Job ID = 1294254 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,041,877 reads read : 9,041,877 reads written : 9,041,877 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:21 9041877 reads; of these: 9041877 (100.00%) were unpaired; of these: 395936 (4.38%) aligned 0 times 6338944 (70.11%) aligned exactly 1 time 2306997 (25.51%) aligned >1 times 95.62% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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_rmdupse_core] 902588 / 8645941 = 0.1044 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 05:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.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 05:57:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:57:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.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 05:57:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:57:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.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 05:57:50: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:57:50: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:57:57: 1000000 INFO @ Mon, 03 Jun 2019 05:57:59: 1000000 INFO @ Mon, 03 Jun 2019 05:58:00: 1000000 INFO @ Mon, 03 Jun 2019 05:58:04: 2000000 INFO @ Mon, 03 Jun 2019 05:58:08: 2000000 INFO @ Mon, 03 Jun 2019 05:58:09: 2000000 INFO @ Mon, 03 Jun 2019 05:58:11: 3000000 INFO @ Mon, 03 Jun 2019 05:58:16: 3000000 INFO @ Mon, 03 Jun 2019 05:58:17: 3000000 INFO @ Mon, 03 Jun 2019 05:58:18: 4000000 INFO @ Mon, 03 Jun 2019 05:58:25: 5000000 INFO @ Mon, 03 Jun 2019 05:58:25: 4000000 INFO @ Mon, 03 Jun 2019 05:58:27: 4000000 INFO @ Mon, 03 Jun 2019 05:58:32: 6000000 INFO @ Mon, 03 Jun 2019 05:58:34: 5000000 INFO @ Mon, 03 Jun 2019 05:58:35: 5000000 INFO @ Mon, 03 Jun 2019 05:58:39: 7000000 INFO @ Mon, 03 Jun 2019 05:58:43: 6000000 INFO @ Mon, 03 Jun 2019 05:58:44: 6000000 INFO @ Mon, 03 Jun 2019 05:58:45: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:58:45: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:58:45: #1 total tags in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:58:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:58:45: #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 05:58:45: #1 tags after filtering in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:58:45: #1 finished! INFO @ Mon, 03 Jun 2019 05:58:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:58:45: #2 number of paired peaks: 187 WARNING @ Mon, 03 Jun 2019 05:58:45: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 03 Jun 2019 05:58:45: start model_add_line... INFO @ Mon, 03 Jun 2019 05:58:45: start X-correlation... INFO @ Mon, 03 Jun 2019 05:58:45: end of X-cor INFO @ Mon, 03 Jun 2019 05:58:45: #2 finished! INFO @ Mon, 03 Jun 2019 05:58:45: #2 predicted fragment length is 38 bps INFO @ Mon, 03 Jun 2019 05:58:45: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 03 Jun 2019 05:58:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05_model.r WARNING @ Mon, 03 Jun 2019 05:58:45: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:58:45: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 03 Jun 2019 05:58:45: #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 05:58:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:58:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:58:52: 7000000 INFO @ Mon, 03 Jun 2019 05:58:53: 7000000 INFO @ Mon, 03 Jun 2019 05:58:58: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:58:58: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:58:58: #1 total tags in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:58:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:58:58: #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 05:58:59: #1 tags after filtering in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:58:59: #1 finished! INFO @ Mon, 03 Jun 2019 05:58:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:58:59: #2 number of paired peaks: 187 WARNING @ Mon, 03 Jun 2019 05:58:59: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 03 Jun 2019 05:58:59: start model_add_line... INFO @ Mon, 03 Jun 2019 05:58:59: start X-correlation... INFO @ Mon, 03 Jun 2019 05:58:59: end of X-cor INFO @ Mon, 03 Jun 2019 05:58:59: #2 finished! INFO @ Mon, 03 Jun 2019 05:58:59: #2 predicted fragment length is 38 bps INFO @ Mon, 03 Jun 2019 05:58:59: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 03 Jun 2019 05:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10_model.r WARNING @ Mon, 03 Jun 2019 05:58:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:58:59: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 03 Jun 2019 05:58:59: #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 05:58:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:59:00: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 05:59:00: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 05:59:00: #1 total tags in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:59:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:59:00: #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 05:59:00: #1 tags after filtering in treatment: 7743353 INFO @ Mon, 03 Jun 2019 05:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:59:00: #1 finished! INFO @ Mon, 03 Jun 2019 05:59:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:59:01: #2 number of paired peaks: 187 WARNING @ Mon, 03 Jun 2019 05:59:01: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Mon, 03 Jun 2019 05:59:01: start model_add_line... INFO @ Mon, 03 Jun 2019 05:59:01: start X-correlation... INFO @ Mon, 03 Jun 2019 05:59:01: end of X-cor INFO @ Mon, 03 Jun 2019 05:59:01: #2 finished! INFO @ Mon, 03 Jun 2019 05:59:01: #2 predicted fragment length is 38 bps INFO @ Mon, 03 Jun 2019 05:59:01: #2 alternative fragment length(s) may be 38 bps INFO @ Mon, 03 Jun 2019 05:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20_model.r WARNING @ Mon, 03 Jun 2019 05:59:01: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:59:01: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Mon, 03 Jun 2019 05:59:01: #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 05:59:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:59:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.05_summits.bed INFO @ Mon, 03 Jun 2019 05:59:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1379 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:59:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:59:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.10_summits.bed INFO @ Mon, 03 Jun 2019 05:59:32: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (913 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX209934/SRX209934.20_summits.bed INFO @ Mon, 03 Jun 2019 05:59:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (503 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。