Job ID = 14171349 SRX = SRX9005684 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 654910 READS because READLEN < 1 Read 5101897 spots for SRR12515085/SRR12515085.sra Written 5101897 spots for SRR12515085/SRR12515085.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171822 ("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_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] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [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] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 406487 / 4177719 = 0.0973 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 11:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.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 11:30:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:30:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:31:03: 1000000 INFO @ Sat, 11 Dec 2021 11:31:09: 2000000 INFO @ Sat, 11 Dec 2021 11:31:16: 3000000 INFO @ Sat, 11 Dec 2021 11:31:23: 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 11:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.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 11:31:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:31:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:31:31: 5000000 INFO @ Sat, 11 Dec 2021 11:31:34: 1000000 INFO @ Sat, 11 Dec 2021 11:31:39: 6000000 INFO @ Sat, 11 Dec 2021 11:31:41: 2000000 INFO @ Sat, 11 Dec 2021 11:31:47: 7000000 INFO @ Sat, 11 Dec 2021 11:31:49: 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 11:31:55: 8000000 INFO @ Sat, 11 Dec 2021 11:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.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 11:31:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:31:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:31:56: 4000000 INFO @ Sat, 11 Dec 2021 11:31:57: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:31:57: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:31:57: #1 total tags in treatment: 3724444 INFO @ Sat, 11 Dec 2021 11:31:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:31:57: #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 11:31:57: #1 tags after filtering in treatment: 3536693 INFO @ Sat, 11 Dec 2021 11:31:57: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 11:31:57: #1 finished! INFO @ Sat, 11 Dec 2021 11:31:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:31:57: #2 number of paired peaks: 4016 INFO @ Sat, 11 Dec 2021 11:31:57: start model_add_line... INFO @ Sat, 11 Dec 2021 11:31:57: start X-correlation... INFO @ Sat, 11 Dec 2021 11:31:57: end of X-cor INFO @ Sat, 11 Dec 2021 11:31:57: #2 finished! INFO @ Sat, 11 Dec 2021 11:31:57: #2 predicted fragment length is 301 bps INFO @ Sat, 11 Dec 2021 11:31:57: #2 alternative fragment length(s) may be 301 bps INFO @ Sat, 11 Dec 2021 11:31:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05_model.r INFO @ Sat, 11 Dec 2021 11:31:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:31:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:32:03: 1000000 INFO @ Sat, 11 Dec 2021 11:32:04: 5000000 INFO @ Sat, 11 Dec 2021 11:32:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.05_summits.bed INFO @ Sat, 11 Dec 2021 11:32:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5317 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:32:10: 2000000 INFO @ Sat, 11 Dec 2021 11:32:11: 6000000 INFO @ Sat, 11 Dec 2021 11:32:17: 3000000 INFO @ Sat, 11 Dec 2021 11:32:19: 7000000 INFO @ Sat, 11 Dec 2021 11:32:24: 4000000 INFO @ Sat, 11 Dec 2021 11:32:26: 8000000 INFO @ Sat, 11 Dec 2021 11:32:28: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:32:28: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:32:28: #1 total tags in treatment: 3724444 INFO @ Sat, 11 Dec 2021 11:32:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:32:28: #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 11:32:28: #1 tags after filtering in treatment: 3536693 INFO @ Sat, 11 Dec 2021 11:32:28: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 11:32:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:32:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:32:28: #2 number of paired peaks: 4016 INFO @ Sat, 11 Dec 2021 11:32:28: start model_add_line... INFO @ Sat, 11 Dec 2021 11:32:28: start X-correlation... INFO @ Sat, 11 Dec 2021 11:32:28: end of X-cor INFO @ Sat, 11 Dec 2021 11:32:28: #2 finished! INFO @ Sat, 11 Dec 2021 11:32:28: #2 predicted fragment length is 301 bps INFO @ Sat, 11 Dec 2021 11:32:28: #2 alternative fragment length(s) may be 301 bps INFO @ Sat, 11 Dec 2021 11:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10_model.r INFO @ Sat, 11 Dec 2021 11:32:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:32:30: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:32:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:32:37: 6000000 INFO @ Sat, 11 Dec 2021 11:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.10_summits.bed INFO @ Sat, 11 Dec 2021 11:32:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3491 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:32:43: 7000000 INFO @ Sat, 11 Dec 2021 11:32:49: 8000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:32:50: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:32:50: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:32:50: #1 total tags in treatment: 3724444 INFO @ Sat, 11 Dec 2021 11:32:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:32:50: #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 11:32:50: #1 tags after filtering in treatment: 3536693 INFO @ Sat, 11 Dec 2021 11:32:50: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 11:32:50: #1 finished! INFO @ Sat, 11 Dec 2021 11:32:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:32:51: #2 number of paired peaks: 4016 INFO @ Sat, 11 Dec 2021 11:32:51: start model_add_line... INFO @ Sat, 11 Dec 2021 11:32:51: start X-correlation... INFO @ Sat, 11 Dec 2021 11:32:51: end of X-cor INFO @ Sat, 11 Dec 2021 11:32:51: #2 finished! INFO @ Sat, 11 Dec 2021 11:32:51: #2 predicted fragment length is 301 bps INFO @ Sat, 11 Dec 2021 11:32:51: #2 alternative fragment length(s) may be 301 bps INFO @ Sat, 11 Dec 2021 11:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20_model.r INFO @ Sat, 11 Dec 2021 11:32:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:32:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005684/SRX9005684.20_summits.bed INFO @ Sat, 11 Dec 2021 11:33:03: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1630 records, 4 fields): 5 millis CompletedMACS2peakCalling