Job ID = 5721250 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,949,206 reads read : 15,898,412 reads written : 15,177,897 reads 0-length : 720,515 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] 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] 3 unmatched pairs [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] 9 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] 3 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 32 unmatched pairs [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] 1 unmatched pairs [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1166700 / 6841904 = 0.1705 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 06:43:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.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 06:43:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:43:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:43:26: 1000000 INFO @ Thu, 16 Apr 2020 06:43:33: 2000000 INFO @ Thu, 16 Apr 2020 06:43:40: 3000000 INFO @ Thu, 16 Apr 2020 06:43:47: 4000000 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 06:43:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.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 06:43:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:43:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:43:55: 5000000 INFO @ Thu, 16 Apr 2020 06:43:57: 1000000 INFO @ Thu, 16 Apr 2020 06:44:02: 6000000 INFO @ Thu, 16 Apr 2020 06:44:04: 2000000 INFO @ Thu, 16 Apr 2020 06:44:10: 7000000 INFO @ Thu, 16 Apr 2020 06:44:12: 3000000 INFO @ Thu, 16 Apr 2020 06:44:17: 8000000 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 06:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.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 06:44:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:44:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:44:19: 4000000 INFO @ Thu, 16 Apr 2020 06:44:25: 9000000 INFO @ Thu, 16 Apr 2020 06:44:27: 1000000 INFO @ Thu, 16 Apr 2020 06:44:27: 5000000 INFO @ Thu, 16 Apr 2020 06:44:33: 10000000 INFO @ Thu, 16 Apr 2020 06:44:35: 2000000 INFO @ Thu, 16 Apr 2020 06:44:36: 6000000 INFO @ Thu, 16 Apr 2020 06:44:41: 11000000 INFO @ Thu, 16 Apr 2020 06:44:43: 3000000 INFO @ Thu, 16 Apr 2020 06:44:44: 7000000 INFO @ Thu, 16 Apr 2020 06:44:49: 12000000 INFO @ Thu, 16 Apr 2020 06:44:52: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:44:52: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:44:52: #1 total tags in treatment: 5561263 INFO @ Thu, 16 Apr 2020 06:44:52: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:44:52: #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 06:44:52: #1 tags after filtering in treatment: 5094801 INFO @ Thu, 16 Apr 2020 06:44:52: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:44:52: #1 finished! INFO @ Thu, 16 Apr 2020 06:44:52: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:44:52: 4000000 INFO @ Thu, 16 Apr 2020 06:44:52: 8000000 INFO @ Thu, 16 Apr 2020 06:44:52: #2 number of paired peaks: 4468 INFO @ Thu, 16 Apr 2020 06:44:52: start model_add_line... INFO @ Thu, 16 Apr 2020 06:44:52: start X-correlation... INFO @ Thu, 16 Apr 2020 06:44:52: end of X-cor INFO @ Thu, 16 Apr 2020 06:44:52: #2 finished! INFO @ Thu, 16 Apr 2020 06:44:52: #2 predicted fragment length is 230 bps INFO @ Thu, 16 Apr 2020 06:44:52: #2 alternative fragment length(s) may be 230 bps INFO @ Thu, 16 Apr 2020 06:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05_model.r WARNING @ Thu, 16 Apr 2020 06:44:52: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:44:52: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Thu, 16 Apr 2020 06:44:52: #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 06:44:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:45:00: 5000000 INFO @ Thu, 16 Apr 2020 06:45:00: 9000000 INFO @ Thu, 16 Apr 2020 06:45:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:45:08: 6000000 INFO @ Thu, 16 Apr 2020 06:45:08: 10000000 INFO @ Thu, 16 Apr 2020 06:45:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:45:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:45:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.05_summits.bed INFO @ Thu, 16 Apr 2020 06:45:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7200 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:45:16: 7000000 INFO @ Thu, 16 Apr 2020 06:45:17: 11000000 INFO @ Thu, 16 Apr 2020 06:45:24: 8000000 INFO @ Thu, 16 Apr 2020 06:45:25: 12000000 INFO @ Thu, 16 Apr 2020 06:45:27: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:45:27: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:45:27: #1 total tags in treatment: 5561263 INFO @ Thu, 16 Apr 2020 06:45:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:45:27: #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 06:45:27: #1 tags after filtering in treatment: 5094801 INFO @ Thu, 16 Apr 2020 06:45:27: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:45:27: #1 finished! INFO @ Thu, 16 Apr 2020 06:45:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:45:28: #2 number of paired peaks: 4468 INFO @ Thu, 16 Apr 2020 06:45:28: start model_add_line... INFO @ Thu, 16 Apr 2020 06:45:28: start X-correlation... INFO @ Thu, 16 Apr 2020 06:45:28: end of X-cor INFO @ Thu, 16 Apr 2020 06:45:28: #2 finished! INFO @ Thu, 16 Apr 2020 06:45:28: #2 predicted fragment length is 230 bps INFO @ Thu, 16 Apr 2020 06:45:28: #2 alternative fragment length(s) may be 230 bps INFO @ Thu, 16 Apr 2020 06:45:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10_model.r WARNING @ Thu, 16 Apr 2020 06:45:28: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:45:28: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Thu, 16 Apr 2020 06:45:28: #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 06:45:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:45:32: 9000000 INFO @ Thu, 16 Apr 2020 06:45:39: 10000000 INFO @ Thu, 16 Apr 2020 06:45:41: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:45:47: 11000000 INFO @ Thu, 16 Apr 2020 06:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.10_summits.bed INFO @ Thu, 16 Apr 2020 06:45:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4892 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:45:54: 12000000 INFO @ Thu, 16 Apr 2020 06:45:56: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:45:56: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:45:56: #1 total tags in treatment: 5561263 INFO @ Thu, 16 Apr 2020 06:45:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:45:56: #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 06:45:56: #1 tags after filtering in treatment: 5094801 INFO @ Thu, 16 Apr 2020 06:45:56: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:45:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:45:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:45:57: #2 number of paired peaks: 4468 INFO @ Thu, 16 Apr 2020 06:45:57: start model_add_line... INFO @ Thu, 16 Apr 2020 06:45:57: start X-correlation... INFO @ Thu, 16 Apr 2020 06:45:57: end of X-cor INFO @ Thu, 16 Apr 2020 06:45:57: #2 finished! INFO @ Thu, 16 Apr 2020 06:45:57: #2 predicted fragment length is 230 bps INFO @ Thu, 16 Apr 2020 06:45:57: #2 alternative fragment length(s) may be 230 bps INFO @ Thu, 16 Apr 2020 06:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20_model.r WARNING @ Thu, 16 Apr 2020 06:45:57: #2 Since the d (230) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:45:57: #2 You may need to consider one of the other alternative d(s): 230 WARNING @ Thu, 16 Apr 2020 06:45:57: #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 06:45:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:46:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050425/SRX7050425.20_summits.bed INFO @ Thu, 16 Apr 2020 06:46:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2832 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。