Job ID = 14171328 SRX = SRX9005677 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 693637 READS because READLEN < 1 Read 6623938 spots for SRR12515078/SRR12515078.sra Written 6623938 spots for SRR12515078/SRR12515078.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171858 ("srTdm6") has been submitted Time loading reference: 00:00:01 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] 3 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] 1 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 700321 / 5533316 = 0.1266 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 11:39:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.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 11:39:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:39:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:39:42: 1000000 INFO @ Sat, 11 Dec 2021 11:39:48: 2000000 INFO @ Sat, 11 Dec 2021 11:39:54: 3000000 INFO @ Sat, 11 Dec 2021 11:40:00: 4000000 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 11:40:06: 5000000 INFO @ Sat, 11 Dec 2021 11:40:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.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 11:40:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:12: 6000000 INFO @ Sat, 11 Dec 2021 11:40:12: 1000000 INFO @ Sat, 11 Dec 2021 11:40:18: 7000000 INFO @ Sat, 11 Dec 2021 11:40:19: 2000000 INFO @ Sat, 11 Dec 2021 11:40:24: 8000000 INFO @ Sat, 11 Dec 2021 11:40:25: 3000000 INFO @ Sat, 11 Dec 2021 11:40:31: 9000000 INFO @ Sat, 11 Dec 2021 11:40:31: 4000000 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 11:40:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.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 11:40:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:37: 10000000 INFO @ Sat, 11 Dec 2021 11:40:38: 5000000 INFO @ Sat, 11 Dec 2021 11:40:40: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:40:40: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:40:40: #1 total tags in treatment: 4789875 INFO @ Sat, 11 Dec 2021 11:40:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:40:40: #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 11:40:40: #1 tags after filtering in treatment: 4640345 INFO @ Sat, 11 Dec 2021 11:40:40: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:40:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:40:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:40:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:40:40: #2 number of paired peaks: 1524 INFO @ Sat, 11 Dec 2021 11:40:40: start model_add_line... INFO @ Sat, 11 Dec 2021 11:40:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:40:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:40:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:40:40: #2 predicted fragment length is 263 bps INFO @ Sat, 11 Dec 2021 11:40:40: #2 alternative fragment length(s) may be 263 bps INFO @ Sat, 11 Dec 2021 11:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05_model.r INFO @ Sat, 11 Dec 2021 11:40:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:40:42: 1000000 INFO @ Sat, 11 Dec 2021 11:40:44: 6000000 INFO @ Sat, 11 Dec 2021 11:40:49: 2000000 INFO @ Sat, 11 Dec 2021 11:40:50: 7000000 INFO @ Sat, 11 Dec 2021 11:40:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:40:55: 3000000 INFO @ Sat, 11 Dec 2021 11:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.05_summits.bed INFO @ Sat, 11 Dec 2021 11:40:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4163 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:40:57: 8000000 INFO @ Sat, 11 Dec 2021 11:41:01: 4000000 INFO @ Sat, 11 Dec 2021 11:41:03: 9000000 INFO @ Sat, 11 Dec 2021 11:41:08: 5000000 INFO @ Sat, 11 Dec 2021 11:41:09: 10000000 INFO @ Sat, 11 Dec 2021 11:41:12: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:41:12: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:41:12: #1 total tags in treatment: 4789875 INFO @ Sat, 11 Dec 2021 11:41:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:41:12: #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 11:41:12: #1 tags after filtering in treatment: 4640345 INFO @ Sat, 11 Dec 2021 11:41:12: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:41:12: #1 finished! INFO @ Sat, 11 Dec 2021 11:41:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:41:12: #2 number of paired peaks: 1524 INFO @ Sat, 11 Dec 2021 11:41:12: start model_add_line... INFO @ Sat, 11 Dec 2021 11:41:12: start X-correlation... INFO @ Sat, 11 Dec 2021 11:41:12: end of X-cor INFO @ Sat, 11 Dec 2021 11:41:12: #2 finished! INFO @ Sat, 11 Dec 2021 11:41:12: #2 predicted fragment length is 263 bps INFO @ Sat, 11 Dec 2021 11:41:12: #2 alternative fragment length(s) may be 263 bps INFO @ Sat, 11 Dec 2021 11:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10_model.r INFO @ Sat, 11 Dec 2021 11:41:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:41:14: 6000000 INFO @ Sat, 11 Dec 2021 11:41:20: 7000000 INFO @ Sat, 11 Dec 2021 11:41:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:41:26: 8000000 INFO @ Sat, 11 Dec 2021 11:41:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:41:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:41:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.10_summits.bed INFO @ Sat, 11 Dec 2021 11:41:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2444 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:41:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:41:38: 10000000 INFO @ Sat, 11 Dec 2021 11:41:41: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:41:41: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:41:41: #1 total tags in treatment: 4789875 INFO @ Sat, 11 Dec 2021 11:41:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:41:41: #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 11:41:41: #1 tags after filtering in treatment: 4640345 INFO @ Sat, 11 Dec 2021 11:41:41: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:41:41: #1 finished! INFO @ Sat, 11 Dec 2021 11:41:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:41:41: #2 number of paired peaks: 1524 INFO @ Sat, 11 Dec 2021 11:41:41: start model_add_line... INFO @ Sat, 11 Dec 2021 11:41:41: start X-correlation... INFO @ Sat, 11 Dec 2021 11:41:41: end of X-cor INFO @ Sat, 11 Dec 2021 11:41:41: #2 finished! INFO @ Sat, 11 Dec 2021 11:41:41: #2 predicted fragment length is 263 bps INFO @ Sat, 11 Dec 2021 11:41:41: #2 alternative fragment length(s) may be 263 bps INFO @ Sat, 11 Dec 2021 11:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20_model.r INFO @ Sat, 11 Dec 2021 11:41:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:41:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:41:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:41:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005677/SRX9005677.20_summits.bed INFO @ Sat, 11 Dec 2021 11:41:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1106 records, 4 fields): 3 millis CompletedMACS2peakCalling