Job ID = 14171327 SRX = SRX9005676 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 652888 READS because READLEN < 1 Read 8269509 spots for SRR12515077/SRR12515077.sra Written 8269509 spots for SRR12515077/SRR12515077.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171886 ("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 12 files... [bam_rmdup_core] processing reference chr2L... [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] 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] 2 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1186376 / 6948842 = 0.1707 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 11:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.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 11:44:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:44:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:44:49: 1000000 INFO @ Sat, 11 Dec 2021 11:44:57: 2000000 INFO @ Sat, 11 Dec 2021 11:45:05: 3000000 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 11:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.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 11:45:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:13: 4000000 INFO @ Sat, 11 Dec 2021 11:45:18: 1000000 INFO @ Sat, 11 Dec 2021 11:45:21: 5000000 INFO @ Sat, 11 Dec 2021 11:45:25: 2000000 INFO @ Sat, 11 Dec 2021 11:45:30: 6000000 INFO @ Sat, 11 Dec 2021 11:45:32: 3000000 INFO @ Sat, 11 Dec 2021 11:45:39: 7000000 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 11:45:40: 4000000 INFO @ Sat, 11 Dec 2021 11:45:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.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 11:45:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:45:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:45:47: 5000000 INFO @ Sat, 11 Dec 2021 11:45:47: 8000000 INFO @ Sat, 11 Dec 2021 11:45:50: 1000000 INFO @ Sat, 11 Dec 2021 11:45:54: 6000000 INFO @ Sat, 11 Dec 2021 11:45:56: 9000000 INFO @ Sat, 11 Dec 2021 11:45:58: 2000000 INFO @ Sat, 11 Dec 2021 11:46:01: 7000000 INFO @ Sat, 11 Dec 2021 11:46:04: 10000000 INFO @ Sat, 11 Dec 2021 11:46:07: 3000000 INFO @ Sat, 11 Dec 2021 11:46:08: 8000000 INFO @ Sat, 11 Dec 2021 11:46:13: 11000000 INFO @ Sat, 11 Dec 2021 11:46:15: 9000000 INFO @ Sat, 11 Dec 2021 11:46:16: 4000000 INFO @ Sat, 11 Dec 2021 11:46:22: 12000000 INFO @ Sat, 11 Dec 2021 11:46:23: 10000000 INFO @ Sat, 11 Dec 2021 11:46:24: 5000000 INFO @ Sat, 11 Dec 2021 11:46:24: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:46:24: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:46:24: #1 total tags in treatment: 5725518 INFO @ Sat, 11 Dec 2021 11:46:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:24: #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 11:46:24: #1 tags after filtering in treatment: 5546674 INFO @ Sat, 11 Dec 2021 11:46:24: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:46:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:25: #2 number of paired peaks: 849 WARNING @ Sat, 11 Dec 2021 11:46:25: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Sat, 11 Dec 2021 11:46:25: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:25: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:25: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:25: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:25: #2 predicted fragment length is 258 bps INFO @ Sat, 11 Dec 2021 11:46:25: #2 alternative fragment length(s) may be 258 bps INFO @ Sat, 11 Dec 2021 11:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05_model.r INFO @ Sat, 11 Dec 2021 11:46:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:31: 11000000 INFO @ Sat, 11 Dec 2021 11:46:33: 6000000 INFO @ Sat, 11 Dec 2021 11:46:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:38: 12000000 INFO @ Sat, 11 Dec 2021 11:46:40: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:46:40: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:46:40: #1 total tags in treatment: 5725518 INFO @ Sat, 11 Dec 2021 11:46:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:46:40: #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 11:46:40: #1 tags after filtering in treatment: 5546674 INFO @ Sat, 11 Dec 2021 11:46:40: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:46:40: #1 finished! INFO @ Sat, 11 Dec 2021 11:46:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:46:40: #2 number of paired peaks: 849 WARNING @ Sat, 11 Dec 2021 11:46:40: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Sat, 11 Dec 2021 11:46:40: start model_add_line... INFO @ Sat, 11 Dec 2021 11:46:40: start X-correlation... INFO @ Sat, 11 Dec 2021 11:46:40: end of X-cor INFO @ Sat, 11 Dec 2021 11:46:40: #2 finished! INFO @ Sat, 11 Dec 2021 11:46:40: #2 predicted fragment length is 258 bps INFO @ Sat, 11 Dec 2021 11:46:40: #2 alternative fragment length(s) may be 258 bps INFO @ Sat, 11 Dec 2021 11:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10_model.r INFO @ Sat, 11 Dec 2021 11:46:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:46:41: 7000000 INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.05_summits.bed INFO @ Sat, 11 Dec 2021 11:46:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3970 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:46:49: 8000000 INFO @ Sat, 11 Dec 2021 11:46:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:46:57: 9000000 INFO @ Sat, 11 Dec 2021 11:46:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:46:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:46:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.10_summits.bed INFO @ Sat, 11 Dec 2021 11:46:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2107 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:47:05: 10000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:47:13: 11000000 INFO @ Sat, 11 Dec 2021 11:47:22: 12000000 INFO @ Sat, 11 Dec 2021 11:47:24: #1 tag size is determined as 125 bps INFO @ Sat, 11 Dec 2021 11:47:24: #1 tag size = 125 INFO @ Sat, 11 Dec 2021 11:47:24: #1 total tags in treatment: 5725518 INFO @ Sat, 11 Dec 2021 11:47:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:47:24: #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 11:47:24: #1 tags after filtering in treatment: 5546674 INFO @ Sat, 11 Dec 2021 11:47:24: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 11:47:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:47:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:47:24: #2 number of paired peaks: 849 WARNING @ Sat, 11 Dec 2021 11:47:24: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Sat, 11 Dec 2021 11:47:24: start model_add_line... INFO @ Sat, 11 Dec 2021 11:47:24: start X-correlation... INFO @ Sat, 11 Dec 2021 11:47:24: end of X-cor INFO @ Sat, 11 Dec 2021 11:47:24: #2 finished! INFO @ Sat, 11 Dec 2021 11:47:24: #2 predicted fragment length is 258 bps INFO @ Sat, 11 Dec 2021 11:47:24: #2 alternative fragment length(s) may be 258 bps INFO @ Sat, 11 Dec 2021 11:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20_model.r INFO @ Sat, 11 Dec 2021 11:47:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:47:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:47:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:47:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:47:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005676/SRX9005676.20_summits.bed INFO @ Sat, 11 Dec 2021 11:47:42: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (875 records, 4 fields): 3 millis CompletedMACS2peakCalling