Job ID = 1295051 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,376,875 reads read : 6,376,875 reads written : 6,376,875 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: 00:02:46 6376875 reads; of these: 6376875 (100.00%) were unpaired; of these: 190907 (2.99%) aligned 0 times 4446052 (69.72%) aligned exactly 1 time 1739916 (27.28%) aligned >1 times 97.01% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 520297 / 6185968 = 0.0841 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 11:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.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 11:31:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.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 11:31:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.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 11:31:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:31:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:32:06: 1000000 INFO @ Mon, 03 Jun 2019 11:32:07: 1000000 INFO @ Mon, 03 Jun 2019 11:32:07: 1000000 INFO @ Mon, 03 Jun 2019 11:32:13: 2000000 INFO @ Mon, 03 Jun 2019 11:32:14: 2000000 INFO @ Mon, 03 Jun 2019 11:32:15: 2000000 INFO @ Mon, 03 Jun 2019 11:32:20: 3000000 INFO @ Mon, 03 Jun 2019 11:32:22: 3000000 INFO @ Mon, 03 Jun 2019 11:32:23: 3000000 INFO @ Mon, 03 Jun 2019 11:32:27: 4000000 INFO @ Mon, 03 Jun 2019 11:32:30: 4000000 INFO @ Mon, 03 Jun 2019 11:32:31: 4000000 INFO @ Mon, 03 Jun 2019 11:32:35: 5000000 INFO @ Mon, 03 Jun 2019 11:32:38: 5000000 INFO @ Mon, 03 Jun 2019 11:32:39: 5000000 INFO @ Mon, 03 Jun 2019 11:32:40: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:32:40: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:32:40: #1 total tags in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:40: #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 11:32:40: #1 tags after filtering in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:40: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:41: #2 number of paired peaks: 328 WARNING @ Mon, 03 Jun 2019 11:32:41: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:41: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:41: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:41: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:41: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:41: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:32:41: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 11:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05_model.r WARNING @ Mon, 03 Jun 2019 11:32:41: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:41: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 11:32:41: #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 11:32:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:43: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:32:43: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:32:43: #1 total tags in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:43: #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 11:32:43: #1 tags after filtering in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:43: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:44: #2 number of paired peaks: 328 WARNING @ Mon, 03 Jun 2019 11:32:44: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:44: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:44: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:44: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:44: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:44: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:32:44: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 11:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20_model.r WARNING @ Mon, 03 Jun 2019 11:32:44: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:44: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 11:32:44: #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 11:32:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:44: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:32:44: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:32:44: #1 total tags in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:32:44: #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 11:32:44: #1 tags after filtering in treatment: 5665671 INFO @ Mon, 03 Jun 2019 11:32:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:32:44: #1 finished! INFO @ Mon, 03 Jun 2019 11:32:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:32:45: #2 number of paired peaks: 328 WARNING @ Mon, 03 Jun 2019 11:32:45: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Mon, 03 Jun 2019 11:32:45: start model_add_line... INFO @ Mon, 03 Jun 2019 11:32:45: start X-correlation... INFO @ Mon, 03 Jun 2019 11:32:45: end of X-cor INFO @ Mon, 03 Jun 2019 11:32:45: #2 finished! INFO @ Mon, 03 Jun 2019 11:32:45: #2 predicted fragment length is 56 bps INFO @ Mon, 03 Jun 2019 11:32:45: #2 alternative fragment length(s) may be 56 bps INFO @ Mon, 03 Jun 2019 11:32:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10_model.r WARNING @ Mon, 03 Jun 2019 11:32:45: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:32:45: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Mon, 03 Jun 2019 11:32:45: #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 11:32:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:32:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:32:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:33:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.05_summits.bed INFO @ Mon, 03 Jun 2019 11:33:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.20_summits.bed INFO @ Mon, 03 Jun 2019 11:33:09: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167246/SRX3167246.10_summits.bed INFO @ Mon, 03 Jun 2019 11:33:10: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (809 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。