Job ID = 16436803 SRX = SRX8948324 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 109141 READS because READLEN < 1 Read 9379472 spots for SRR12453881/SRR12453881.sra Written 9379472 spots for SRR12453881/SRR12453881.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436947 ("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] 12 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 4 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] 1181573 / 9074659 = 0.1302 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 12:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.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 12:05:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:05:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:05:28: 1000000 INFO @ Tue, 02 Aug 2022 12:05:35: 2000000 INFO @ Tue, 02 Aug 2022 12:05:43: 3000000 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 12:05:50: 4000000 INFO @ Tue, 02 Aug 2022 12:05:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.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 12:05:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:05:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:05:57: 5000000 INFO @ Tue, 02 Aug 2022 12:06:00: 1000000 INFO @ Tue, 02 Aug 2022 12:06:05: 6000000 INFO @ Tue, 02 Aug 2022 12:06:09: 2000000 INFO @ Tue, 02 Aug 2022 12:06:13: 7000000 INFO @ Tue, 02 Aug 2022 12:06:17: 3000000 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 12:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.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 12:06:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:06:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:06:21: 8000000 INFO @ Tue, 02 Aug 2022 12:06:25: 4000000 INFO @ Tue, 02 Aug 2022 12:06:29: 9000000 INFO @ Tue, 02 Aug 2022 12:06:29: 1000000 INFO @ Tue, 02 Aug 2022 12:06:34: 5000000 INFO @ Tue, 02 Aug 2022 12:06:37: 10000000 INFO @ Tue, 02 Aug 2022 12:06:37: 2000000 INFO @ Tue, 02 Aug 2022 12:06:42: 6000000 INFO @ Tue, 02 Aug 2022 12:06:45: 11000000 INFO @ Tue, 02 Aug 2022 12:06:46: 3000000 INFO @ Tue, 02 Aug 2022 12:06:50: 7000000 INFO @ Tue, 02 Aug 2022 12:06:53: 12000000 INFO @ Tue, 02 Aug 2022 12:06:54: 4000000 INFO @ Tue, 02 Aug 2022 12:06:59: 8000000 INFO @ Tue, 02 Aug 2022 12:07:02: 13000000 INFO @ Tue, 02 Aug 2022 12:07:03: 5000000 INFO @ Tue, 02 Aug 2022 12:07:07: 9000000 INFO @ Tue, 02 Aug 2022 12:07:10: 14000000 INFO @ Tue, 02 Aug 2022 12:07:11: 6000000 INFO @ Tue, 02 Aug 2022 12:07:15: 10000000 INFO @ Tue, 02 Aug 2022 12:07:18: 15000000 INFO @ Tue, 02 Aug 2022 12:07:19: 7000000 INFO @ Tue, 02 Aug 2022 12:07:23: 11000000 INFO @ Tue, 02 Aug 2022 12:07:26: 16000000 INFO @ Tue, 02 Aug 2022 12:07:26: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:07:26: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:07:26: #1 total tags in treatment: 7837212 INFO @ Tue, 02 Aug 2022 12:07:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:07:26: #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 12:07:27: #1 tags after filtering in treatment: 5779906 INFO @ Tue, 02 Aug 2022 12:07:27: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 12:07:27: #1 finished! INFO @ Tue, 02 Aug 2022 12:07:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:07:27: 8000000 INFO @ Tue, 02 Aug 2022 12:07:28: #2 number of paired peaks: 9175 INFO @ Tue, 02 Aug 2022 12:07:28: start model_add_line... INFO @ Tue, 02 Aug 2022 12:07:28: start X-correlation... INFO @ Tue, 02 Aug 2022 12:07:28: end of X-cor INFO @ Tue, 02 Aug 2022 12:07:28: #2 finished! INFO @ Tue, 02 Aug 2022 12:07:28: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:07:28: #2 alternative fragment length(s) may be 2,148 bps INFO @ Tue, 02 Aug 2022 12:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05_model.r INFO @ Tue, 02 Aug 2022 12:07:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:07:31: 12000000 INFO @ Tue, 02 Aug 2022 12:07:35: 9000000 INFO @ Tue, 02 Aug 2022 12:07:39: 13000000 INFO @ Tue, 02 Aug 2022 12:07:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:07:42: 10000000 INFO @ Tue, 02 Aug 2022 12:07:47: 14000000 INFO @ Tue, 02 Aug 2022 12:07:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:07:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:07:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.05_summits.bed INFO @ Tue, 02 Aug 2022 12:07:48: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (394 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:07:49: 11000000 INFO @ Tue, 02 Aug 2022 12:07:55: 15000000 INFO @ Tue, 02 Aug 2022 12:07:57: 12000000 INFO @ Tue, 02 Aug 2022 12:08:03: 16000000 INFO @ Tue, 02 Aug 2022 12:08:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:08:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:08:03: #1 total tags in treatment: 7837212 INFO @ Tue, 02 Aug 2022 12:08:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:08:03: #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 12:08:03: #1 tags after filtering in treatment: 5779906 INFO @ Tue, 02 Aug 2022 12:08:03: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 12:08:03: #1 finished! INFO @ Tue, 02 Aug 2022 12:08:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:08:04: 13000000 INFO @ Tue, 02 Aug 2022 12:08:04: #2 number of paired peaks: 9175 INFO @ Tue, 02 Aug 2022 12:08:04: start model_add_line... INFO @ Tue, 02 Aug 2022 12:08:04: start X-correlation... INFO @ Tue, 02 Aug 2022 12:08:04: end of X-cor INFO @ Tue, 02 Aug 2022 12:08:04: #2 finished! INFO @ Tue, 02 Aug 2022 12:08:04: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:08:04: #2 alternative fragment length(s) may be 2,148 bps INFO @ Tue, 02 Aug 2022 12:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10_model.r INFO @ Tue, 02 Aug 2022 12:08:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:08:11: 14000000 INFO @ Tue, 02 Aug 2022 12:08:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:08:19: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:08:25: 16000000 INFO @ Tue, 02 Aug 2022 12:08:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:08:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:08:25: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:08:25: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:08:25: #1 total tags in treatment: 7837212 INFO @ Tue, 02 Aug 2022 12:08:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:08:25: #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 12:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.10_summits.bed INFO @ Tue, 02 Aug 2022 12:08:26: Done! INFO @ Tue, 02 Aug 2022 12:08:26: #1 tags after filtering in treatment: 5779906 INFO @ Tue, 02 Aug 2022 12:08:26: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 02 Aug 2022 12:08:26: #1 finished! INFO @ Tue, 02 Aug 2022 12:08:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:08:26: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:08:27: #2 number of paired peaks: 9175 INFO @ Tue, 02 Aug 2022 12:08:27: start model_add_line... INFO @ Tue, 02 Aug 2022 12:08:27: start X-correlation... INFO @ Tue, 02 Aug 2022 12:08:27: end of X-cor INFO @ Tue, 02 Aug 2022 12:08:27: #2 finished! INFO @ Tue, 02 Aug 2022 12:08:27: #2 predicted fragment length is 148 bps INFO @ Tue, 02 Aug 2022 12:08:27: #2 alternative fragment length(s) may be 2,148 bps INFO @ Tue, 02 Aug 2022 12:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20_model.r INFO @ Tue, 02 Aug 2022 12:08:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:08:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:08:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:08:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:08:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8948324/SRX8948324.20_summits.bed INFO @ Tue, 02 Aug 2022 12:08:45: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。