Job ID = 5721255 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,272,699 reads read : 18,545,398 reads written : 17,853,953 reads 0-length : 691,445 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: 00:00:01 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] 1 unmatched pairs [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] 1 unmatched pairs [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] 1 unmatched pairs [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] 432 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] 1414192 / 8036679 = 0.1760 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 06:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.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 06:53:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:53:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:53:57: 1000000 INFO @ Thu, 16 Apr 2020 06:54:06: 2000000 INFO @ Thu, 16 Apr 2020 06:54:15: 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 06:54:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.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 06:54:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:54:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:54:24: 4000000 INFO @ Thu, 16 Apr 2020 06:54:28: 1000000 INFO @ Thu, 16 Apr 2020 06:54:34: 5000000 INFO @ Thu, 16 Apr 2020 06:54:38: 2000000 INFO @ Thu, 16 Apr 2020 06:54:44: 6000000 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 06:54:47: 3000000 INFO @ Thu, 16 Apr 2020 06:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.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 06:54:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:54:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:54:53: 7000000 INFO @ Thu, 16 Apr 2020 06:54:57: 4000000 INFO @ Thu, 16 Apr 2020 06:54:59: 1000000 INFO @ Thu, 16 Apr 2020 06:55:03: 8000000 INFO @ Thu, 16 Apr 2020 06:55:08: 5000000 INFO @ Thu, 16 Apr 2020 06:55:09: 2000000 INFO @ Thu, 16 Apr 2020 06:55:13: 9000000 INFO @ Thu, 16 Apr 2020 06:55:18: 6000000 INFO @ Thu, 16 Apr 2020 06:55:19: 3000000 INFO @ Thu, 16 Apr 2020 06:55:23: 10000000 INFO @ Thu, 16 Apr 2020 06:55:28: 7000000 INFO @ Thu, 16 Apr 2020 06:55:29: 4000000 INFO @ Thu, 16 Apr 2020 06:55:33: 11000000 INFO @ Thu, 16 Apr 2020 06:55:37: 8000000 INFO @ Thu, 16 Apr 2020 06:55:39: 5000000 INFO @ Thu, 16 Apr 2020 06:55:43: 12000000 INFO @ Thu, 16 Apr 2020 06:55:47: 9000000 INFO @ Thu, 16 Apr 2020 06:55:49: 6000000 INFO @ Thu, 16 Apr 2020 06:55:54: 13000000 INFO @ Thu, 16 Apr 2020 06:55:57: 10000000 INFO @ Thu, 16 Apr 2020 06:55:59: 7000000 INFO @ Thu, 16 Apr 2020 06:56:03: 14000000 INFO @ Thu, 16 Apr 2020 06:56:07: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:56:07: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:56:07: #1 total tags in treatment: 6579510 INFO @ Thu, 16 Apr 2020 06:56:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:56:07: #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 06:56:07: #1 tags after filtering in treatment: 6069124 INFO @ Thu, 16 Apr 2020 06:56:07: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:56:07: #1 finished! INFO @ Thu, 16 Apr 2020 06:56:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:56:07: 11000000 INFO @ Thu, 16 Apr 2020 06:56:08: #2 number of paired peaks: 1832 INFO @ Thu, 16 Apr 2020 06:56:08: start model_add_line... INFO @ Thu, 16 Apr 2020 06:56:08: start X-correlation... INFO @ Thu, 16 Apr 2020 06:56:08: end of X-cor INFO @ Thu, 16 Apr 2020 06:56:08: #2 finished! INFO @ Thu, 16 Apr 2020 06:56:08: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 06:56:08: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 06:56:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05_model.r WARNING @ Thu, 16 Apr 2020 06:56:08: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:56:08: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Thu, 16 Apr 2020 06:56:08: #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 06:56:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:56:08: 8000000 INFO @ Thu, 16 Apr 2020 06:56:17: 12000000 INFO @ Thu, 16 Apr 2020 06:56:18: 9000000 INFO @ Thu, 16 Apr 2020 06:56:23: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:56:26: 13000000 INFO @ Thu, 16 Apr 2020 06:56:26: 10000000 INFO @ Thu, 16 Apr 2020 06:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:56:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:56:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.05_summits.bed INFO @ Thu, 16 Apr 2020 06:56:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2067 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:56:35: 14000000 INFO @ Thu, 16 Apr 2020 06:56:35: 11000000 INFO @ Thu, 16 Apr 2020 06:56:38: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:56:38: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:56:38: #1 total tags in treatment: 6579510 INFO @ Thu, 16 Apr 2020 06:56:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:56:38: #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 06:56:38: #1 tags after filtering in treatment: 6069124 INFO @ Thu, 16 Apr 2020 06:56:38: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:56:38: #1 finished! INFO @ Thu, 16 Apr 2020 06:56:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:56:39: #2 number of paired peaks: 1832 INFO @ Thu, 16 Apr 2020 06:56:39: start model_add_line... INFO @ Thu, 16 Apr 2020 06:56:39: start X-correlation... INFO @ Thu, 16 Apr 2020 06:56:39: end of X-cor INFO @ Thu, 16 Apr 2020 06:56:39: #2 finished! INFO @ Thu, 16 Apr 2020 06:56:39: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 06:56:39: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 06:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10_model.r WARNING @ Thu, 16 Apr 2020 06:56:39: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:56:39: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Thu, 16 Apr 2020 06:56:39: #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 06:56:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:56:44: 12000000 INFO @ Thu, 16 Apr 2020 06:56:53: 13000000 INFO @ Thu, 16 Apr 2020 06:56:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.10_summits.bed INFO @ Thu, 16 Apr 2020 06:57:01: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1364 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:57:01: 14000000 INFO @ Thu, 16 Apr 2020 06:57:05: #1 tag size is determined as 124 bps INFO @ Thu, 16 Apr 2020 06:57:05: #1 tag size = 124 INFO @ Thu, 16 Apr 2020 06:57:05: #1 total tags in treatment: 6579510 INFO @ Thu, 16 Apr 2020 06:57:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:57:05: #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 06:57:05: #1 tags after filtering in treatment: 6069124 INFO @ Thu, 16 Apr 2020 06:57:05: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 16 Apr 2020 06:57:05: #1 finished! INFO @ Thu, 16 Apr 2020 06:57:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:57:05: #2 number of paired peaks: 1832 INFO @ Thu, 16 Apr 2020 06:57:05: start model_add_line... INFO @ Thu, 16 Apr 2020 06:57:05: start X-correlation... INFO @ Thu, 16 Apr 2020 06:57:05: end of X-cor INFO @ Thu, 16 Apr 2020 06:57:05: #2 finished! INFO @ Thu, 16 Apr 2020 06:57:05: #2 predicted fragment length is 224 bps INFO @ Thu, 16 Apr 2020 06:57:05: #2 alternative fragment length(s) may be 224 bps INFO @ Thu, 16 Apr 2020 06:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20_model.r WARNING @ Thu, 16 Apr 2020 06:57:05: #2 Since the d (224) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:57:05: #2 You may need to consider one of the other alternative d(s): 224 WARNING @ Thu, 16 Apr 2020 06:57:05: #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 06:57:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:57:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7050428/SRX7050428.20_summits.bed INFO @ Thu, 16 Apr 2020 06:57:27: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (838 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。