28:42: #2 alternative fragment length(s) may be 300 bps INFO @ Sat, 11 Dec 2021 11:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05_model.r INFO @ Sat, 11 Dec 2021 11:28:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:28:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:28:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.05_summits.bed INFO @ Sat, 11 Dec 2021 11:28:42: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 11:29:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.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 @ Sat, 11 Dec 2021 11:29:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:29:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:29:09: 1000000 INFO @ Sat, 11 Dec 2021 11:29:12: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:29:12: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:29:12: #1 total tags in treatment: 90294 INFO @ Sat, 11 Dec 2021 11:29:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:29:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:29:12: #1 tags after filtering in treatment: 86499 INFO @ Sat, 11 Dec 2021 11:29:12: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:29:12: #1 finished! INFO @ Sat, 11 Dec 2021 11:29:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:29:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:29:12: #2 number of paired peaks: 4741 INFO @ Sat, 11 Dec 2021 11:29:12: start model_add_line... INFO @ Sat, 11 Dec 2021 11:29:12: start X-correlation... INFO @ Sat, 11 Dec 2021 11:29:12: end of X-cor INFO @ Sat, 11 Dec 2021 11:29:12: #2 finished! INFO @ Sat, 11 Dec 2021 11:29:12: #2 predicted fragment length is 300 bps INFO @ Sat, 11 Dec 2021 11:29:12: #2 alternative fragment length(s) may be 300 bps INFO @ Sat, 11 Dec 2021 11:29:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10_model.r INFO @ Sat, 11 Dec 2021 11:29:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:29:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:29:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.10_summits.bed INFO @ Sat, 11 Dec 2021 11:29:12: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 11:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.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 @ Sat, 11 Dec 2021 11:29:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:29:32: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:29:39: 1000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:29:42: #1 tag size is determined as 97 bps INFO @ Sat, 11 Dec 2021 11:29:42: #1 tag size = 97 INFO @ Sat, 11 Dec 2021 11:29:42: #1 total tags in treatment: 90294 INFO @ Sat, 11 Dec 2021 11:29:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:29:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:29:42: #1 tags after filtering in treatment: 86499 INFO @ Sat, 11 Dec 2021 11:29:42: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 11 Dec 2021 11:29:42: #1 finished! INFO @ Sat, 11 Dec 2021 11:29:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:29:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:29:42: #2 number of paired peaks: 4741 INFO @ Sat, 11 Dec 2021 11:29:42: start model_add_line... INFO @ Sat, 11 Dec 2021 11:29:42: start X-correlation... INFO @ Sat, 11 Dec 2021 11:29:42: end of X-cor INFO @ Sat, 11 Dec 2021 11:29:42: #2 finished! INFO @ Sat, 11 Dec 2021 11:29:42: #2 predicted fragment length is 300 bps INFO @ Sat, 11 Dec 2021 11:29:42: #2 alternative fragment length(s) may be 300 bps INFO @ Sat, 11 Dec 2021 11:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20_model.r INFO @ Sat, 11 Dec 2021 11:29:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:29:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005689/SRX9005689.20_summits.bed INFO @ Sat, 11 Dec 2021 11:29:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling