Job ID = 1294259 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,840,671 reads read : 5,681,342 reads written : 5,681,342 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: 00:06:04 2840671 reads; of these: 2840671 (100.00%) were paired; of these: 586531 (20.65%) aligned concordantly 0 times 1872565 (65.92%) aligned concordantly exactly 1 time 381575 (13.43%) aligned concordantly >1 times ---- 586531 pairs aligned concordantly 0 times; of these: 130785 (22.30%) aligned discordantly 1 time ---- 455746 pairs aligned 0 times concordantly or discordantly; of these: 911492 mates make up the pairs; of these: 603647 (66.23%) aligned 0 times 204489 (22.43%) aligned exactly 1 time 103356 (11.34%) aligned >1 times 89.37% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 13093 / 2281286 = 0.0057 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 @ Mon, 03 Jun 2019 05:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.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 @ Mon, 03 Jun 2019 05:58:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:58:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.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 @ Mon, 03 Jun 2019 05:58:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:58:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.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 @ Mon, 03 Jun 2019 05:58:41: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:58:41: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:58:49: 1000000 INFO @ Mon, 03 Jun 2019 05:58:51: 1000000 INFO @ Mon, 03 Jun 2019 05:58:51: 1000000 INFO @ Mon, 03 Jun 2019 05:58:58: 2000000 INFO @ Mon, 03 Jun 2019 05:59:01: 2000000 INFO @ Mon, 03 Jun 2019 05:59:01: 2000000 INFO @ Mon, 03 Jun 2019 05:59:07: 3000000 INFO @ Mon, 03 Jun 2019 05:59:12: 3000000 INFO @ Mon, 03 Jun 2019 05:59:12: 3000000 INFO @ Mon, 03 Jun 2019 05:59:15: 4000000 INFO @ Mon, 03 Jun 2019 05:59:22: 4000000 INFO @ Mon, 03 Jun 2019 05:59:22: 4000000 INFO @ Mon, 03 Jun 2019 05:59:23: 5000000 INFO @ Mon, 03 Jun 2019 05:59:24: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 05:59:24: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 05:59:24: #1 total tags in treatment: 2241096 INFO @ Mon, 03 Jun 2019 05:59:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:59:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:59:24: #1 tags after filtering in treatment: 2192860 INFO @ Mon, 03 Jun 2019 05:59:24: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 05:59:24: #1 finished! INFO @ Mon, 03 Jun 2019 05:59:24: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:59:24: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 05:59:24: 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 @ Mon, 03 Jun 2019 05:59:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:59:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:59:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:59:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:59:24: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 05:59:24: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 05:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20_model.r WARNING @ Mon, 03 Jun 2019 05:59:24: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:59:24: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Mon, 03 Jun 2019 05:59:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:59:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:59:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:32: 5000000 INFO @ Mon, 03 Jun 2019 05:59:32: 5000000 INFO @ Mon, 03 Jun 2019 05:59:32: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 05:59:32: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 05:59:32: #1 total tags in treatment: 2241096 INFO @ Mon, 03 Jun 2019 05:59:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:59:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:59:32: #1 tags after filtering in treatment: 2192860 INFO @ Mon, 03 Jun 2019 05:59:32: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 05:59:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:59:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:59:32: #1 tag size is determined as 70 bps INFO @ Mon, 03 Jun 2019 05:59:32: #1 tag size = 70 INFO @ Mon, 03 Jun 2019 05:59:32: #1 total tags in treatment: 2241096 INFO @ Mon, 03 Jun 2019 05:59:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:59:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:59:32: #1 tags after filtering in treatment: 2192860 INFO @ Mon, 03 Jun 2019 05:59:32: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 05:59:32: #1 finished! INFO @ Mon, 03 Jun 2019 05:59:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:59:33: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 05:59:33: 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 @ Mon, 03 Jun 2019 05:59:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:59:33: start X-correlation... INFO @ Mon, 03 Jun 2019 05:59:33: end of X-cor INFO @ Mon, 03 Jun 2019 05:59:33: #2 finished! INFO @ Mon, 03 Jun 2019 05:59:33: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 05:59:33: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 05:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10_model.r WARNING @ Mon, 03 Jun 2019 05:59:33: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:59:33: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Mon, 03 Jun 2019 05:59:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:59:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:59:33: #2 number of paired peaks: 280 WARNING @ Mon, 03 Jun 2019 05:59:33: 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 @ Mon, 03 Jun 2019 05:59:33: start model_add_line... INFO @ Mon, 03 Jun 2019 05:59:33: start X-correlation... INFO @ Mon, 03 Jun 2019 05:59:33: end of X-cor INFO @ Mon, 03 Jun 2019 05:59:33: #2 finished! INFO @ Mon, 03 Jun 2019 05:59:33: #2 predicted fragment length is 117 bps INFO @ Mon, 03 Jun 2019 05:59:33: #2 alternative fragment length(s) may be 117 bps INFO @ Mon, 03 Jun 2019 05:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05_model.r WARNING @ Mon, 03 Jun 2019 05:59:33: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:59:33: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Mon, 03 Jun 2019 05:59:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:59:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.20_summits.bed INFO @ Mon, 03 Jun 2019 05:59:34: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:59:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.05_summits.bed INFO @ Mon, 03 Jun 2019 05:59:43: Done! INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX215623/SRX215623.10_summits.bed INFO @ Mon, 03 Jun 2019 05:59:43: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (265 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。