Job ID = 9025450 sra ファイルのダウンロード中... Completed: 1381980K bytes transferred in 14 seconds (786013K 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 14324 0 14324 0 0 1882 0 --:--:-- 0:00:07 --:--:-- 11208 100 57070 0 57070 0 0 6631 0 --:--:-- 0:00:08 --:--:-- 25096 100 69833 0 69833 0 0 7960 0 --:--:-- 0:00:08 --:--:-- 28620 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 44398214 spots for /home/okishinya/chipatlas/results/ce10/SRX1007135/SRR1993095.sra Written 44398214 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: 00:07:56 44398214 reads; of these: 44398214 (100.00%) were unpaired; of these: 11217161 (25.26%) aligned 0 times 28082948 (63.25%) aligned exactly 1 time 5098105 (11.48%) aligned >1 times 74.74% overall alignment rate Time searching: 00:07:56 Overall time: 00:07:56 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] 8841219 / 33181053 = 0.2665 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 04:07:08: # Command line: callpeak -t SRX1007135.bam -f BAM -g ce -n SRX1007135.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007135.20 # format = BAM # ChIP-seq file = ['SRX1007135.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 04:07:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:08: # Command line: callpeak -t SRX1007135.bam -f BAM -g ce -n SRX1007135.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007135.05 # format = BAM # ChIP-seq file = ['SRX1007135.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 04:07:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:08: # Command line: callpeak -t SRX1007135.bam -f BAM -g ce -n SRX1007135.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007135.10 # format = BAM # ChIP-seq file = ['SRX1007135.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 04:07:08: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:07:08: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:07:14: 1000000 INFO @ Sat, 03 Jun 2017 04:07:14: 1000000 INFO @ Sat, 03 Jun 2017 04:07:14: 1000000 INFO @ Sat, 03 Jun 2017 04:07:19: 2000000 INFO @ Sat, 03 Jun 2017 04:07:19: 2000000 INFO @ Sat, 03 Jun 2017 04:07:19: 2000000 INFO @ Sat, 03 Jun 2017 04:07:24: 3000000 INFO @ Sat, 03 Jun 2017 04:07:25: 3000000 INFO @ Sat, 03 Jun 2017 04:07:25: 3000000 INFO @ Sat, 03 Jun 2017 04:07:29: 4000000 INFO @ Sat, 03 Jun 2017 04:07:31: 4000000 INFO @ Sat, 03 Jun 2017 04:07:31: 4000000 INFO @ Sat, 03 Jun 2017 04:07:34: 5000000 INFO @ Sat, 03 Jun 2017 04:07:36: 5000000 INFO @ Sat, 03 Jun 2017 04:07:36: 5000000 INFO @ Sat, 03 Jun 2017 04:07:39: 6000000 INFO @ Sat, 03 Jun 2017 04:07:42: 6000000 INFO @ Sat, 03 Jun 2017 04:07:42: 6000000 INFO @ Sat, 03 Jun 2017 04:07:45: 7000000 INFO @ Sat, 03 Jun 2017 04:07:47: 7000000 INFO @ Sat, 03 Jun 2017 04:07:49: 7000000 INFO @ Sat, 03 Jun 2017 04:07:51: 8000000 INFO @ Sat, 03 Jun 2017 04:07:52: 8000000 INFO @ Sat, 03 Jun 2017 04:07:55: 8000000 INFO @ Sat, 03 Jun 2017 04:07:57: 9000000 INFO @ Sat, 03 Jun 2017 04:07:57: 9000000 INFO @ Sat, 03 Jun 2017 04:08:01: 9000000 INFO @ Sat, 03 Jun 2017 04:08:03: 10000000 INFO @ Sat, 03 Jun 2017 04:08:03: 10000000 INFO @ Sat, 03 Jun 2017 04:08:08: 10000000 INFO @ Sat, 03 Jun 2017 04:08:09: 11000000 INFO @ Sat, 03 Jun 2017 04:08:10: 11000000 INFO @ Sat, 03 Jun 2017 04:08:16: 11000000 INFO @ Sat, 03 Jun 2017 04:08:16: 12000000 INFO @ Sat, 03 Jun 2017 04:08:16: 12000000 INFO @ Sat, 03 Jun 2017 04:08:22: 13000000 INFO @ Sat, 03 Jun 2017 04:08:23: 13000000 INFO @ Sat, 03 Jun 2017 04:08:23: 12000000 INFO @ Sat, 03 Jun 2017 04:08:29: 14000000 INFO @ Sat, 03 Jun 2017 04:08:29: 14000000 INFO @ Sat, 03 Jun 2017 04:08:30: 13000000 INFO @ Sat, 03 Jun 2017 04:08:35: 15000000 INFO @ Sat, 03 Jun 2017 04:08:36: 15000000 INFO @ Sat, 03 Jun 2017 04:08:38: 14000000 INFO @ Sat, 03 Jun 2017 04:08:41: 16000000 INFO @ Sat, 03 Jun 2017 04:08:43: 16000000 INFO @ Sat, 03 Jun 2017 04:08:45: 15000000 INFO @ Sat, 03 Jun 2017 04:08:48: 17000000 INFO @ Sat, 03 Jun 2017 04:08:49: 17000000 INFO @ Sat, 03 Jun 2017 04:08:52: 16000000 INFO @ Sat, 03 Jun 2017 04:08:54: 18000000 INFO @ Sat, 03 Jun 2017 04:08:56: 18000000 INFO @ Sat, 03 Jun 2017 04:08:59: 17000000 INFO @ Sat, 03 Jun 2017 04:09:00: 19000000 INFO @ Sat, 03 Jun 2017 04:09:03: 19000000 INFO @ Sat, 03 Jun 2017 04:09:07: 20000000 INFO @ Sat, 03 Jun 2017 04:09:07: 18000000 INFO @ Sat, 03 Jun 2017 04:09:09: 20000000 INFO @ Sat, 03 Jun 2017 04:09:13: 21000000 INFO @ Sat, 03 Jun 2017 04:09:14: 19000000 INFO @ Sat, 03 Jun 2017 04:09:16: 21000000 INFO @ Sat, 03 Jun 2017 04:09:19: 22000000 INFO @ Sat, 03 Jun 2017 04:09:21: 20000000 INFO @ Sat, 03 Jun 2017 04:09:22: 22000000 INFO @ Sat, 03 Jun 2017 04:09:26: 23000000 INFO @ Sat, 03 Jun 2017 04:09:29: 21000000 INFO @ Sat, 03 Jun 2017 04:09:29: 23000000 INFO @ Sat, 03 Jun 2017 04:09:32: 24000000 INFO @ Sat, 03 Jun 2017 04:09:35: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:35: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:35: #1 total tags in treatment: 24339834 INFO @ Sat, 03 Jun 2017 04:09:35: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:35: #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 04:09:35: 22000000 INFO @ Sat, 03 Jun 2017 04:09:36: 24000000 INFO @ Sat, 03 Jun 2017 04:09:38: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:38: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:38: #1 total tags in treatment: 24339834 INFO @ Sat, 03 Jun 2017 04:09:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:38: #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 04:09:39: #1 tags after filtering in treatment: 24331719 INFO @ Sat, 03 Jun 2017 04:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:39: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:41: 23000000 INFO @ Sat, 03 Jun 2017 04:09:43: #1 tags after filtering in treatment: 24331719 INFO @ Sat, 03 Jun 2017 04:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:44: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 04:09:44: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:44: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:47: 24000000 INFO @ Sat, 03 Jun 2017 04:09:48: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 04:09:48: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:48: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:50: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 04:09:50: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 04:09:50: #1 total tags in treatment: 24339834 INFO @ Sat, 03 Jun 2017 04:09:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:09:50: #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 04:09:54: #1 tags after filtering in treatment: 24331719 INFO @ Sat, 03 Jun 2017 04:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:09:54: #1 finished! INFO @ Sat, 03 Jun 2017 04:09:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:09:54: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:54: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:54: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:54: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 04:09:54: #2 alternative fragment length(s) may be 2,41,577 bps INFO @ Sat, 03 Jun 2017 04:09:54: #2.2 Generate R script for model : SRX1007135.10_model.r WARNING @ Sat, 03 Jun 2017 04:09:54: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:54: #2 You may need to consider one of the other alternative d(s): 2,41,577 WARNING @ Sat, 03 Jun 2017 04:09:54: #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 04:09:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:09:58: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 04:09:58: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 04:09:58: start model_add_line... INFO @ Sat, 03 Jun 2017 04:09:58: start X-correlation... INFO @ Sat, 03 Jun 2017 04:09:58: end of X-cor INFO @ Sat, 03 Jun 2017 04:09:58: #2 finished! INFO @ Sat, 03 Jun 2017 04:09:58: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 04:09:58: #2 alternative fragment length(s) may be 2,41,577 bps INFO @ Sat, 03 Jun 2017 04:09:58: #2.2 Generate R script for model : SRX1007135.20_model.r WARNING @ Sat, 03 Jun 2017 04:09:58: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:09:58: #2 You may need to consider one of the other alternative d(s): 2,41,577 WARNING @ Sat, 03 Jun 2017 04:09:58: #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 04:09:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:10:08: start X-correlation... INFO @ Sat, 03 Jun 2017 04:10:08: end of X-cor INFO @ Sat, 03 Jun 2017 04:10:08: #2 finished! INFO @ Sat, 03 Jun 2017 04:10:08: #2 predicted fragment length is 41 bps INFO @ Sat, 03 Jun 2017 04:10:08: #2 alternative fragment length(s) may be 2,41,577 bps INFO @ Sat, 03 Jun 2017 04:10:08: #2.2 Generate R script for model : SRX1007135.05_model.r WARNING @ Sat, 03 Jun 2017 04:10:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:10:08: #2 You may need to consider one of the other alternative d(s): 2,41,577 WARNING @ Sat, 03 Jun 2017 04:10:08: #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 04:10:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:11:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:11:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:11:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:12:53: #4 Write output xls file... SRX1007135.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:12:53: #4 Write peak in narrowPeak format file... SRX1007135.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:12:53: #4 Write summits bed file... SRX1007135.20_summits.bed INFO @ Sat, 03 Jun 2017 04:12:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1818 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:07: #4 Write output xls file... SRX1007135.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:07: #4 Write peak in narrowPeak format file... SRX1007135.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:07: #4 Write summits bed file... SRX1007135.10_summits.bed INFO @ Sat, 03 Jun 2017 04:13:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6084 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:13:14: #4 Write output xls file... SRX1007135.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:13:14: #4 Write peak in narrowPeak format file... SRX1007135.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:13:14: #4 Write summits bed file... SRX1007135.05_summits.bed INFO @ Sat, 03 Jun 2017 04:13:14: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (12300 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。