Job ID = 14171461 SRX = SRX10971699 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:43:53 prefetch.2.10.7: 1) Downloading 'SRR14631850'... 2021-12-11T02:43:53 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:45:14 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:45:14 prefetch.2.10.7: 1) 'SRR14631850' was downloaded successfully 2021-12-11T02:45:14 prefetch.2.10.7: 'SRR14631850' has 0 unresolved dependencies Rejected 3016213 READS because READLEN < 1 Read 15113169 spots for SRR14631850/SRR14631850.sra Written 15113169 spots for SRR14631850/SRR14631850.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172081 ("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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 2 unmatched pairs [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] 3 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4663205 / 11221369 = 0.4156 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 12:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.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 12:39:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:39:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:39:51: 1000000 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 12:40:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.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 12:40:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:08: 2000000 INFO @ Sat, 11 Dec 2021 12:40:21: 1000000 INFO @ Sat, 11 Dec 2021 12:40:30: 3000000 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 12:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.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 12:40:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:41: 2000000 INFO @ Sat, 11 Dec 2021 12:40:51: 4000000 INFO @ Sat, 11 Dec 2021 12:41:00: 3000000 INFO @ Sat, 11 Dec 2021 12:41:06: 1000000 INFO @ Sat, 11 Dec 2021 12:41:10: 5000000 INFO @ Sat, 11 Dec 2021 12:41:17: 4000000 INFO @ Sat, 11 Dec 2021 12:41:28: 6000000 INFO @ Sat, 11 Dec 2021 12:41:35: 5000000 INFO @ Sat, 11 Dec 2021 12:41:38: 2000000 INFO @ Sat, 11 Dec 2021 12:41:46: 7000000 INFO @ Sat, 11 Dec 2021 12:41:51: 6000000 INFO @ Sat, 11 Dec 2021 12:42:06: 8000000 INFO @ Sat, 11 Dec 2021 12:42:08: 7000000 INFO @ Sat, 11 Dec 2021 12:42:08: 3000000 INFO @ Sat, 11 Dec 2021 12:42:25: 9000000 INFO @ Sat, 11 Dec 2021 12:42:26: 8000000 INFO @ Sat, 11 Dec 2021 12:42:39: 10000000 INFO @ Sat, 11 Dec 2021 12:42:44: 9000000 INFO @ Sat, 11 Dec 2021 12:42:45: 4000000 INFO @ Sat, 11 Dec 2021 12:42:56: 11000000 INFO @ Sat, 11 Dec 2021 12:42:58: 10000000 INFO @ Sat, 11 Dec 2021 12:43:12: 12000000 INFO @ Sat, 11 Dec 2021 12:43:14: 11000000 INFO @ Sat, 11 Dec 2021 12:43:16: 5000000 INFO @ Sat, 11 Dec 2021 12:43:29: 13000000 INFO @ Sat, 11 Dec 2021 12:43:31: 12000000 INFO @ Sat, 11 Dec 2021 12:43:47: 14000000 INFO @ Sat, 11 Dec 2021 12:43:48: 6000000 INFO @ Sat, 11 Dec 2021 12:43:48: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:44:04: 15000000 INFO @ Sat, 11 Dec 2021 12:44:06: 14000000 INFO @ Sat, 11 Dec 2021 12:44:16: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:44:16: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:44:16: #1 total tags in treatment: 6351818 INFO @ Sat, 11 Dec 2021 12:44:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:16: #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 12:44:17: #1 tags after filtering in treatment: 5970503 INFO @ Sat, 11 Dec 2021 12:44:17: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:44:17: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:18: #2 number of paired peaks: 5624 INFO @ Sat, 11 Dec 2021 12:44:18: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:18: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:18: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:18: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:18: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 12:44:18: #2 alternative fragment length(s) may be 283 bps INFO @ Sat, 11 Dec 2021 12:44:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05_model.r INFO @ Sat, 11 Dec 2021 12:44:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:44:21: 7000000 INFO @ Sat, 11 Dec 2021 12:44:23: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:44:35: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:44:35: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:44:35: #1 total tags in treatment: 6351818 INFO @ Sat, 11 Dec 2021 12:44:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:35: #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 12:44:35: #1 tags after filtering in treatment: 5970503 INFO @ Sat, 11 Dec 2021 12:44:35: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:44:35: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:36: #2 number of paired peaks: 5624 INFO @ Sat, 11 Dec 2021 12:44:36: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:36: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:36: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:36: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:36: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 12:44:36: #2 alternative fragment length(s) may be 283 bps INFO @ Sat, 11 Dec 2021 12:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10_model.r INFO @ Sat, 11 Dec 2021 12:44:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:44:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.05_summits.bed INFO @ Sat, 11 Dec 2021 12:44:55: Done! INFO @ Sat, 11 Dec 2021 12:44:55: 8000000 pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (6954 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:45:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.10_summits.bed INFO @ Sat, 11 Dec 2021 12:45:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5708 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:45:23: 9000000 INFO @ Sat, 11 Dec 2021 12:45:47: 10000000 INFO @ Sat, 11 Dec 2021 12:46:14: 11000000 INFO @ Sat, 11 Dec 2021 12:46:41: 12000000 INFO @ Sat, 11 Dec 2021 12:47:14: 13000000 INFO @ Sat, 11 Dec 2021 12:47:42: 14000000 INFO @ Sat, 11 Dec 2021 12:48:10: 15000000 INFO @ Sat, 11 Dec 2021 12:48:29: #1 tag size is determined as 124 bps INFO @ Sat, 11 Dec 2021 12:48:29: #1 tag size = 124 INFO @ Sat, 11 Dec 2021 12:48:29: #1 total tags in treatment: 6351818 INFO @ Sat, 11 Dec 2021 12:48:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:48:29: #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 12:48:29: #1 tags after filtering in treatment: 5970503 INFO @ Sat, 11 Dec 2021 12:48:29: #1 Redundant rate of treatment: 0.06 INFO @ Sat, 11 Dec 2021 12:48:29: #1 finished! INFO @ Sat, 11 Dec 2021 12:48:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:48:30: #2 number of paired peaks: 5624 INFO @ Sat, 11 Dec 2021 12:48:30: start model_add_line... INFO @ Sat, 11 Dec 2021 12:48:30: start X-correlation... INFO @ Sat, 11 Dec 2021 12:48:30: end of X-cor INFO @ Sat, 11 Dec 2021 12:48:30: #2 finished! INFO @ Sat, 11 Dec 2021 12:48:30: #2 predicted fragment length is 283 bps INFO @ Sat, 11 Dec 2021 12:48:30: #2 alternative fragment length(s) may be 283 bps INFO @ Sat, 11 Dec 2021 12:48:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20_model.r INFO @ Sat, 11 Dec 2021 12:48:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:48:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:48:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:49:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:49:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:49:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971699/SRX10971699.20_summits.bed INFO @ Sat, 11 Dec 2021 12:49:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3998 records, 4 fields): 8 millis CompletedMACS2peakCalling