Job ID = 16438679 SRX = SRX14748158 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 5760 READS because READLEN < 1 Read 6126576 spots for SRR18645005/SRR18645005.sra Written 6126576 spots for SRR18645005/SRR18645005.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438970 ("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 -1 than in file specified with -2 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] 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] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 202031 / 5732203 = 0.0352 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 14:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.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 14:20:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:20:19: 1000000 INFO @ Tue, 02 Aug 2022 14:20:25: 2000000 INFO @ Tue, 02 Aug 2022 14:20:32: 3000000 INFO @ Tue, 02 Aug 2022 14:20:38: 4000000 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 14:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.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 14:20:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:20:45: 5000000 INFO @ Tue, 02 Aug 2022 14:20:49: 1000000 INFO @ Tue, 02 Aug 2022 14:20:53: 6000000 INFO @ Tue, 02 Aug 2022 14:20:56: 2000000 INFO @ Tue, 02 Aug 2022 14:21:00: 7000000 INFO @ Tue, 02 Aug 2022 14:21:02: 3000000 INFO @ Tue, 02 Aug 2022 14:21:08: 8000000 INFO @ Tue, 02 Aug 2022 14:21:09: 4000000 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 14:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.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 14:21:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:21:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:21:15: 9000000 INFO @ Tue, 02 Aug 2022 14:21:16: 5000000 INFO @ Tue, 02 Aug 2022 14:21:19: 1000000 INFO @ Tue, 02 Aug 2022 14:21:22: 6000000 INFO @ Tue, 02 Aug 2022 14:21:23: 10000000 INFO @ Tue, 02 Aug 2022 14:21:25: 2000000 INFO @ Tue, 02 Aug 2022 14:21:29: 7000000 INFO @ Tue, 02 Aug 2022 14:21:31: 11000000 INFO @ Tue, 02 Aug 2022 14:21:32: 3000000 INFO @ Tue, 02 Aug 2022 14:21:33: #1 tag size is determined as 69 bps INFO @ Tue, 02 Aug 2022 14:21:33: #1 tag size = 69 INFO @ Tue, 02 Aug 2022 14:21:33: #1 total tags in treatment: 5522744 INFO @ Tue, 02 Aug 2022 14:21:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:21:33: #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 14:21:33: #1 tags after filtering in treatment: 5284340 INFO @ Tue, 02 Aug 2022 14:21:33: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:21:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:21:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:21:34: #2 number of paired peaks: 1399 INFO @ Tue, 02 Aug 2022 14:21:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:21:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:21:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:21:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:21:34: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 14:21:34: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 14:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05_model.r INFO @ Tue, 02 Aug 2022 14:21:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:21:35: 8000000 INFO @ Tue, 02 Aug 2022 14:21:38: 4000000 INFO @ Tue, 02 Aug 2022 14:21:42: 9000000 INFO @ Tue, 02 Aug 2022 14:21:45: 5000000 INFO @ Tue, 02 Aug 2022 14:21:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:21:48: 10000000 INFO @ Tue, 02 Aug 2022 14:21:51: 6000000 INFO @ Tue, 02 Aug 2022 14:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.05_summits.bed INFO @ Tue, 02 Aug 2022 14:21:53: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1601 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:21:55: 11000000 INFO @ Tue, 02 Aug 2022 14:21:57: #1 tag size is determined as 69 bps INFO @ Tue, 02 Aug 2022 14:21:57: #1 tag size = 69 INFO @ Tue, 02 Aug 2022 14:21:57: #1 total tags in treatment: 5522744 INFO @ Tue, 02 Aug 2022 14:21:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:21:57: #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 14:21:57: #1 tags after filtering in treatment: 5284340 INFO @ Tue, 02 Aug 2022 14:21:57: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:21:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:21:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:21:58: #2 number of paired peaks: 1399 INFO @ Tue, 02 Aug 2022 14:21:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:21:58: start X-correlation... INFO @ Tue, 02 Aug 2022 14:21:58: end of X-cor INFO @ Tue, 02 Aug 2022 14:21:58: #2 finished! INFO @ Tue, 02 Aug 2022 14:21:58: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 14:21:58: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 14:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10_model.r INFO @ Tue, 02 Aug 2022 14:21:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:21:58: 7000000 INFO @ Tue, 02 Aug 2022 14:22:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:22:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:22:10: 9000000 INFO @ Tue, 02 Aug 2022 14:22:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:22:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.10_summits.bed INFO @ Tue, 02 Aug 2022 14:22:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (942 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:22:16: 10000000 INFO @ Tue, 02 Aug 2022 14:22:22: 11000000 INFO @ Tue, 02 Aug 2022 14:22:24: #1 tag size is determined as 69 bps INFO @ Tue, 02 Aug 2022 14:22:24: #1 tag size = 69 INFO @ Tue, 02 Aug 2022 14:22:24: #1 total tags in treatment: 5522744 INFO @ Tue, 02 Aug 2022 14:22:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:22:24: #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 14:22:25: #1 tags after filtering in treatment: 5284340 INFO @ Tue, 02 Aug 2022 14:22:25: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 14:22:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:22:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:22:25: #2 number of paired peaks: 1399 INFO @ Tue, 02 Aug 2022 14:22:25: start model_add_line... INFO @ Tue, 02 Aug 2022 14:22:25: start X-correlation... INFO @ Tue, 02 Aug 2022 14:22:25: end of X-cor INFO @ Tue, 02 Aug 2022 14:22:25: #2 finished! INFO @ Tue, 02 Aug 2022 14:22:25: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 14:22:25: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 14:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20_model.r INFO @ Tue, 02 Aug 2022 14:22:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:22:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:22:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:22:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14748158/SRX14748158.20_summits.bed INFO @ Tue, 02 Aug 2022 14:22:44: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (540 records, 4 fields): 154 millis CompletedMACS2peakCalling