Job ID = 1293388 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,170,315 reads read : 4,340,630 reads written : 4,340,630 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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 Multiseed full-index search: 00:05:59 2170315 reads; of these: 2170315 (100.00%) were paired; of these: 263451 (12.14%) aligned concordantly 0 times 1457367 (67.15%) aligned concordantly exactly 1 time 449497 (20.71%) aligned concordantly >1 times ---- 263451 pairs aligned concordantly 0 times; of these: 43080 (16.35%) aligned discordantly 1 time ---- 220371 pairs aligned 0 times concordantly or discordantly; of these: 440742 mates make up the pairs; of these: 336922 (76.44%) aligned 0 times 62986 (14.29%) aligned exactly 1 time 40834 (9.26%) aligned >1 times 92.24% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 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] 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] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 10241 / 1943354 = 0.0053 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sun, 02 Jun 2019 23:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.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 @ Sun, 02 Jun 2019 23:33:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:33:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.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 @ Sun, 02 Jun 2019 23:33:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:33:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.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 @ Sun, 02 Jun 2019 23:33:11: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:33:11: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:33:19: 1000000 INFO @ Sun, 02 Jun 2019 23:33:22: 1000000 INFO @ Sun, 02 Jun 2019 23:33:22: 1000000 INFO @ Sun, 02 Jun 2019 23:33:28: 2000000 INFO @ Sun, 02 Jun 2019 23:33:33: 2000000 INFO @ Sun, 02 Jun 2019 23:33:34: 2000000 INFO @ Sun, 02 Jun 2019 23:33:36: 3000000 INFO @ Sun, 02 Jun 2019 23:33:45: 3000000 INFO @ Sun, 02 Jun 2019 23:33:45: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:33:45: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:33:45: #1 total tags in treatment: 1896678 INFO @ Sun, 02 Jun 2019 23:33:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:33:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:33:45: #1 tags after filtering in treatment: 1858316 INFO @ Sun, 02 Jun 2019 23:33:45: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 02 Jun 2019 23:33:45: #1 finished! INFO @ Sun, 02 Jun 2019 23:33:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:33:45: 3000000 INFO @ Sun, 02 Jun 2019 23:33:45: #2 number of paired peaks: 2593 INFO @ Sun, 02 Jun 2019 23:33:45: start model_add_line... INFO @ Sun, 02 Jun 2019 23:33:45: start X-correlation... INFO @ Sun, 02 Jun 2019 23:33:45: end of X-cor INFO @ Sun, 02 Jun 2019 23:33:45: #2 finished! INFO @ Sun, 02 Jun 2019 23:33:45: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 23:33:45: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 23:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20_model.r WARNING @ Sun, 02 Jun 2019 23:33:45: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:33:45: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 02 Jun 2019 23:33:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:33:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:33:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:33:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.20_summits.bed INFO @ Sun, 02 Jun 2019 23:33:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:33:56: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:33:56: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:33:56: #1 total tags in treatment: 1896678 INFO @ Sun, 02 Jun 2019 23:33:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:33:56: #1 tags after filtering in treatment: 1858316 INFO @ Sun, 02 Jun 2019 23:33:56: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 02 Jun 2019 23:33:56: #1 finished! INFO @ Sun, 02 Jun 2019 23:33:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:33:56: #1 tag size is determined as 82 bps INFO @ Sun, 02 Jun 2019 23:33:56: #1 tag size = 82 INFO @ Sun, 02 Jun 2019 23:33:56: #1 total tags in treatment: 1896678 INFO @ Sun, 02 Jun 2019 23:33:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:33:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:33:56: #1 tags after filtering in treatment: 1858316 INFO @ Sun, 02 Jun 2019 23:33:56: #1 Redundant rate of treatment: 0.02 INFO @ Sun, 02 Jun 2019 23:33:56: #1 finished! INFO @ Sun, 02 Jun 2019 23:33:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:33:56: #2 number of paired peaks: 2593 INFO @ Sun, 02 Jun 2019 23:33:56: start model_add_line... INFO @ Sun, 02 Jun 2019 23:33:56: start X-correlation... INFO @ Sun, 02 Jun 2019 23:33:56: end of X-cor INFO @ Sun, 02 Jun 2019 23:33:56: #2 finished! INFO @ Sun, 02 Jun 2019 23:33:56: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 23:33:56: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 23:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10_model.r INFO @ Sun, 02 Jun 2019 23:33:56: #2 number of paired peaks: 2593 INFO @ Sun, 02 Jun 2019 23:33:56: start model_add_line... WARNING @ Sun, 02 Jun 2019 23:33:56: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:33:56: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 02 Jun 2019 23:33:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:33:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:33:56: start X-correlation... INFO @ Sun, 02 Jun 2019 23:33:56: end of X-cor INFO @ Sun, 02 Jun 2019 23:33:56: #2 finished! INFO @ Sun, 02 Jun 2019 23:33:56: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 23:33:56: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 23:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05_model.r WARNING @ Sun, 02 Jun 2019 23:33:56: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 23:33:56: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 02 Jun 2019 23:33:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 23:33:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:34:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:34:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.10_summits.bed INFO @ Sun, 02 Jun 2019 23:34:05: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1243 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1973304/ERX1973304.05_summits.bed INFO @ Sun, 02 Jun 2019 23:34:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2961 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。