Job ID = 8696851 sra ファイルのダウンロード中... Completed: 861925K bytes transferred in 11 seconds (600132K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 26919 0 26919 0 0 3134 0 --:--:-- 0:00:08 --:--:-- 14123 100 31392 0 31392 0 0 3582 0 --:--:-- 0:00:08 --:--:-- 15099 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 32467660 spots for /home/okishinya/chipatlas/results/dm3/SRX110786/SRR388368.sra Written 32467660 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:58 32467660 reads; of these: 32467660 (100.00%) were unpaired; of these: 3199125 (9.85%) aligned 0 times 23555687 (72.55%) aligned exactly 1 time 5712848 (17.60%) aligned >1 times 90.15% overall alignment rate Time searching: 00:16:59 Overall time: 00:16:59 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] 7036011 / 29268535 = 0.2404 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 @ Fri, 10 Mar 2017 12:54:47: # Command line: callpeak -t SRX110786.bam -f BAM -g dm -n SRX110786.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110786.20 # format = BAM # ChIP-seq file = ['SRX110786.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 @ Fri, 10 Mar 2017 12:54:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:54:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:54:47: # Command line: callpeak -t SRX110786.bam -f BAM -g dm -n SRX110786.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110786.10 # format = BAM # ChIP-seq file = ['SRX110786.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 @ Fri, 10 Mar 2017 12:54:47: # Command line: callpeak -t SRX110786.bam -f BAM -g dm -n SRX110786.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110786.05 # format = BAM # ChIP-seq file = ['SRX110786.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 @ Fri, 10 Mar 2017 12:54:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:54:47: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:54:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:54:47: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:54:55: 1000000 INFO @ Fri, 10 Mar 2017 12:54:55: 1000000 INFO @ Fri, 10 Mar 2017 12:54:56: 1000000 INFO @ Fri, 10 Mar 2017 12:55:02: 2000000 INFO @ Fri, 10 Mar 2017 12:55:04: 2000000 INFO @ Fri, 10 Mar 2017 12:55:04: 2000000 INFO @ Fri, 10 Mar 2017 12:55:10: 3000000 INFO @ Fri, 10 Mar 2017 12:55:12: 3000000 INFO @ Fri, 10 Mar 2017 12:55:12: 3000000 INFO @ Fri, 10 Mar 2017 12:55:17: 4000000 INFO @ Fri, 10 Mar 2017 12:55:20: 4000000 INFO @ Fri, 10 Mar 2017 12:55:20: 4000000 INFO @ Fri, 10 Mar 2017 12:55:24: 5000000 INFO @ Fri, 10 Mar 2017 12:55:28: 5000000 INFO @ Fri, 10 Mar 2017 12:55:28: 5000000 INFO @ Fri, 10 Mar 2017 12:55:31: 6000000 INFO @ Fri, 10 Mar 2017 12:55:36: 6000000 INFO @ Fri, 10 Mar 2017 12:55:36: 6000000 INFO @ Fri, 10 Mar 2017 12:55:38: 7000000 INFO @ Fri, 10 Mar 2017 12:55:44: 7000000 INFO @ Fri, 10 Mar 2017 12:55:44: 7000000 INFO @ Fri, 10 Mar 2017 12:55:45: 8000000 INFO @ Fri, 10 Mar 2017 12:55:52: 8000000 INFO @ Fri, 10 Mar 2017 12:55:52: 8000000 INFO @ Fri, 10 Mar 2017 12:55:53: 9000000 INFO @ Fri, 10 Mar 2017 12:56:00: 10000000 INFO @ Fri, 10 Mar 2017 12:56:00: 9000000 INFO @ Fri, 10 Mar 2017 12:56:00: 9000000 INFO @ Fri, 10 Mar 2017 12:56:08: 11000000 INFO @ Fri, 10 Mar 2017 12:56:09: 10000000 INFO @ Fri, 10 Mar 2017 12:56:10: 10000000 INFO @ Fri, 10 Mar 2017 12:56:18: 12000000 INFO @ Fri, 10 Mar 2017 12:56:19: 11000000 INFO @ Fri, 10 Mar 2017 12:56:21: 11000000 INFO @ Fri, 10 Mar 2017 12:56:28: 13000000 INFO @ Fri, 10 Mar 2017 12:56:29: 12000000 INFO @ Fri, 10 Mar 2017 12:56:35: 12000000 INFO @ Fri, 10 Mar 2017 12:56:45: 14000000 INFO @ Fri, 10 Mar 2017 12:56:47: 13000000 INFO @ Fri, 10 Mar 2017 12:56:49: 13000000 INFO @ Fri, 10 Mar 2017 12:57:02: 15000000 INFO @ Fri, 10 Mar 2017 12:57:04: 14000000 INFO @ Fri, 10 Mar 2017 12:57:04: 14000000 INFO @ Fri, 10 Mar 2017 12:57:14: 15000000 INFO @ Fri, 10 Mar 2017 12:57:17: 16000000 INFO @ Fri, 10 Mar 2017 12:57:19: 15000000 INFO @ Fri, 10 Mar 2017 12:57:22: 16000000 INFO @ Fri, 10 Mar 2017 12:57:29: 17000000 INFO @ Fri, 10 Mar 2017 12:57:31: 17000000 INFO @ Fri, 10 Mar 2017 12:57:33: 16000000 INFO @ Fri, 10 Mar 2017 12:57:37: 18000000 INFO @ Fri, 10 Mar 2017 12:57:45: 18000000 INFO @ Fri, 10 Mar 2017 12:57:45: 19000000 INFO @ Fri, 10 Mar 2017 12:57:47: 17000000 INFO @ Fri, 10 Mar 2017 12:57:53: 20000000 INFO @ Fri, 10 Mar 2017 12:57:59: 19000000 INFO @ Fri, 10 Mar 2017 12:58:00: 18000000 INFO @ Fri, 10 Mar 2017 12:58:01: 21000000 INFO @ Fri, 10 Mar 2017 12:58:08: 19000000 INFO @ Fri, 10 Mar 2017 12:58:09: 22000000 INFO @ Fri, 10 Mar 2017 12:58:11: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:58:11: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:58:11: #1 total tags in treatment: 22232524 INFO @ Fri, 10 Mar 2017 12:58:11: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:58:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:58:13: 20000000 INFO @ Fri, 10 Mar 2017 12:58:16: #1 tags after filtering in treatment: 22228396 INFO @ Fri, 10 Mar 2017 12:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:58:16: #1 finished! INFO @ Fri, 10 Mar 2017 12:58:16: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:58:17: 20000000 INFO @ Fri, 10 Mar 2017 12:58:21: #2 number of paired peaks: 305 WARNING @ Fri, 10 Mar 2017 12:58:21: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 10 Mar 2017 12:58:21: start model_add_line... INFO @ Fri, 10 Mar 2017 12:58:26: 21000000 INFO @ Fri, 10 Mar 2017 12:58:26: 21000000 INFO @ Fri, 10 Mar 2017 12:58:28: start X-correlation... INFO @ Fri, 10 Mar 2017 12:58:28: end of X-cor INFO @ Fri, 10 Mar 2017 12:58:28: #2 finished! INFO @ Fri, 10 Mar 2017 12:58:28: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Mar 2017 12:58:28: #2 alternative fragment length(s) may be 4,73,550 bps INFO @ Fri, 10 Mar 2017 12:58:28: #2.2 Generate R script for model : SRX110786.05_model.r WARNING @ Fri, 10 Mar 2017 12:58:28: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:58:28: #2 You may need to consider one of the other alternative d(s): 4,73,550 WARNING @ Fri, 10 Mar 2017 12:58:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:58:28: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:58:36: 22000000 INFO @ Fri, 10 Mar 2017 12:58:36: 22000000 INFO @ Fri, 10 Mar 2017 12:58:39: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:58:39: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:58:39: #1 total tags in treatment: 22232524 INFO @ Fri, 10 Mar 2017 12:58:39: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:58:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:58:39: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:58:39: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:58:39: #1 total tags in treatment: 22232524 INFO @ Fri, 10 Mar 2017 12:58:39: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:58:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:58:43: #1 tags after filtering in treatment: 22228396 INFO @ Fri, 10 Mar 2017 12:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:58:43: #1 finished! INFO @ Fri, 10 Mar 2017 12:58:43: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:58:44: #1 tags after filtering in treatment: 22228396 INFO @ Fri, 10 Mar 2017 12:58:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:58:44: #1 finished! INFO @ Fri, 10 Mar 2017 12:58:44: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:58:48: #2 number of paired peaks: 305 WARNING @ Fri, 10 Mar 2017 12:58:48: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 10 Mar 2017 12:58:48: start model_add_line... INFO @ Fri, 10 Mar 2017 12:58:49: #2 number of paired peaks: 305 WARNING @ Fri, 10 Mar 2017 12:58:49: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Fri, 10 Mar 2017 12:58:49: start model_add_line... INFO @ Fri, 10 Mar 2017 12:58:55: start X-correlation... INFO @ Fri, 10 Mar 2017 12:58:55: end of X-cor INFO @ Fri, 10 Mar 2017 12:58:55: #2 finished! INFO @ Fri, 10 Mar 2017 12:58:55: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Mar 2017 12:58:55: #2 alternative fragment length(s) may be 4,73,550 bps INFO @ Fri, 10 Mar 2017 12:58:55: #2.2 Generate R script for model : SRX110786.20_model.r WARNING @ Fri, 10 Mar 2017 12:58:55: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:58:55: #2 You may need to consider one of the other alternative d(s): 4,73,550 WARNING @ Fri, 10 Mar 2017 12:58:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:58:55: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:58:55: start X-correlation... INFO @ Fri, 10 Mar 2017 12:58:55: end of X-cor INFO @ Fri, 10 Mar 2017 12:58:55: #2 finished! INFO @ Fri, 10 Mar 2017 12:58:55: #2 predicted fragment length is 73 bps INFO @ Fri, 10 Mar 2017 12:58:55: #2 alternative fragment length(s) may be 4,73,550 bps INFO @ Fri, 10 Mar 2017 12:58:55: #2.2 Generate R script for model : SRX110786.10_model.r WARNING @ Fri, 10 Mar 2017 12:58:55: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:58:55: #2 You may need to consider one of the other alternative d(s): 4,73,550 WARNING @ Fri, 10 Mar 2017 12:58:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:58:55: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 13:00:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:01:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:01:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 13:02:25: #4 Write output xls file... SRX110786.05_peaks.xls INFO @ Fri, 10 Mar 2017 13:02:25: #4 Write peak in narrowPeak format file... SRX110786.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:02:25: #4 Write summits bed file... SRX110786.05_summits.bed INFO @ Fri, 10 Mar 2017 13:02:25: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11131 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:02:49: #4 Write output xls file... SRX110786.10_peaks.xls INFO @ Fri, 10 Mar 2017 13:02:50: #4 Write peak in narrowPeak format file... SRX110786.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:02:50: #4 Write summits bed file... SRX110786.10_summits.bed INFO @ Fri, 10 Mar 2017 13:02:50: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6087 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 13:02:56: #4 Write output xls file... SRX110786.20_peaks.xls INFO @ Fri, 10 Mar 2017 13:02:56: #4 Write peak in narrowPeak format file... SRX110786.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 13:02:56: #4 Write summits bed file... SRX110786.20_summits.bed INFO @ Fri, 10 Mar 2017 13:02:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1413 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。