Job ID = 9030317 sra ファイルのダウンロード中... Completed: 426561K bytes transferred in 6 seconds (551020K 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 --:--:-- 0:00:06 --:--:-- 0 100 14323 0 14323 0 0 1892 0 --:--:-- 0:00:07 --:--:-- 12520 100 38317 0 38317 0 0 4474 0 --:--:-- 0:00:08 --:--:-- 17905 100 57449 0 57449 0 0 6339 0 --:--:-- 0:00:09 --:--:-- 21777 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 13809114 spots for /home/okishinya/chipatlas/results/dm3/SRX287975/SRR870164.sra Written 13809114 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: 00:06:49 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 547884 (3.97%) aligned 0 times 8994262 (65.13%) aligned exactly 1 time 4266968 (30.90%) aligned >1 times 96.03% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 1852931 / 13261230 = 0.1397 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 17:46:22: # Command line: callpeak -t SRX287975.bam -f BAM -g dm -n SRX287975.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX287975.10 # format = BAM # ChIP-seq file = ['SRX287975.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 17:46:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:46:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:46:22: # Command line: callpeak -t SRX287975.bam -f BAM -g dm -n SRX287975.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX287975.20 # format = BAM # ChIP-seq file = ['SRX287975.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 17:46:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:46:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:46:22: # Command line: callpeak -t SRX287975.bam -f BAM -g dm -n SRX287975.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX287975.05 # format = BAM # ChIP-seq file = ['SRX287975.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 17:46:22: #1 read tag files... INFO @ Sat, 03 Jun 2017 17:46:22: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 17:46:28: 1000000 INFO @ Sat, 03 Jun 2017 17:46:29: 1000000 INFO @ Sat, 03 Jun 2017 17:46:30: 1000000 INFO @ Sat, 03 Jun 2017 17:46:34: 2000000 INFO @ Sat, 03 Jun 2017 17:46:35: 2000000 INFO @ Sat, 03 Jun 2017 17:46:36: 2000000 INFO @ Sat, 03 Jun 2017 17:46:41: 3000000 INFO @ Sat, 03 Jun 2017 17:46:42: 3000000 INFO @ Sat, 03 Jun 2017 17:46:42: 3000000 INFO @ Sat, 03 Jun 2017 17:46:47: 4000000 INFO @ Sat, 03 Jun 2017 17:46:48: 4000000 INFO @ Sat, 03 Jun 2017 17:46:48: 4000000 INFO @ Sat, 03 Jun 2017 17:46:54: 5000000 INFO @ Sat, 03 Jun 2017 17:46:54: 5000000 INFO @ Sat, 03 Jun 2017 17:46:55: 5000000 INFO @ Sat, 03 Jun 2017 17:47:00: 6000000 INFO @ Sat, 03 Jun 2017 17:47:00: 6000000 INFO @ Sat, 03 Jun 2017 17:47:01: 6000000 INFO @ Sat, 03 Jun 2017 17:47:06: 7000000 INFO @ Sat, 03 Jun 2017 17:47:06: 7000000 INFO @ Sat, 03 Jun 2017 17:47:08: 7000000 INFO @ Sat, 03 Jun 2017 17:47:12: 8000000 INFO @ Sat, 03 Jun 2017 17:47:13: 8000000 INFO @ Sat, 03 Jun 2017 17:47:15: 8000000 INFO @ Sat, 03 Jun 2017 17:47:18: 9000000 INFO @ Sat, 03 Jun 2017 17:47:19: 9000000 INFO @ Sat, 03 Jun 2017 17:47:21: 9000000 INFO @ Sat, 03 Jun 2017 17:47:24: 10000000 INFO @ Sat, 03 Jun 2017 17:47:26: 10000000 INFO @ Sat, 03 Jun 2017 17:47:28: 10000000 INFO @ Sat, 03 Jun 2017 17:47:30: 11000000 INFO @ Sat, 03 Jun 2017 17:47:32: 11000000 INFO @ Sat, 03 Jun 2017 17:47:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:47:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:47:33: #1 total tags in treatment: 11408299 INFO @ Sat, 03 Jun 2017 17:47:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:47:33: #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 17:47:34: 11000000 INFO @ Sat, 03 Jun 2017 17:47:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:47:35: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:47:35: #1 total tags in treatment: 11408299 INFO @ Sat, 03 Jun 2017 17:47:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:47:35: #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 17:47:35: #1 tags after filtering in treatment: 11406013 INFO @ Sat, 03 Jun 2017 17:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:47:35: #1 finished! INFO @ Sat, 03 Jun 2017 17:47:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:47:37: #1 tags after filtering in treatment: 11406013 INFO @ Sat, 03 Jun 2017 17:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:47:37: #1 finished! INFO @ Sat, 03 Jun 2017 17:47:37: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:47:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 17:47:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 17:47:37: #1 total tags in treatment: 11408299 INFO @ Sat, 03 Jun 2017 17:47:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 17:47:37: #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 17:47:37: #2 number of paired peaks: 403 WARNING @ Sat, 03 Jun 2017 17:47:37: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Jun 2017 17:47:37: start model_add_line... INFO @ Sat, 03 Jun 2017 17:47:39: #2 number of paired peaks: 403 WARNING @ Sat, 03 Jun 2017 17:47:39: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Jun 2017 17:47:39: start model_add_line... INFO @ Sat, 03 Jun 2017 17:47:39: #1 tags after filtering in treatment: 11406013 INFO @ Sat, 03 Jun 2017 17:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 17:47:39: #1 finished! INFO @ Sat, 03 Jun 2017 17:47:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 17:47:40: start X-correlation... INFO @ Sat, 03 Jun 2017 17:47:40: end of X-cor INFO @ Sat, 03 Jun 2017 17:47:40: #2 finished! INFO @ Sat, 03 Jun 2017 17:47:40: #2 predicted fragment length is 45 bps INFO @ Sat, 03 Jun 2017 17:47:40: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 03 Jun 2017 17:47:40: #2.2 Generate R script for model : SRX287975.10_model.r WARNING @ Sat, 03 Jun 2017 17:47:40: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:47:40: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 03 Jun 2017 17:47:40: #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 17:47:40: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:47:41: #2 number of paired peaks: 403 WARNING @ Sat, 03 Jun 2017 17:47:41: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Sat, 03 Jun 2017 17:47:41: start model_add_line... INFO @ Sat, 03 Jun 2017 17:47:41: start X-correlation... INFO @ Sat, 03 Jun 2017 17:47:41: end of X-cor INFO @ Sat, 03 Jun 2017 17:47:41: #2 finished! INFO @ Sat, 03 Jun 2017 17:47:41: #2 predicted fragment length is 45 bps INFO @ Sat, 03 Jun 2017 17:47:41: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 03 Jun 2017 17:47:41: #2.2 Generate R script for model : SRX287975.20_model.r WARNING @ Sat, 03 Jun 2017 17:47:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:47:41: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 03 Jun 2017 17:47:41: #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 17:47:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:47:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:47:44: start X-correlation... INFO @ Sat, 03 Jun 2017 17:47:44: end of X-cor INFO @ Sat, 03 Jun 2017 17:47:44: #2 finished! INFO @ Sat, 03 Jun 2017 17:47:44: #2 predicted fragment length is 45 bps INFO @ Sat, 03 Jun 2017 17:47:44: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 03 Jun 2017 17:47:44: #2.2 Generate R script for model : SRX287975.05_model.r WARNING @ Sat, 03 Jun 2017 17:47:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 17:47:44: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 03 Jun 2017 17:47:44: #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 17:47:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 17:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 17:48:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:48:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:48:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write output xls file... SRX287975.10_peaks.xls INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write output xls file... SRX287975.20_peaks.xls INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write peak in narrowPeak format file... SRX287975.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write peak in narrowPeak format file... SRX287975.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write summits bed file... SRX287975.10_summits.bed INFO @ Sat, 03 Jun 2017 17:49:26: Done! INFO @ Sat, 03 Jun 2017 17:49:26: #4 Write summits bed file... SRX287975.20_summits.bed INFO @ Sat, 03 Jun 2017 17:49:26: Done! pass1 - making usageList (13 chroms): 2 millis pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1401 records, 4 fields): 4 millis pass2 - checking and writing primary data (1846 records, 4 fields): 8 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 17:49:32: #4 Write output xls file... SRX287975.05_peaks.xls INFO @ Sat, 03 Jun 2017 17:49:32: #4 Write peak in narrowPeak format file... SRX287975.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 17:49:32: #4 Write summits bed file... SRX287975.05_summits.bed INFO @ Sat, 03 Jun 2017 17:49:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2089 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。