Job ID = 9025596 sra ファイルのダウンロード中... Completed: 579548K bytes transferred in 213 seconds (22210K 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 14324 0 14324 0 0 1839 0 --:--:-- 0:00:07 --:--:-- 10447 100 38318 0 38318 0 0 4362 0 --:--:-- 0:00:08 --:--:-- 16188 100 52767 0 52767 0 0 5787 0 --:--:-- 0:00:09 --:--:-- 19543 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 21113861 spots for /home/okishinya/chipatlas/results/ce10/SRX1936241/SRR3879848.sra Written 21113861 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: 00:00:01 Multiseed full-index search: 00:06:06 21113861 reads; of these: 21113861 (100.00%) were unpaired; of these: 1032559 (4.89%) aligned 0 times 17121897 (81.09%) aligned exactly 1 time 2959405 (14.02%) aligned >1 times 95.11% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2260963 / 20081302 = 0.1126 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 04:42:05: # Command line: callpeak -t SRX1936241.bam -f BAM -g ce -n SRX1936241.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1936241.20 # format = BAM # ChIP-seq file = ['SRX1936241.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:42:05: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:05: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:05: # Command line: callpeak -t SRX1936241.bam -f BAM -g ce -n SRX1936241.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1936241.05 # format = BAM # ChIP-seq file = ['SRX1936241.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:42:05: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:05: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:05: # Command line: callpeak -t SRX1936241.bam -f BAM -g ce -n SRX1936241.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1936241.10 # format = BAM # ChIP-seq file = ['SRX1936241.bam'] # control file = None # effective genome size = 9.00e+07 # 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 04:42:05: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:05: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:12: 1000000 INFO @ Sat, 03 Jun 2017 04:42:12: 1000000 INFO @ Sat, 03 Jun 2017 04:42:14: 1000000 INFO @ Sat, 03 Jun 2017 04:42:19: 2000000 INFO @ Sat, 03 Jun 2017 04:42:19: 2000000 INFO @ Sat, 03 Jun 2017 04:42:22: 2000000 INFO @ Sat, 03 Jun 2017 04:42:27: 3000000 INFO @ Sat, 03 Jun 2017 04:42:27: 3000000 INFO @ Sat, 03 Jun 2017 04:42:30: 3000000 INFO @ Sat, 03 Jun 2017 04:42:34: 4000000 INFO @ Sat, 03 Jun 2017 04:42:34: 4000000 INFO @ Sat, 03 Jun 2017 04:42:38: 4000000 INFO @ Sat, 03 Jun 2017 04:42:41: 5000000 INFO @ Sat, 03 Jun 2017 04:42:41: 5000000 INFO @ Sat, 03 Jun 2017 04:42:46: 5000000 INFO @ Sat, 03 Jun 2017 04:42:49: 6000000 INFO @ Sat, 03 Jun 2017 04:42:49: 6000000 INFO @ Sat, 03 Jun 2017 04:42:54: 6000000 INFO @ Sat, 03 Jun 2017 04:42:56: 7000000 INFO @ Sat, 03 Jun 2017 04:42:57: 7000000 INFO @ Sat, 03 Jun 2017 04:43:02: 7000000 INFO @ Sat, 03 Jun 2017 04:43:03: 8000000 INFO @ Sat, 03 Jun 2017 04:43:06: 8000000 INFO @ Sat, 03 Jun 2017 04:43:10: 9000000 INFO @ Sat, 03 Jun 2017 04:43:11: 8000000 INFO @ Sat, 03 Jun 2017 04:43:16: 9000000 INFO @ Sat, 03 Jun 2017 04:43:17: 10000000 INFO @ Sat, 03 Jun 2017 04:43:19: 9000000 INFO @ Sat, 03 Jun 2017 04:43:24: 11000000 INFO @ Sat, 03 Jun 2017 04:43:25: 10000000 INFO @ Sat, 03 Jun 2017 04:43:27: 10000000 INFO @ Sat, 03 Jun 2017 04:43:31: 12000000 INFO @ Sat, 03 Jun 2017 04:43:35: 11000000 INFO @ Sat, 03 Jun 2017 04:43:35: 11000000 INFO @ Sat, 03 Jun 2017 04:43:39: 13000000 INFO @ Sat, 03 Jun 2017 04:43:43: 12000000 INFO @ Sat, 03 Jun 2017 04:43:44: 12000000 INFO @ Sat, 03 Jun 2017 04:43:46: 14000000 INFO @ Sat, 03 Jun 2017 04:43:51: 13000000 INFO @ Sat, 03 Jun 2017 04:43:53: 15000000 INFO @ Sat, 03 Jun 2017 04:43:53: 13000000 INFO @ Sat, 03 Jun 2017 04:44:00: 14000000 INFO @ Sat, 03 Jun 2017 04:44:00: 16000000 INFO @ Sat, 03 Jun 2017 04:44:03: 14000000 INFO @ Sat, 03 Jun 2017 04:44:07: 17000000 INFO @ Sat, 03 Jun 2017 04:44:08: 15000000 INFO @ Sat, 03 Jun 2017 04:44:12: 15000000 INFO @ Sat, 03 Jun 2017 04:44:13: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:44:13: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:44:13: #1 total tags in treatment: 17820339 INFO @ Sat, 03 Jun 2017 04:44:13: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:44:13: #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 04:44:16: 16000000 INFO @ Sat, 03 Jun 2017 04:44:16: #1 tags after filtering in treatment: 17817124 INFO @ Sat, 03 Jun 2017 04:44:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:44:16: #1 finished! INFO @ Sat, 03 Jun 2017 04:44:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:44:20: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 04:44:20: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Jun 2017 04:44:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:44:21: 16000000 INFO @ Sat, 03 Jun 2017 04:44:24: start X-correlation... INFO @ Sat, 03 Jun 2017 04:44:24: end of X-cor INFO @ Sat, 03 Jun 2017 04:44:24: #2 finished! INFO @ Sat, 03 Jun 2017 04:44:24: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:44:24: #2 alternative fragment length(s) may be 1,49,538,571 bps INFO @ Sat, 03 Jun 2017 04:44:24: #2.2 Generate R script for model : SRX1936241.05_model.r WARNING @ Sat, 03 Jun 2017 04:44:24: #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 04:44:24: #2 You may need to consider one of the other alternative d(s): 1,49,538,571 WARNING @ Sat, 03 Jun 2017 04:44:24: #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 04:44:24: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:44:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:44:24: 17000000 INFO @ Sat, 03 Jun 2017 04:44:31: 17000000 INFO @ Sat, 03 Jun 2017 04:44:31: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:44:31: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:44:31: #1 total tags in treatment: 17820339 INFO @ Sat, 03 Jun 2017 04:44:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:44:31: #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 04:44:34: #1 tags after filtering in treatment: 17817124 INFO @ Sat, 03 Jun 2017 04:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:44:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:44:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:44:37: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 04:44:37: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Jun 2017 04:44:37: start model_add_line... INFO @ Sat, 03 Jun 2017 04:44:38: #1 tag size is determined as 52 bps INFO @ Sat, 03 Jun 2017 04:44:38: #1 tag size = 52 INFO @ Sat, 03 Jun 2017 04:44:38: #1 total tags in treatment: 17820339 INFO @ Sat, 03 Jun 2017 04:44:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:44:38: #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 04:44:41: start X-correlation... INFO @ Sat, 03 Jun 2017 04:44:41: end of X-cor INFO @ Sat, 03 Jun 2017 04:44:41: #2 finished! INFO @ Sat, 03 Jun 2017 04:44:41: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:44:41: #2 alternative fragment length(s) may be 1,49,538,571 bps INFO @ Sat, 03 Jun 2017 04:44:41: #2.2 Generate R script for model : SRX1936241.20_model.r WARNING @ Sat, 03 Jun 2017 04:44:41: #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 04:44:41: #2 You may need to consider one of the other alternative d(s): 1,49,538,571 WARNING @ Sat, 03 Jun 2017 04:44:41: #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 04:44:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:44:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:44:42: #1 tags after filtering in treatment: 17817124 INFO @ Sat, 03 Jun 2017 04:44:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:44:42: #1 finished! INFO @ Sat, 03 Jun 2017 04:44:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:44:45: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 04:44:45: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 03 Jun 2017 04:44:45: start model_add_line... INFO @ Sat, 03 Jun 2017 04:44:49: start X-correlation... INFO @ Sat, 03 Jun 2017 04:44:49: end of X-cor INFO @ Sat, 03 Jun 2017 04:44:49: #2 finished! INFO @ Sat, 03 Jun 2017 04:44:49: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:44:49: #2 alternative fragment length(s) may be 1,49,538,571 bps INFO @ Sat, 03 Jun 2017 04:44:49: #2.2 Generate R script for model : SRX1936241.10_model.r WARNING @ Sat, 03 Jun 2017 04:44:49: #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 04:44:49: #2 You may need to consider one of the other alternative d(s): 1,49,538,571 WARNING @ Sat, 03 Jun 2017 04:44:49: #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 04:44:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:44:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:45:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:59: #4 Write output xls file... SRX1936241.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:46:59: #4 Write peak in narrowPeak format file... SRX1936241.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:46:59: #4 Write summits bed file... SRX1936241.05_summits.bed INFO @ Sat, 03 Jun 2017 04:46:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:47:14: #4 Write output xls file... SRX1936241.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:47:14: #4 Write peak in narrowPeak format file... SRX1936241.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:47:14: #4 Write summits bed file... SRX1936241.20_summits.bed INFO @ Sat, 03 Jun 2017 04:47:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (133 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:47:16: #4 Write output xls file... SRX1936241.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:47:16: #4 Write peak in narrowPeak format file... SRX1936241.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:47:16: #4 Write summits bed file... SRX1936241.10_summits.bed INFO @ Sat, 03 Jun 2017 04:47:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。