Job ID = 16436578 SRX = SRX8948320 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 115754 READS because READLEN < 1 Read 10463164 spots for SRR12453877/SRR12453877.sra Written 10463164 spots for SRR12453877/SRR12453877.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436843 ("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] 53 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 8 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] 2427353 / 10134667 = 0.2395 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 11:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.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 11:56:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:56:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:56:41: 1000000 INFO @ Tue, 02 Aug 2022 11:56:46: 2000000 INFO @ Tue, 02 Aug 2022 11:56:52: 3000000 INFO @ Tue, 02 Aug 2022 11:56:57: 4000000 INFO @ Tue, 02 Aug 2022 11:57:03: 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 11:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.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 11:57:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:57:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:57:09: 6000000 INFO @ Tue, 02 Aug 2022 11:57:11: 1000000 INFO @ Tue, 02 Aug 2022 11:57:15: 7000000 INFO @ Tue, 02 Aug 2022 11:57:17: 2000000 INFO @ Tue, 02 Aug 2022 11:57:21: 8000000 INFO @ Tue, 02 Aug 2022 11:57:23: 3000000 INFO @ Tue, 02 Aug 2022 11:57:27: 9000000 INFO @ Tue, 02 Aug 2022 11:57:28: 4000000 INFO @ Tue, 02 Aug 2022 11:57:32: 10000000 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 11:57:34: 5000000 INFO @ Tue, 02 Aug 2022 11:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.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 11:57:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:57:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:57:38: 11000000 INFO @ Tue, 02 Aug 2022 11:57:39: 6000000 INFO @ Tue, 02 Aug 2022 11:57:41: 1000000 INFO @ Tue, 02 Aug 2022 11:57:44: 12000000 INFO @ Tue, 02 Aug 2022 11:57:45: 7000000 INFO @ Tue, 02 Aug 2022 11:57:47: 2000000 INFO @ Tue, 02 Aug 2022 11:57:50: 13000000 INFO @ Tue, 02 Aug 2022 11:57:51: 8000000 INFO @ Tue, 02 Aug 2022 11:57:53: 3000000 INFO @ Tue, 02 Aug 2022 11:57:56: 14000000 INFO @ Tue, 02 Aug 2022 11:57:56: 9000000 INFO @ Tue, 02 Aug 2022 11:57:58: 4000000 INFO @ Tue, 02 Aug 2022 11:58:01: 15000000 INFO @ Tue, 02 Aug 2022 11:58:01: 10000000 INFO @ Tue, 02 Aug 2022 11:58:04: 5000000 INFO @ Tue, 02 Aug 2022 11:58:05: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:58:05: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:58:05: #1 total tags in treatment: 7689327 INFO @ Tue, 02 Aug 2022 11:58:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:05: #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 11:58:05: #1 tags after filtering in treatment: 5980910 INFO @ Tue, 02 Aug 2022 11:58:05: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 11:58:05: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:06: #2 number of paired peaks: 7171 INFO @ Tue, 02 Aug 2022 11:58:06: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:06: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:06: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:06: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:06: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 11:58:06: #2 alternative fragment length(s) may be 2,154 bps INFO @ Tue, 02 Aug 2022 11:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05_model.r INFO @ Tue, 02 Aug 2022 11:58:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:58:07: 11000000 INFO @ Tue, 02 Aug 2022 11:58:10: 6000000 INFO @ Tue, 02 Aug 2022 11:58:13: 12000000 INFO @ Tue, 02 Aug 2022 11:58:16: 7000000 INFO @ Tue, 02 Aug 2022 11:58:19: 13000000 INFO @ Tue, 02 Aug 2022 11:58:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:21: 8000000 INFO @ Tue, 02 Aug 2022 11:58:25: 14000000 INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.05_summits.bed INFO @ Tue, 02 Aug 2022 11:58:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 138 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:58:27: 9000000 INFO @ Tue, 02 Aug 2022 11:58:30: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:58:32: 10000000 INFO @ Tue, 02 Aug 2022 11:58:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:58:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:58:34: #1 total tags in treatment: 7689327 INFO @ Tue, 02 Aug 2022 11:58:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:58:34: #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 11:58:34: #1 tags after filtering in treatment: 5980910 INFO @ Tue, 02 Aug 2022 11:58:34: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 11:58:34: #1 finished! INFO @ Tue, 02 Aug 2022 11:58:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:58:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:58:35: #2 number of paired peaks: 7171 INFO @ Tue, 02 Aug 2022 11:58:35: start model_add_line... INFO @ Tue, 02 Aug 2022 11:58:35: start X-correlation... INFO @ Tue, 02 Aug 2022 11:58:35: end of X-cor INFO @ Tue, 02 Aug 2022 11:58:35: #2 finished! INFO @ Tue, 02 Aug 2022 11:58:35: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 11:58:35: #2 alternative fragment length(s) may be 2,154 bps INFO @ Tue, 02 Aug 2022 11:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10_model.r INFO @ Tue, 02 Aug 2022 11:58:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:58:38: 11000000 INFO @ Tue, 02 Aug 2022 11:58:43: 12000000 INFO @ Tue, 02 Aug 2022 11:58:47: 13000000 INFO @ Tue, 02 Aug 2022 11:58:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:58:52: 14000000 INFO @ Tue, 02 Aug 2022 11:58:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:58:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:58:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.10_summits.bed INFO @ Tue, 02 Aug 2022 11:58:54: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:58:57: 15000000 INFO @ Tue, 02 Aug 2022 11:59:00: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 11:59:00: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 11:59:00: #1 total tags in treatment: 7689327 INFO @ Tue, 02 Aug 2022 11:59:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:59:00: #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 11:59:01: #1 tags after filtering in treatment: 5980910 INFO @ Tue, 02 Aug 2022 11:59:01: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 11:59:01: #1 finished! INFO @ Tue, 02 Aug 2022 11:59:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:59:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:59:01: #2 number of paired peaks: 7171 INFO @ Tue, 02 Aug 2022 11:59:01: start model_add_line... INFO @ Tue, 02 Aug 2022 11:59:01: start X-correlation... INFO @ Tue, 02 Aug 2022 11:59:01: end of X-cor INFO @ Tue, 02 Aug 2022 11:59:01: #2 finished! INFO @ Tue, 02 Aug 2022 11:59:01: #2 predicted fragment length is 154 bps INFO @ Tue, 02 Aug 2022 11:59:01: #2 alternative fragment length(s) may be 2,154 bps INFO @ Tue, 02 Aug 2022 11:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20_model.r INFO @ Tue, 02 Aug 2022 11:59:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:59:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948320/SRX8948320.20_summits.bed INFO @ Tue, 02 Aug 2022 11:59:22: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 29 millis CompletedMACS2peakCalling