Job ID = 11171308 sra ファイルのダウンロード中... Completed: 120927K bytes transferred in 5 seconds (174151K bits/sec), in 1 file. Completed: 119195K bytes transferred in 5 seconds (191957K bits/sec), in 1 file. Completed: 119537K bytes transferred in 5 seconds (186751K bits/sec), in 1 file. Completed: 118727K bytes transferred in 6 seconds (156372K 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 6335611 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850466.sra Written 6335611 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850466.sra Read 6326047 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850465.sra Written 6326047 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850465.sra Read 6284885 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850467.sra Written 6284885 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850467.sra Read 6413143 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850464.sra Written 6413143 spots for /home/okishinya/chipatlas/results/dm3/SRX3020551/SRR5850464.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 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: 00:10:57 25359686 reads; of these: 25359686 (100.00%) were unpaired; of these: 712260 (2.81%) aligned 0 times 16148308 (63.68%) aligned exactly 1 time 8499118 (33.51%) aligned >1 times 97.19% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 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] 4305292 / 24647426 = 0.1747 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 @ Sat, 08 Sep 2018 13:52:15: # Command line: callpeak -t SRX3020551.bam -f BAM -g dm -n SRX3020551.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020551.05 # format = BAM # ChIP-seq file = ['SRX3020551.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 @ Sat, 08 Sep 2018 13:52:15: # Command line: callpeak -t SRX3020551.bam -f BAM -g dm -n SRX3020551.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020551.10 # format = BAM # ChIP-seq file = ['SRX3020551.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 @ Sat, 08 Sep 2018 13:52:15: # Command line: callpeak -t SRX3020551.bam -f BAM -g dm -n SRX3020551.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020551.20 # format = BAM # ChIP-seq file = ['SRX3020551.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 @ Sat, 08 Sep 2018 13:52:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:52:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:52:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:52:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:52:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:52:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:52:21: 1000000 INFO @ Sat, 08 Sep 2018 13:52:21: 1000000 INFO @ Sat, 08 Sep 2018 13:52:21: 1000000 INFO @ Sat, 08 Sep 2018 13:52:28: 2000000 INFO @ Sat, 08 Sep 2018 13:52:28: 2000000 INFO @ Sat, 08 Sep 2018 13:52:28: 2000000 INFO @ Sat, 08 Sep 2018 13:52:34: 3000000 INFO @ Sat, 08 Sep 2018 13:52:34: 3000000 INFO @ Sat, 08 Sep 2018 13:52:34: 3000000 INFO @ Sat, 08 Sep 2018 13:52:40: 4000000 INFO @ Sat, 08 Sep 2018 13:52:40: 4000000 INFO @ Sat, 08 Sep 2018 13:52:41: 4000000 INFO @ Sat, 08 Sep 2018 13:52:47: 5000000 INFO @ Sat, 08 Sep 2018 13:52:47: 5000000 INFO @ Sat, 08 Sep 2018 13:52:47: 5000000 INFO @ Sat, 08 Sep 2018 13:52:53: 6000000 INFO @ Sat, 08 Sep 2018 13:52:53: 6000000 INFO @ Sat, 08 Sep 2018 13:52:54: 6000000 INFO @ Sat, 08 Sep 2018 13:53:00: 7000000 INFO @ Sat, 08 Sep 2018 13:53:00: 7000000 INFO @ Sat, 08 Sep 2018 13:53:01: 7000000 INFO @ Sat, 08 Sep 2018 13:53:06: 8000000 INFO @ Sat, 08 Sep 2018 13:53:06: 8000000 INFO @ Sat, 08 Sep 2018 13:53:08: 8000000 INFO @ Sat, 08 Sep 2018 13:53:13: 9000000 INFO @ Sat, 08 Sep 2018 13:53:13: 9000000 INFO @ Sat, 08 Sep 2018 13:53:15: 9000000 INFO @ Sat, 08 Sep 2018 13:53:19: 10000000 INFO @ Sat, 08 Sep 2018 13:53:19: 10000000 INFO @ Sat, 08 Sep 2018 13:53:21: 10000000 INFO @ Sat, 08 Sep 2018 13:53:25: 11000000 INFO @ Sat, 08 Sep 2018 13:53:26: 11000000 INFO @ Sat, 08 Sep 2018 13:53:28: 11000000 INFO @ Sat, 08 Sep 2018 13:53:32: 12000000 INFO @ Sat, 08 Sep 2018 13:53:32: 12000000 INFO @ Sat, 08 Sep 2018 13:53:35: 12000000 INFO @ Sat, 08 Sep 2018 13:53:38: 13000000 INFO @ Sat, 08 Sep 2018 13:53:38: 13000000 INFO @ Sat, 08 Sep 2018 13:53:42: 13000000 INFO @ Sat, 08 Sep 2018 13:53:45: 14000000 INFO @ Sat, 08 Sep 2018 13:53:45: 14000000 INFO @ Sat, 08 Sep 2018 13:53:48: 14000000 INFO @ Sat, 08 Sep 2018 13:53:51: 15000000 INFO @ Sat, 08 Sep 2018 13:53:51: 15000000 INFO @ Sat, 08 Sep 2018 13:53:55: 15000000 INFO @ Sat, 08 Sep 2018 13:53:58: 16000000 INFO @ Sat, 08 Sep 2018 13:53:58: 16000000 INFO @ Sat, 08 Sep 2018 13:54:02: 16000000 INFO @ Sat, 08 Sep 2018 13:54:05: 17000000 INFO @ Sat, 08 Sep 2018 13:54:05: 17000000 INFO @ Sat, 08 Sep 2018 13:54:09: 17000000 INFO @ Sat, 08 Sep 2018 13:54:11: 18000000 INFO @ Sat, 08 Sep 2018 13:54:11: 18000000 INFO @ Sat, 08 Sep 2018 13:54:16: 18000000 INFO @ Sat, 08 Sep 2018 13:54:18: 19000000 INFO @ Sat, 08 Sep 2018 13:54:18: 19000000 INFO @ Sat, 08 Sep 2018 13:54:22: 19000000 INFO @ Sat, 08 Sep 2018 13:54:24: 20000000 INFO @ Sat, 08 Sep 2018 13:54:24: 20000000 INFO @ Sat, 08 Sep 2018 13:54:27: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:54:27: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:54:27: #1 total tags in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:54:27: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:54:27: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:54:27: #1 total tags in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:54:27: #1 tags after filtering in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:27: #1 tags after filtering in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:28: #2 number of paired peaks: 178 WARNING @ Sat, 08 Sep 2018 13:54:28: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:28: #2 number of paired peaks: 178 WARNING @ Sat, 08 Sep 2018 13:54:28: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:28: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:54:28: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 08 Sep 2018 13:54:28: #2.2 Generate R script for model : SRX3020551.05_model.r WARNING @ Sat, 08 Sep 2018 13:54:28: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:28: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 08 Sep 2018 13:54:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:29: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:29: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:29: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:29: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:54:29: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 08 Sep 2018 13:54:29: #2.2 Generate R script for model : SRX3020551.10_model.r WARNING @ Sat, 08 Sep 2018 13:54:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:29: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 08 Sep 2018 13:54:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:29: 20000000 INFO @ Sat, 08 Sep 2018 13:54:31: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:54:31: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:54:31: #1 total tags in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:31: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:54:32: #1 tags after filtering in treatment: 20342134 INFO @ Sat, 08 Sep 2018 13:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:32: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:32: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:33: #2 number of paired peaks: 178 WARNING @ Sat, 08 Sep 2018 13:54:33: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:33: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:33: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:33: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:33: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:33: #2 predicted fragment length is 50 bps INFO @ Sat, 08 Sep 2018 13:54:33: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sat, 08 Sep 2018 13:54:33: #2.2 Generate R script for model : SRX3020551.20_model.r WARNING @ Sat, 08 Sep 2018 13:54:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:33: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sat, 08 Sep 2018 13:54:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:55:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write output xls file... SRX3020551.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write peak in narrowPeak format file... SRX3020551.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write summits bed file... SRX3020551.10_summits.bed INFO @ Sat, 08 Sep 2018 13:55:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1965 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write output xls file... SRX3020551.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write peak in narrowPeak format file... SRX3020551.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:29: #4 Write summits bed file... SRX3020551.05_summits.bed INFO @ Sat, 08 Sep 2018 13:55:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3280 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:32: #4 Write output xls file... SRX3020551.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:32: #4 Write peak in narrowPeak format file... SRX3020551.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:32: #4 Write summits bed file... SRX3020551.20_summits.bed INFO @ Sat, 08 Sep 2018 13:55:32: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (582 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。