Job ID = 14171384 SRX = SRX9005695 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Rejected 1023016 READS because READLEN < 1 Read 5059176 spots for SRR12515096/SRR12515096.sra Written 5059176 spots for SRR12515096/SRR12515096.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171881 ("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] 7 unmatched pairs [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] 12 unmatched pairs [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] 19 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 15 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] 5 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 7 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 944645 / 3639493 = 0.2596 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 11:40:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.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 11:40:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:43: 1000000 INFO @ Sat, 11 Dec 2021 11:40:49: 2000000 INFO @ Sat, 11 Dec 2021 11:40:55: 3000000 INFO @ Sat, 11 Dec 2021 11:41:02: 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 11:41:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.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 11:41:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:08: 5000000 INFO @ Sat, 11 Dec 2021 11:41:14: 1000000 INFO @ Sat, 11 Dec 2021 11:41:14: 6000000 INFO @ Sat, 11 Dec 2021 11:41:16: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:41:16: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:41:16: #1 total tags in treatment: 2642885 INFO @ Sat, 11 Dec 2021 11:41:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:41:16: #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 11:41:16: #1 tags after filtering in treatment: 2594915 INFO @ Sat, 11 Dec 2021 11:41:16: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:41:16: #1 finished! INFO @ Sat, 11 Dec 2021 11:41:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:41:16: #2 number of paired peaks: 280 WARNING @ Sat, 11 Dec 2021 11:41:16: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 11 Dec 2021 11:41:16: start model_add_line... INFO @ Sat, 11 Dec 2021 11:41:16: start X-correlation... INFO @ Sat, 11 Dec 2021 11:41:16: end of X-cor INFO @ Sat, 11 Dec 2021 11:41:16: #2 finished! INFO @ Sat, 11 Dec 2021 11:41:16: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 11:41:16: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Dec 2021 11:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05_model.r WARNING @ Sat, 11 Dec 2021 11:41:16: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:41:16: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 11 Dec 2021 11:41:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:41:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:41:20: 2000000 INFO @ Sat, 11 Dec 2021 11:41:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:41:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:41:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:41:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.05_summits.bed INFO @ Sat, 11 Dec 2021 11:41:24: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (489 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:41:26: 3000000 INFO @ Sat, 11 Dec 2021 11:41:33: 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 11:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.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 11:41:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:39: 5000000 INFO @ Sat, 11 Dec 2021 11:41:43: 1000000 INFO @ Sat, 11 Dec 2021 11:41:46: 6000000 INFO @ Sat, 11 Dec 2021 11:41:47: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:41:47: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:41:47: #1 total tags in treatment: 2642885 INFO @ Sat, 11 Dec 2021 11:41:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:41:47: #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 11:41:47: #1 tags after filtering in treatment: 2594915 INFO @ Sat, 11 Dec 2021 11:41:47: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:41:47: #1 finished! INFO @ Sat, 11 Dec 2021 11:41:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:41:47: #2 number of paired peaks: 280 WARNING @ Sat, 11 Dec 2021 11:41:47: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 11 Dec 2021 11:41:47: start model_add_line... INFO @ Sat, 11 Dec 2021 11:41:47: start X-correlation... INFO @ Sat, 11 Dec 2021 11:41:47: end of X-cor INFO @ Sat, 11 Dec 2021 11:41:47: #2 finished! INFO @ Sat, 11 Dec 2021 11:41:47: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 11:41:47: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Dec 2021 11:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10_model.r WARNING @ Sat, 11 Dec 2021 11:41:47: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:41:47: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 11 Dec 2021 11:41:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:41:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:41:50: 2000000 INFO @ Sat, 11 Dec 2021 11:41:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:41:56: 3000000 INFO @ Sat, 11 Dec 2021 11:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.10_summits.bed INFO @ Sat, 11 Dec 2021 11:41:56: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:42:01: 4000000 INFO @ Sat, 11 Dec 2021 11:42:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:42:13: 6000000 INFO @ Sat, 11 Dec 2021 11:42:15: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 11:42:15: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 11:42:15: #1 total tags in treatment: 2642885 INFO @ Sat, 11 Dec 2021 11:42:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:15: #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 11:42:15: #1 tags after filtering in treatment: 2594915 INFO @ Sat, 11 Dec 2021 11:42:15: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 11 Dec 2021 11:42:15: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:15: #2 number of paired peaks: 280 WARNING @ Sat, 11 Dec 2021 11:42:15: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:15: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:15: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:15: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:15: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:15: #2 predicted fragment length is 129 bps INFO @ Sat, 11 Dec 2021 11:42:15: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 11 Dec 2021 11:42:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20_model.r WARNING @ Sat, 11 Dec 2021 11:42:15: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:42:15: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Sat, 11 Dec 2021 11:42:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:42:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9005695/SRX9005695.20_summits.bed INFO @ Sat, 11 Dec 2021 11:42:24: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。