Job ID = 10714550 sra ファイルのダウンロード中... Completed: 570301K bytes transferred in 25 seconds (180230K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 25448999 spots for /home/okishinya/chipatlas/results/dm3/SRX2583184/SRR5279384.sra Written 25448999 spots for /home/okishinya/chipatlas/results/dm3/SRX2583184/SRR5279384.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Multiseed full-index search: 00:10:45 25448999 reads; of these: 25448999 (100.00%) were unpaired; of these: 763279 (3.00%) aligned 0 times 18555203 (72.91%) aligned exactly 1 time 6130517 (24.09%) aligned >1 times 97.00% overall alignment rate Time searching: 00:10:46 Overall time: 00:10:46 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3555469 / 24685720 = 0.1440 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, 03 Jun 2018 13:40:10: # Command line: callpeak -t SRX2583184.bam -f BAM -g dm -n SRX2583184.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2583184.05 # format = BAM # ChIP-seq file = ['SRX2583184.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, 03 Jun 2018 13:40:10: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:10: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:10: # Command line: callpeak -t SRX2583184.bam -f BAM -g dm -n SRX2583184.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2583184.20 # format = BAM # ChIP-seq file = ['SRX2583184.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, 03 Jun 2018 13:40:10: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:10: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:10: # Command line: callpeak -t SRX2583184.bam -f BAM -g dm -n SRX2583184.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2583184.10 # format = BAM # ChIP-seq file = ['SRX2583184.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, 03 Jun 2018 13:40:10: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:40:10: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:40:17: 1000000 INFO @ Sun, 03 Jun 2018 13:40:17: 1000000 INFO @ Sun, 03 Jun 2018 13:40:17: 1000000 INFO @ Sun, 03 Jun 2018 13:40:24: 2000000 INFO @ Sun, 03 Jun 2018 13:40:24: 2000000 INFO @ Sun, 03 Jun 2018 13:40:24: 2000000 INFO @ Sun, 03 Jun 2018 13:40:31: 3000000 INFO @ Sun, 03 Jun 2018 13:40:31: 3000000 INFO @ Sun, 03 Jun 2018 13:40:31: 3000000 INFO @ Sun, 03 Jun 2018 13:40:38: 4000000 INFO @ Sun, 03 Jun 2018 13:40:38: 4000000 INFO @ Sun, 03 Jun 2018 13:40:38: 4000000 INFO @ Sun, 03 Jun 2018 13:40:45: 5000000 INFO @ Sun, 03 Jun 2018 13:40:45: 5000000 INFO @ Sun, 03 Jun 2018 13:40:45: 5000000 INFO @ Sun, 03 Jun 2018 13:40:52: 6000000 INFO @ Sun, 03 Jun 2018 13:40:52: 6000000 INFO @ Sun, 03 Jun 2018 13:40:52: 6000000 INFO @ Sun, 03 Jun 2018 13:40:59: 7000000 INFO @ Sun, 03 Jun 2018 13:41:00: 7000000 INFO @ Sun, 03 Jun 2018 13:41:00: 7000000 INFO @ Sun, 03 Jun 2018 13:41:06: 8000000 INFO @ Sun, 03 Jun 2018 13:41:07: 8000000 INFO @ Sun, 03 Jun 2018 13:41:07: 8000000 INFO @ Sun, 03 Jun 2018 13:41:13: 9000000 INFO @ Sun, 03 Jun 2018 13:41:14: 9000000 INFO @ Sun, 03 Jun 2018 13:41:14: 9000000 INFO @ Sun, 03 Jun 2018 13:41:20: 10000000 INFO @ Sun, 03 Jun 2018 13:41:21: 10000000 INFO @ Sun, 03 Jun 2018 13:41:21: 10000000 INFO @ Sun, 03 Jun 2018 13:41:28: 11000000 INFO @ Sun, 03 Jun 2018 13:41:28: 11000000 INFO @ Sun, 03 Jun 2018 13:41:28: 11000000 INFO @ Sun, 03 Jun 2018 13:41:35: 12000000 INFO @ Sun, 03 Jun 2018 13:41:35: 12000000 INFO @ Sun, 03 Jun 2018 13:41:36: 12000000 INFO @ Sun, 03 Jun 2018 13:41:42: 13000000 INFO @ Sun, 03 Jun 2018 13:41:42: 13000000 INFO @ Sun, 03 Jun 2018 13:41:43: 13000000 INFO @ Sun, 03 Jun 2018 13:41:49: 14000000 INFO @ Sun, 03 Jun 2018 13:41:49: 14000000 INFO @ Sun, 03 Jun 2018 13:41:50: 14000000 INFO @ Sun, 03 Jun 2018 13:41:56: 15000000 INFO @ Sun, 03 Jun 2018 13:41:56: 15000000 INFO @ Sun, 03 Jun 2018 13:41:58: 15000000 INFO @ Sun, 03 Jun 2018 13:42:03: 16000000 INFO @ Sun, 03 Jun 2018 13:42:03: 16000000 INFO @ Sun, 03 Jun 2018 13:42:05: 16000000 INFO @ Sun, 03 Jun 2018 13:42:10: 17000000 INFO @ Sun, 03 Jun 2018 13:42:10: 17000000 INFO @ Sun, 03 Jun 2018 13:42:12: 17000000 INFO @ Sun, 03 Jun 2018 13:42:17: 18000000 INFO @ Sun, 03 Jun 2018 13:42:17: 18000000 INFO @ Sun, 03 Jun 2018 13:42:19: 18000000 INFO @ Sun, 03 Jun 2018 13:42:24: 19000000 INFO @ Sun, 03 Jun 2018 13:42:24: 19000000 INFO @ Sun, 03 Jun 2018 13:42:26: 19000000 INFO @ Sun, 03 Jun 2018 13:42:31: 20000000 INFO @ Sun, 03 Jun 2018 13:42:31: 20000000 INFO @ Sun, 03 Jun 2018 13:42:34: 20000000 INFO @ Sun, 03 Jun 2018 13:42:38: 21000000 INFO @ Sun, 03 Jun 2018 13:42:38: 21000000 INFO @ Sun, 03 Jun 2018 13:42:39: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:42:39: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:42:39: #1 total tags in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:39: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:42:39: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:42:39: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:42:39: #1 total tags in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:39: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:42:40: #1 tags after filtering in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:42:40: #1 finished! INFO @ Sun, 03 Jun 2018 13:42:40: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:42:40: #1 tags after filtering in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:42:40: #1 finished! INFO @ Sun, 03 Jun 2018 13:42:40: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:42:41: 21000000 INFO @ Sun, 03 Jun 2018 13:42:41: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:42:41: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:42:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:42:41: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:42:41: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:42:41: start model_add_line... INFO @ Sun, 03 Jun 2018 13:42:42: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:42:42: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:42:42: #1 total tags in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:42:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:42:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:42:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:42:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:42:42: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:42:42: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 03 Jun 2018 13:42:42: #2.2 Generate R script for model : SRX2583184.10_model.r WARNING @ Sun, 03 Jun 2018 13:42:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:42:42: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 03 Jun 2018 13:42:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:42:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:42:42: start X-correlation... INFO @ Sun, 03 Jun 2018 13:42:42: end of X-cor INFO @ Sun, 03 Jun 2018 13:42:42: #2 finished! INFO @ Sun, 03 Jun 2018 13:42:42: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:42:42: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 03 Jun 2018 13:42:42: #2.2 Generate R script for model : SRX2583184.05_model.r WARNING @ Sun, 03 Jun 2018 13:42:42: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:42:42: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 03 Jun 2018 13:42:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:42:42: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:42:42: #1 tags after filtering in treatment: 21130251 INFO @ Sun, 03 Jun 2018 13:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:42:42: #1 finished! INFO @ Sun, 03 Jun 2018 13:42:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:42:43: #2 number of paired peaks: 276 WARNING @ Sun, 03 Jun 2018 13:42:43: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 03 Jun 2018 13:42:43: start model_add_line... INFO @ Sun, 03 Jun 2018 13:42:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:42:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:42:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:42:44: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:42:44: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 03 Jun 2018 13:42:44: #2.2 Generate R script for model : SRX2583184.20_model.r WARNING @ Sun, 03 Jun 2018 13:42:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:42:44: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 03 Jun 2018 13:42:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:42:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:43:22: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:43:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:43:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:43:43: #4 Write output xls file... SRX2583184.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:43:43: #4 Write peak in narrowPeak format file... SRX2583184.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:43:43: #4 Write summits bed file... SRX2583184.05_summits.bed INFO @ Sun, 03 Jun 2018 13:43:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3480 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:43:44: #4 Write output xls file... SRX2583184.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:43:44: #4 Write peak in narrowPeak format file... SRX2583184.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:43:44: #4 Write summits bed file... SRX2583184.10_summits.bed INFO @ Sun, 03 Jun 2018 13:43:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2240 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:43:48: #4 Write output xls file... SRX2583184.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:43:48: #4 Write peak in narrowPeak format file... SRX2583184.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:43:48: #4 Write summits bed file... SRX2583184.20_summits.bed INFO @ Sun, 03 Jun 2018 13:43:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1204 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。