Job ID = 14171458 SRX = SRX10971697 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-11T02:43:23 prefetch.2.10.7: 1) Downloading 'SRR14631848'... 2021-12-11T02:43:23 prefetch.2.10.7: Downloading via HTTPS... 2021-12-11T02:43:59 prefetch.2.10.7: HTTPS download succeed 2021-12-11T02:43:59 prefetch.2.10.7: 'SRR14631848' is valid 2021-12-11T02:43:59 prefetch.2.10.7: 1) 'SRR14631848' was downloaded successfully 2021-12-11T02:43:59 prefetch.2.10.7: 'SRR14631848' has 0 unresolved dependencies Rejected 1012474 READS because READLEN < 1 Read 5780680 spots for SRR14631848/SRR14631848.sra Written 5780680 spots for SRR14631848/SRR14631848.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171968 ("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] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [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] 1 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] processing reference chrX... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 776539 / 4325493 = 0.1795 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 11:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.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 11:58:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:58:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:58:13: 1000000 INFO @ Sat, 11 Dec 2021 11:58:23: 2000000 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 11:58:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.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 11:58:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:58:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:58:34: 3000000 INFO @ Sat, 11 Dec 2021 11:58:43: 1000000 INFO @ Sat, 11 Dec 2021 11:58:46: 4000000 INFO @ Sat, 11 Dec 2021 11:58:53: 2000000 INFO @ Sat, 11 Dec 2021 11:58:57: 5000000 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 11:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.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 11:59:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:59:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:59:03: 3000000 INFO @ Sat, 11 Dec 2021 11:59:09: 6000000 INFO @ Sat, 11 Dec 2021 11:59:13: 1000000 INFO @ Sat, 11 Dec 2021 11:59:14: 4000000 INFO @ Sat, 11 Dec 2021 11:59:21: 7000000 INFO @ Sat, 11 Dec 2021 11:59:24: 2000000 INFO @ Sat, 11 Dec 2021 11:59:24: 5000000 INFO @ Sat, 11 Dec 2021 11:59:31: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:59:31: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:59:31: #1 total tags in treatment: 3483091 INFO @ Sat, 11 Dec 2021 11:59:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:59:31: #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 11:59:31: #1 tags after filtering in treatment: 3389537 INFO @ Sat, 11 Dec 2021 11:59:31: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:59:31: #1 finished! INFO @ Sat, 11 Dec 2021 11:59:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:59:32: #2 number of paired peaks: 4345 INFO @ Sat, 11 Dec 2021 11:59:32: start model_add_line... INFO @ Sat, 11 Dec 2021 11:59:32: start X-correlation... INFO @ Sat, 11 Dec 2021 11:59:32: end of X-cor INFO @ Sat, 11 Dec 2021 11:59:32: #2 finished! INFO @ Sat, 11 Dec 2021 11:59:32: #2 predicted fragment length is 285 bps INFO @ Sat, 11 Dec 2021 11:59:32: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 11 Dec 2021 11:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05_model.r INFO @ Sat, 11 Dec 2021 11:59:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:59:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:59:34: 3000000 INFO @ Sat, 11 Dec 2021 11:59:34: 6000000 INFO @ Sat, 11 Dec 2021 11:59:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:59:42: 4000000 INFO @ Sat, 11 Dec 2021 11:59:43: 7000000 INFO @ Sat, 11 Dec 2021 11:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.05_summits.bed INFO @ Sat, 11 Dec 2021 11:59:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5443 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:59:51: 5000000 INFO @ Sat, 11 Dec 2021 11:59:51: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:59:51: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:59:51: #1 total tags in treatment: 3483091 INFO @ Sat, 11 Dec 2021 11:59:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:59:51: #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 11:59:51: #1 tags after filtering in treatment: 3389537 INFO @ Sat, 11 Dec 2021 11:59:51: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:59:51: #1 finished! INFO @ Sat, 11 Dec 2021 11:59:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:59:51: #2 number of paired peaks: 4345 INFO @ Sat, 11 Dec 2021 11:59:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:59:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:59:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:59:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:59:51: #2 predicted fragment length is 285 bps INFO @ Sat, 11 Dec 2021 11:59:51: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 11 Dec 2021 11:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10_model.r INFO @ Sat, 11 Dec 2021 11:59:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:59:59: 6000000 INFO @ Sat, 11 Dec 2021 12:00:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.10_summits.bed INFO @ Sat, 11 Dec 2021 12:00:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3612 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:00:06: 7000000 INFO @ Sat, 11 Dec 2021 12:00:13: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 12:00:13: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 12:00:13: #1 total tags in treatment: 3483091 INFO @ Sat, 11 Dec 2021 12:00:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:00:13: #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 12:00:13: #1 tags after filtering in treatment: 3389537 INFO @ Sat, 11 Dec 2021 12:00:13: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 12:00:13: #1 finished! INFO @ Sat, 11 Dec 2021 12:00:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:00:13: #2 number of paired peaks: 4345 INFO @ Sat, 11 Dec 2021 12:00:13: start model_add_line... INFO @ Sat, 11 Dec 2021 12:00:13: start X-correlation... INFO @ Sat, 11 Dec 2021 12:00:13: end of X-cor INFO @ Sat, 11 Dec 2021 12:00:13: #2 finished! INFO @ Sat, 11 Dec 2021 12:00:13: #2 predicted fragment length is 285 bps INFO @ Sat, 11 Dec 2021 12:00:13: #2 alternative fragment length(s) may be 285 bps INFO @ Sat, 11 Dec 2021 12:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20_model.r INFO @ Sat, 11 Dec 2021 12:00:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:00:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10971697/SRX10971697.20_summits.bed INFO @ Sat, 11 Dec 2021 12:00:25: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 8 millis CompletedMACS2peakCalling