Job ID = 9029214 sra ファイルのダウンロード中... Completed: 303366K bytes transferred in 7 seconds (325351K 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 12007 0 12007 0 0 1630 0 --:--:-- 0:00:07 --:--:-- 11086 100 38318 0 38318 0 0 4582 0 --:--:-- 0:00:08 --:--:-- 18439 100 54110 0 54110 0 0 6195 0 --:--:-- 0:00:08 --:--:-- 22076 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 14386095 spots for /home/okishinya/chipatlas/results/dm3/SRX1433354/SRR2919819.sra Written 14386095 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: 00:06:11 14386095 reads; of these: 14386095 (100.00%) were unpaired; of these: 309278 (2.15%) aligned 0 times 10845706 (75.39%) aligned exactly 1 time 3231111 (22.46%) aligned >1 times 97.85% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 1816431 / 14076817 = 0.1290 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 13:02:11: # Command line: callpeak -t SRX1433354.bam -f BAM -g dm -n SRX1433354.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433354.05 # format = BAM # ChIP-seq file = ['SRX1433354.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 13:02:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:02:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:02:11: # Command line: callpeak -t SRX1433354.bam -f BAM -g dm -n SRX1433354.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433354.20 # format = BAM # ChIP-seq file = ['SRX1433354.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 13:02:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:02:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:02:11: # Command line: callpeak -t SRX1433354.bam -f BAM -g dm -n SRX1433354.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433354.10 # format = BAM # ChIP-seq file = ['SRX1433354.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 13:02:11: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:02:11: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:02:17: 1000000 INFO @ Sat, 03 Jun 2017 13:02:18: 1000000 INFO @ Sat, 03 Jun 2017 13:02:18: 1000000 INFO @ Sat, 03 Jun 2017 13:02:24: 2000000 INFO @ Sat, 03 Jun 2017 13:02:26: 2000000 INFO @ Sat, 03 Jun 2017 13:02:26: 2000000 INFO @ Sat, 03 Jun 2017 13:02:31: 3000000 INFO @ Sat, 03 Jun 2017 13:02:33: 3000000 INFO @ Sat, 03 Jun 2017 13:02:34: 3000000 INFO @ Sat, 03 Jun 2017 13:02:37: 4000000 INFO @ Sat, 03 Jun 2017 13:02:41: 4000000 INFO @ Sat, 03 Jun 2017 13:02:41: 4000000 INFO @ Sat, 03 Jun 2017 13:02:44: 5000000 INFO @ Sat, 03 Jun 2017 13:02:49: 5000000 INFO @ Sat, 03 Jun 2017 13:02:49: 5000000 INFO @ Sat, 03 Jun 2017 13:02:53: 6000000 INFO @ Sat, 03 Jun 2017 13:02:57: 6000000 INFO @ Sat, 03 Jun 2017 13:02:57: 6000000 INFO @ Sat, 03 Jun 2017 13:03:02: 7000000 INFO @ Sat, 03 Jun 2017 13:03:05: 7000000 INFO @ Sat, 03 Jun 2017 13:03:05: 7000000 INFO @ Sat, 03 Jun 2017 13:03:11: 8000000 INFO @ Sat, 03 Jun 2017 13:03:13: 8000000 INFO @ Sat, 03 Jun 2017 13:03:13: 8000000 INFO @ Sat, 03 Jun 2017 13:03:20: 9000000 INFO @ Sat, 03 Jun 2017 13:03:21: 9000000 INFO @ Sat, 03 Jun 2017 13:03:21: 9000000 INFO @ Sat, 03 Jun 2017 13:03:29: 10000000 INFO @ Sat, 03 Jun 2017 13:03:29: 10000000 INFO @ Sat, 03 Jun 2017 13:03:29: 10000000 INFO @ Sat, 03 Jun 2017 13:03:37: 11000000 INFO @ Sat, 03 Jun 2017 13:03:37: 11000000 INFO @ Sat, 03 Jun 2017 13:03:37: 11000000 INFO @ Sat, 03 Jun 2017 13:03:45: 12000000 INFO @ Sat, 03 Jun 2017 13:03:45: 12000000 INFO @ Sat, 03 Jun 2017 13:03:46: 12000000 INFO @ Sat, 03 Jun 2017 13:03:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:03:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:03:47: #1 total tags in treatment: 12260386 INFO @ Sat, 03 Jun 2017 13:03:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:47: #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 13:03:47: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:03:47: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:03:47: #1 total tags in treatment: 12260386 INFO @ Sat, 03 Jun 2017 13:03:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:47: #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 13:03:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:03:48: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:03:48: #1 total tags in treatment: 12260386 INFO @ Sat, 03 Jun 2017 13:03:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:03:48: #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 13:03:49: #1 tags after filtering in treatment: 12258424 INFO @ Sat, 03 Jun 2017 13:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:49: #1 tags after filtering in treatment: 12258424 INFO @ Sat, 03 Jun 2017 13:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:50: #1 tags after filtering in treatment: 12258424 INFO @ Sat, 03 Jun 2017 13:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:03:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:03:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:03:51: #2 number of paired peaks: 289 WARNING @ Sat, 03 Jun 2017 13:03:51: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 03 Jun 2017 13:03:51: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:51: #2 number of paired peaks: 289 WARNING @ Sat, 03 Jun 2017 13:03:51: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 03 Jun 2017 13:03:51: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:52: #2 number of paired peaks: 289 WARNING @ Sat, 03 Jun 2017 13:03:52: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Sat, 03 Jun 2017 13:03:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:03:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:54: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 13:03:54: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 13:03:54: #2.2 Generate R script for model : SRX1433354.10_model.r WARNING @ Sat, 03 Jun 2017 13:03:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:03:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 13:03:54: #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 13:03:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:03:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:54: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 13:03:54: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 13:03:54: #2.2 Generate R script for model : SRX1433354.05_model.r WARNING @ Sat, 03 Jun 2017 13:03:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:03:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 13:03:54: #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 13:03:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:03:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:03:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:03:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:03:55: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 13:03:55: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 03 Jun 2017 13:03:55: #2.2 Generate R script for model : SRX1433354.20_model.r WARNING @ Sat, 03 Jun 2017 13:03:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:03:55: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 03 Jun 2017 13:03:55: #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 13:03:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:03:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:05:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:05:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:05:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:05:47: #4 Write output xls file... SRX1433354.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:05:47: #4 Write peak in narrowPeak format file... SRX1433354.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:05:47: #4 Write summits bed file... SRX1433354.05_summits.bed INFO @ Sat, 03 Jun 2017 13:05:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1567 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:05:51: #4 Write output xls file... SRX1433354.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:05:51: #4 Write peak in narrowPeak format file... SRX1433354.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:05:51: #4 Write summits bed file... SRX1433354.20_summits.bed INFO @ Sat, 03 Jun 2017 13:05:52: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (833 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:05:54: #4 Write output xls file... SRX1433354.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:05:54: #4 Write peak in narrowPeak format file... SRX1433354.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:05:54: #4 Write summits bed file... SRX1433354.10_summits.bed INFO @ Sat, 03 Jun 2017 13:05:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1130 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。