Job ID = 9031968 sra ファイルのダウンロード中... Completed: 1302800K bytes transferred in 13 seconds (783983K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1916 0 --:--:-- 0:00:07 --:--:-- 13933 100 46318 0 46318 0 0 5577 0 --:--:-- 0:00:08 --:--:-- 24928 100 73217 0 73217 0 0 8477 0 --:--:-- 0:00:08 --:--:-- 33432 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... Written 20492134 spots for /home/okishinya/chipatlas/results/dm3/SRX645140/SRR1505740.sra Written 20492134 spots total 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: 00:00:00 Multiseed full-index search: 00:13:53 20492134 reads; of these: 20492134 (100.00%) were unpaired; of these: 9530306 (46.51%) aligned 0 times 7730668 (37.73%) aligned exactly 1 time 3231160 (15.77%) aligned >1 times 53.49% overall alignment rate Time searching: 00:13:53 Overall time: 00:13:53 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 8 files... [bam_rmdupse_core] 808556 / 10961828 = 0.0738 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, 03 Jun 2017 22:27:15: # Command line: callpeak -t SRX645140.bam -f BAM -g dm -n SRX645140.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX645140.05 # format = BAM # ChIP-seq file = ['SRX645140.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 INFO @ Sat, 03 Jun 2017 22:27:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:27:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:27:15: # Command line: callpeak -t SRX645140.bam -f BAM -g dm -n SRX645140.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX645140.10 # format = BAM # ChIP-seq file = ['SRX645140.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 INFO @ Sat, 03 Jun 2017 22:27:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:27:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:27:15: # Command line: callpeak -t SRX645140.bam -f BAM -g dm -n SRX645140.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX645140.20 # format = BAM # ChIP-seq file = ['SRX645140.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 INFO @ Sat, 03 Jun 2017 22:27:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 22:27:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 22:27:24: 1000000 INFO @ Sat, 03 Jun 2017 22:27:24: 1000000 INFO @ Sat, 03 Jun 2017 22:27:24: 1000000 INFO @ Sat, 03 Jun 2017 22:27:32: 2000000 INFO @ Sat, 03 Jun 2017 22:27:32: 2000000 INFO @ Sat, 03 Jun 2017 22:27:32: 2000000 INFO @ Sat, 03 Jun 2017 22:27:40: 3000000 INFO @ Sat, 03 Jun 2017 22:27:40: 3000000 INFO @ Sat, 03 Jun 2017 22:27:41: 3000000 INFO @ Sat, 03 Jun 2017 22:27:48: 4000000 INFO @ Sat, 03 Jun 2017 22:27:48: 4000000 INFO @ Sat, 03 Jun 2017 22:27:49: 4000000 INFO @ Sat, 03 Jun 2017 22:27:57: 5000000 INFO @ Sat, 03 Jun 2017 22:27:57: 5000000 INFO @ Sat, 03 Jun 2017 22:27:57: 5000000 INFO @ Sat, 03 Jun 2017 22:28:05: 6000000 INFO @ Sat, 03 Jun 2017 22:28:05: 6000000 INFO @ Sat, 03 Jun 2017 22:28:05: 6000000 INFO @ Sat, 03 Jun 2017 22:28:13: 7000000 INFO @ Sat, 03 Jun 2017 22:28:13: 7000000 INFO @ Sat, 03 Jun 2017 22:28:13: 7000000 INFO @ Sat, 03 Jun 2017 22:28:21: 8000000 INFO @ Sat, 03 Jun 2017 22:28:22: 8000000 INFO @ Sat, 03 Jun 2017 22:28:22: 8000000 INFO @ Sat, 03 Jun 2017 22:28:29: 9000000 INFO @ Sat, 03 Jun 2017 22:28:30: 9000000 INFO @ Sat, 03 Jun 2017 22:28:30: 9000000 INFO @ Sat, 03 Jun 2017 22:28:37: 10000000 INFO @ Sat, 03 Jun 2017 22:28:38: 10000000 INFO @ Sat, 03 Jun 2017 22:28:38: 10000000 INFO @ Sat, 03 Jun 2017 22:28:39: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 22:28:39: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 22:28:39: #1 total tags in treatment: 10153272 INFO @ Sat, 03 Jun 2017 22:28:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 22:28:39: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 22:28:39: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 22:28:39: #1 total tags in treatment: 10153272 INFO @ Sat, 03 Jun 2017 22:28:39: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:28:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 22:28:40: #1 tag size is determined as 100 bps INFO @ Sat, 03 Jun 2017 22:28:40: #1 tag size = 100 INFO @ Sat, 03 Jun 2017 22:28:40: #1 total tags in treatment: 10153272 INFO @ Sat, 03 Jun 2017 22:28:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 22:28:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 22:28:41: #1 tags after filtering in treatment: 10120433 INFO @ Sat, 03 Jun 2017 22:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:28:41: #1 finished! INFO @ Sat, 03 Jun 2017 22:28:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:28:41: #1 tags after filtering in treatment: 10120433 INFO @ Sat, 03 Jun 2017 22:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:28:41: #1 finished! INFO @ Sat, 03 Jun 2017 22:28:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:28:41: #1 tags after filtering in treatment: 10120433 INFO @ Sat, 03 Jun 2017 22:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 22:28:41: #1 finished! INFO @ Sat, 03 Jun 2017 22:28:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 22:28:42: #2 number of paired peaks: 115 WARNING @ Sat, 03 Jun 2017 22:28:42: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Jun 2017 22:28:42: start model_add_line... INFO @ Sat, 03 Jun 2017 22:28:43: #2 number of paired peaks: 115 WARNING @ Sat, 03 Jun 2017 22:28:43: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Jun 2017 22:28:43: start model_add_line... INFO @ Sat, 03 Jun 2017 22:28:43: #2 number of paired peaks: 115 WARNING @ Sat, 03 Jun 2017 22:28:43: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Sat, 03 Jun 2017 22:28:43: start model_add_line... INFO @ Sat, 03 Jun 2017 22:28:43: start X-correlation... INFO @ Sat, 03 Jun 2017 22:28:43: end of X-cor INFO @ Sat, 03 Jun 2017 22:28:43: #2 finished! INFO @ Sat, 03 Jun 2017 22:28:43: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Jun 2017 22:28:43: #2 alternative fragment length(s) may be 88,531,562 bps INFO @ Sat, 03 Jun 2017 22:28:43: #2.2 Generate R script for model : SRX645140.20_model.r WARNING @ Sat, 03 Jun 2017 22:28:43: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:28:43: #2 You may need to consider one of the other alternative d(s): 88,531,562 WARNING @ Sat, 03 Jun 2017 22:28:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 22:28:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:28:44: start X-correlation... INFO @ Sat, 03 Jun 2017 22:28:44: end of X-cor INFO @ Sat, 03 Jun 2017 22:28:44: #2 finished! INFO @ Sat, 03 Jun 2017 22:28:44: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Jun 2017 22:28:44: #2 alternative fragment length(s) may be 88,531,562 bps INFO @ Sat, 03 Jun 2017 22:28:44: #2.2 Generate R script for model : SRX645140.05_model.r WARNING @ Sat, 03 Jun 2017 22:28:44: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:28:44: #2 You may need to consider one of the other alternative d(s): 88,531,562 WARNING @ Sat, 03 Jun 2017 22:28:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 22:28:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:28:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:28:44: start X-correlation... INFO @ Sat, 03 Jun 2017 22:28:44: end of X-cor INFO @ Sat, 03 Jun 2017 22:28:44: #2 finished! INFO @ Sat, 03 Jun 2017 22:28:44: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Jun 2017 22:28:44: #2 alternative fragment length(s) may be 88,531,562 bps INFO @ Sat, 03 Jun 2017 22:28:44: #2.2 Generate R script for model : SRX645140.10_model.r WARNING @ Sat, 03 Jun 2017 22:28:44: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 22:28:44: #2 You may need to consider one of the other alternative d(s): 88,531,562 WARNING @ Sat, 03 Jun 2017 22:28:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 22:28:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 22:28:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 22:29:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:29:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:29:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 22:30:25: #4 Write output xls file... SRX645140.20_peaks.xls INFO @ Sat, 03 Jun 2017 22:30:25: #4 Write peak in narrowPeak format file... SRX645140.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:30:25: #4 Write summits bed file... SRX645140.20_summits.bed INFO @ Sat, 03 Jun 2017 22:30:25: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (642 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write output xls file... SRX645140.05_peaks.xls INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write peak in narrowPeak format file... SRX645140.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write summits bed file... SRX645140.05_summits.bed INFO @ Sat, 03 Jun 2017 22:30:27: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1386 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write output xls file... SRX645140.10_peaks.xls INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write peak in narrowPeak format file... SRX645140.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 22:30:27: #4 Write summits bed file... SRX645140.10_summits.bed INFO @ Sat, 03 Jun 2017 22:30:27: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (967 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。