Job ID = 16436542 SRX = SRX8948319 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 120841 READS because READLEN < 1 Read 10297414 spots for SRR12453876/SRR12453876.sra Written 10297414 spots for SRR12453876/SRR12453876.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436807 ("srTdm6") has been submitted Time loading reference: 00:00:01 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] 208 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 74 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] 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] 4983540 / 9930712 = 0.5018 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 11:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.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 11:48:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:22: 1000000 INFO @ Tue, 02 Aug 2022 11:48:27: 2000000 INFO @ Tue, 02 Aug 2022 11:48:31: 3000000 INFO @ Tue, 02 Aug 2022 11:48:36: 4000000 INFO @ Tue, 02 Aug 2022 11:48:41: 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 11:48:45: 6000000 INFO @ Tue, 02 Aug 2022 11:48:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.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 11:48:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:48:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:48:50: 7000000 INFO @ Tue, 02 Aug 2022 11:48:53: 1000000 INFO @ Tue, 02 Aug 2022 11:48:55: 8000000 INFO @ Tue, 02 Aug 2022 11:48:58: 2000000 INFO @ Tue, 02 Aug 2022 11:49:01: 9000000 INFO @ Tue, 02 Aug 2022 11:49:03: 3000000 INFO @ Tue, 02 Aug 2022 11:49:06: 10000000 INFO @ Tue, 02 Aug 2022 11:49:06: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:49:06: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:49:06: #1 total tags in treatment: 4883240 INFO @ Tue, 02 Aug 2022 11:49:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:49:06: #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 11:49:07: #1 tags after filtering in treatment: 3904947 INFO @ Tue, 02 Aug 2022 11:49:07: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:49:07: #1 finished! INFO @ Tue, 02 Aug 2022 11:49:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:49:07: #2 number of paired peaks: 9150 INFO @ Tue, 02 Aug 2022 11:49:07: start model_add_line... INFO @ Tue, 02 Aug 2022 11:49:07: start X-correlation... INFO @ Tue, 02 Aug 2022 11:49:07: end of X-cor INFO @ Tue, 02 Aug 2022 11:49:07: #2 finished! INFO @ Tue, 02 Aug 2022 11:49:07: #2 predicted fragment length is 292 bps INFO @ Tue, 02 Aug 2022 11:49:07: #2 alternative fragment length(s) may be 2,292,305 bps INFO @ Tue, 02 Aug 2022 11:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05_model.r INFO @ Tue, 02 Aug 2022 11:49:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:49:08: 4000000 INFO @ Tue, 02 Aug 2022 11:49:13: 5000000 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 11:49:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.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 11:49:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:49:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:49:17: 6000000 INFO @ Tue, 02 Aug 2022 11:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.05_summits.bed INFO @ Tue, 02 Aug 2022 11:49:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:49:22: 7000000 INFO @ Tue, 02 Aug 2022 11:49:22: 1000000 INFO @ Tue, 02 Aug 2022 11:49:27: 8000000 INFO @ Tue, 02 Aug 2022 11:49:27: 2000000 INFO @ Tue, 02 Aug 2022 11:49:32: 9000000 INFO @ Tue, 02 Aug 2022 11:49:33: 3000000 INFO @ Tue, 02 Aug 2022 11:49:38: 10000000 INFO @ Tue, 02 Aug 2022 11:49:38: 4000000 INFO @ Tue, 02 Aug 2022 11:49:38: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:49:38: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:49:38: #1 total tags in treatment: 4883240 INFO @ Tue, 02 Aug 2022 11:49:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:49:38: #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 11:49:38: #1 tags after filtering in treatment: 3904947 INFO @ Tue, 02 Aug 2022 11:49:38: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:49:38: #1 finished! INFO @ Tue, 02 Aug 2022 11:49:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:49:39: #2 number of paired peaks: 9150 INFO @ Tue, 02 Aug 2022 11:49:39: start model_add_line... INFO @ Tue, 02 Aug 2022 11:49:39: start X-correlation... INFO @ Tue, 02 Aug 2022 11:49:39: end of X-cor INFO @ Tue, 02 Aug 2022 11:49:39: #2 finished! INFO @ Tue, 02 Aug 2022 11:49:39: #2 predicted fragment length is 292 bps INFO @ Tue, 02 Aug 2022 11:49:39: #2 alternative fragment length(s) may be 2,292,305 bps INFO @ Tue, 02 Aug 2022 11:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10_model.r INFO @ Tue, 02 Aug 2022 11:49:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:49:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:49:42: 5000000 INFO @ Tue, 02 Aug 2022 11:49:47: 6000000 INFO @ Tue, 02 Aug 2022 11:49:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:49:52: 7000000 INFO @ Tue, 02 Aug 2022 11:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.10_summits.bed INFO @ Tue, 02 Aug 2022 11:49:53: Done! pass1 - making usageList (8 chroms): 1 millis BedGraph に変換しました。 BigWig に変換中... pass2 - checking and writing primary data (86 records, 4 fields): 311 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:49:56: 8000000 INFO @ Tue, 02 Aug 2022 11:50:01: 9000000 INFO @ Tue, 02 Aug 2022 11:50:06: 10000000 INFO @ Tue, 02 Aug 2022 11:50:06: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 11:50:06: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 11:50:06: #1 total tags in treatment: 4883240 INFO @ Tue, 02 Aug 2022 11:50:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:50:06: #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 11:50:07: #1 tags after filtering in treatment: 3904947 INFO @ Tue, 02 Aug 2022 11:50:07: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 02 Aug 2022 11:50:07: #1 finished! INFO @ Tue, 02 Aug 2022 11:50:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:50:07: #2 number of paired peaks: 9150 INFO @ Tue, 02 Aug 2022 11:50:07: start model_add_line... INFO @ Tue, 02 Aug 2022 11:50:07: start X-correlation... INFO @ Tue, 02 Aug 2022 11:50:07: end of X-cor INFO @ Tue, 02 Aug 2022 11:50:07: #2 finished! INFO @ Tue, 02 Aug 2022 11:50:07: #2 predicted fragment length is 292 bps INFO @ Tue, 02 Aug 2022 11:50:07: #2 alternative fragment length(s) may be 2,292,305 bps INFO @ Tue, 02 Aug 2022 11:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20_model.r INFO @ Tue, 02 Aug 2022 11:50:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:50:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:50:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948319/SRX8948319.20_summits.bed INFO @ Tue, 02 Aug 2022 11:50:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 25 millis CompletedMACS2peakCalling