Job ID = 5721235 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,867,685 reads read : 15,735,370 reads written : 14,401,703 reads 0-length : 1,333,667 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... 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] 2 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] 4 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] 115 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1219356 / 6000814 = 0.2032 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.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 @ Thu, 16 Apr 2020 06:39:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:39:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:39:31: 1000000 INFO @ Thu, 16 Apr 2020 06:39:39: 2000000 INFO @ Thu, 16 Apr 2020 06:39:46: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:39:53: 4000000 INFO @ Thu, 16 Apr 2020 06:39:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.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 @ Thu, 16 Apr 2020 06:39:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:39:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:40:00: 5000000 INFO @ Thu, 16 Apr 2020 06:40:01: 1000000 INFO @ Thu, 16 Apr 2020 06:40:07: 6000000 INFO @ Thu, 16 Apr 2020 06:40:08: 2000000 INFO @ Thu, 16 Apr 2020 06:40:14: 7000000 INFO @ Thu, 16 Apr 2020 06:40:15: 3000000 INFO @ Thu, 16 Apr 2020 06:40:22: 8000000 INFO @ Thu, 16 Apr 2020 06:40:22: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 16 Apr 2020 06:40:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.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 @ Thu, 16 Apr 2020 06:40:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:40:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:40:29: 9000000 INFO @ Thu, 16 Apr 2020 06:40:30: 5000000 INFO @ Thu, 16 Apr 2020 06:40:31: 1000000 INFO @ Thu, 16 Apr 2020 06:40:36: 10000000 INFO @ Thu, 16 Apr 2020 06:40:37: 6000000 INFO @ Thu, 16 Apr 2020 06:40:38: 2000000 INFO @ Thu, 16 Apr 2020 06:40:44: 11000000 INFO @ Thu, 16 Apr 2020 06:40:44: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:40:44: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:40:44: #1 total tags in treatment: 4692875 INFO @ Thu, 16 Apr 2020 06:40:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:40:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:40:44: #1 tags after filtering in treatment: 4450096 INFO @ Thu, 16 Apr 2020 06:40:44: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:40:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:40:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:40:44: 7000000 INFO @ Thu, 16 Apr 2020 06:40:45: #2 number of paired peaks: 2432 INFO @ Thu, 16 Apr 2020 06:40:45: start model_add_line... INFO @ Thu, 16 Apr 2020 06:40:45: start X-correlation... INFO @ Thu, 16 Apr 2020 06:40:45: end of X-cor INFO @ Thu, 16 Apr 2020 06:40:45: #2 finished! INFO @ Thu, 16 Apr 2020 06:40:45: #2 predicted fragment length is 242 bps INFO @ Thu, 16 Apr 2020 06:40:45: #2 alternative fragment length(s) may be 242 bps INFO @ Thu, 16 Apr 2020 06:40:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05_model.r WARNING @ Thu, 16 Apr 2020 06:40:45: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:40:45: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Thu, 16 Apr 2020 06:40:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:40:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:40:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:40:45: 3000000 INFO @ Thu, 16 Apr 2020 06:40:52: 8000000 INFO @ Thu, 16 Apr 2020 06:40:53: 4000000 INFO @ Thu, 16 Apr 2020 06:40:56: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:40:59: 9000000 INFO @ Thu, 16 Apr 2020 06:41:00: 5000000 INFO @ Thu, 16 Apr 2020 06:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.05_summits.bed INFO @ Thu, 16 Apr 2020 06:41:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4825 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:41:06: 10000000 INFO @ Thu, 16 Apr 2020 06:41:07: 6000000 INFO @ Thu, 16 Apr 2020 06:41:14: 11000000 INFO @ Thu, 16 Apr 2020 06:41:14: 7000000 INFO @ Thu, 16 Apr 2020 06:41:14: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:41:14: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:41:14: #1 total tags in treatment: 4692875 INFO @ Thu, 16 Apr 2020 06:41:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:41:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:41:14: #1 tags after filtering in treatment: 4450096 INFO @ Thu, 16 Apr 2020 06:41:14: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:41:14: #1 finished! INFO @ Thu, 16 Apr 2020 06:41:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:41:15: #2 number of paired peaks: 2432 INFO @ Thu, 16 Apr 2020 06:41:15: start model_add_line... INFO @ Thu, 16 Apr 2020 06:41:15: start X-correlation... INFO @ Thu, 16 Apr 2020 06:41:15: end of X-cor INFO @ Thu, 16 Apr 2020 06:41:15: #2 finished! INFO @ Thu, 16 Apr 2020 06:41:15: #2 predicted fragment length is 242 bps INFO @ Thu, 16 Apr 2020 06:41:15: #2 alternative fragment length(s) may be 242 bps INFO @ Thu, 16 Apr 2020 06:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10_model.r WARNING @ Thu, 16 Apr 2020 06:41:15: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:41:15: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Thu, 16 Apr 2020 06:41:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:41:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:41:21: 8000000 INFO @ Thu, 16 Apr 2020 06:41:26: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:41:29: 9000000 INFO @ Thu, 16 Apr 2020 06:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.10_summits.bed INFO @ Thu, 16 Apr 2020 06:41:31: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2303 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:41:36: 10000000 INFO @ Thu, 16 Apr 2020 06:41:44: 11000000 INFO @ Thu, 16 Apr 2020 06:41:44: #1 tag size is determined as 123 bps INFO @ Thu, 16 Apr 2020 06:41:44: #1 tag size = 123 INFO @ Thu, 16 Apr 2020 06:41:44: #1 total tags in treatment: 4692875 INFO @ Thu, 16 Apr 2020 06:41:44: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:41:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:41:44: #1 tags after filtering in treatment: 4450096 INFO @ Thu, 16 Apr 2020 06:41:44: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:41:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:41:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:41:44: #2 number of paired peaks: 2432 INFO @ Thu, 16 Apr 2020 06:41:44: start model_add_line... INFO @ Thu, 16 Apr 2020 06:41:45: start X-correlation... INFO @ Thu, 16 Apr 2020 06:41:45: end of X-cor INFO @ Thu, 16 Apr 2020 06:41:45: #2 finished! INFO @ Thu, 16 Apr 2020 06:41:45: #2 predicted fragment length is 242 bps INFO @ Thu, 16 Apr 2020 06:41:45: #2 alternative fragment length(s) may be 242 bps INFO @ Thu, 16 Apr 2020 06:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20_model.r WARNING @ Thu, 16 Apr 2020 06:41:45: #2 Since the d (242) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:41:45: #2 You may need to consider one of the other alternative d(s): 242 WARNING @ Thu, 16 Apr 2020 06:41:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:41:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:41:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:42:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:42:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:42:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050420/SRX7050420.20_summits.bed INFO @ Thu, 16 Apr 2020 06:42:00: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (856 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。