Job ID = 9028741 sra ファイルのダウンロード中... Completed: 902852K bytes transferred in 10 seconds (679299K 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 --:--:-- 0 101 5455 0 5455 0 0 751 0 --:--:-- 0:00:07 --:--:-- 8240 100 28797 0 28797 0 0 3486 0 --:--:-- 0:00:08 --:--:-- 17368 100 73685 0 73685 0 0 7962 0 --:--:-- 0:00:09 --:--:-- 27774 100 85209 0 85209 0 0 9045 0 --:--:-- 0:00:09 --:--:-- 30226 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 34467748 spots for /home/okishinya/chipatlas/results/ce10/SRX707298/SRR1582081.sra Written 34467748 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: 00:11:09 34467748 reads; of these: 34467748 (100.00%) were unpaired; of these: 1561735 (4.53%) aligned 0 times 27723897 (80.43%) aligned exactly 1 time 5182116 (15.03%) aligned >1 times 95.47% overall alignment rate Time searching: 00:11:09 Overall time: 00:11:09 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 16 files... [bam_rmdupse_core] 7568625 / 32906013 = 0.2300 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 11:56:59: # Command line: callpeak -t SRX707298.bam -f BAM -g ce -n SRX707298.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX707298.20 # format = BAM # ChIP-seq file = ['SRX707298.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 11:56:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:56:59: # Command line: callpeak -t SRX707298.bam -f BAM -g ce -n SRX707298.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX707298.10 # format = BAM # ChIP-seq file = ['SRX707298.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 11:56:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:56:59: # Command line: callpeak -t SRX707298.bam -f BAM -g ce -n SRX707298.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX707298.05 # format = BAM # ChIP-seq file = ['SRX707298.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 11:56:59: #1 read tag files... INFO @ Sat, 03 Jun 2017 11:56:59: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 11:57:05: 1000000 INFO @ Sat, 03 Jun 2017 11:57:05: 1000000 INFO @ Sat, 03 Jun 2017 11:57:06: 1000000 INFO @ Sat, 03 Jun 2017 11:57:11: 2000000 INFO @ Sat, 03 Jun 2017 11:57:11: 2000000 INFO @ Sat, 03 Jun 2017 11:57:13: 2000000 INFO @ Sat, 03 Jun 2017 11:57:18: 3000000 INFO @ Sat, 03 Jun 2017 11:57:18: 3000000 INFO @ Sat, 03 Jun 2017 11:57:21: 3000000 INFO @ Sat, 03 Jun 2017 11:57:25: 4000000 INFO @ Sat, 03 Jun 2017 11:57:25: 4000000 INFO @ Sat, 03 Jun 2017 11:57:29: 4000000 INFO @ Sat, 03 Jun 2017 11:57:31: 5000000 INFO @ Sat, 03 Jun 2017 11:57:31: 5000000 INFO @ Sat, 03 Jun 2017 11:57:36: 5000000 INFO @ Sat, 03 Jun 2017 11:57:38: 6000000 INFO @ Sat, 03 Jun 2017 11:57:38: 6000000 INFO @ Sat, 03 Jun 2017 11:57:44: 6000000 INFO @ Sat, 03 Jun 2017 11:57:44: 7000000 INFO @ Sat, 03 Jun 2017 11:57:45: 7000000 INFO @ Sat, 03 Jun 2017 11:57:51: 8000000 INFO @ Sat, 03 Jun 2017 11:57:51: 8000000 INFO @ Sat, 03 Jun 2017 11:57:52: 7000000 INFO @ Sat, 03 Jun 2017 11:57:58: 9000000 INFO @ Sat, 03 Jun 2017 11:57:58: 9000000 INFO @ Sat, 03 Jun 2017 11:57:59: 8000000 INFO @ Sat, 03 Jun 2017 11:58:04: 10000000 INFO @ Sat, 03 Jun 2017 11:58:05: 10000000 INFO @ Sat, 03 Jun 2017 11:58:07: 9000000 INFO @ Sat, 03 Jun 2017 11:58:11: 11000000 INFO @ Sat, 03 Jun 2017 11:58:12: 11000000 INFO @ Sat, 03 Jun 2017 11:58:15: 10000000 INFO @ Sat, 03 Jun 2017 11:58:18: 12000000 INFO @ Sat, 03 Jun 2017 11:58:19: 12000000 INFO @ Sat, 03 Jun 2017 11:58:23: 11000000 INFO @ Sat, 03 Jun 2017 11:58:25: 13000000 INFO @ Sat, 03 Jun 2017 11:58:26: 13000000 INFO @ Sat, 03 Jun 2017 11:58:31: 12000000 INFO @ Sat, 03 Jun 2017 11:58:32: 14000000 INFO @ Sat, 03 Jun 2017 11:58:33: 14000000 INFO @ Sat, 03 Jun 2017 11:58:39: 15000000 INFO @ Sat, 03 Jun 2017 11:58:39: 13000000 INFO @ Sat, 03 Jun 2017 11:58:40: 15000000 INFO @ Sat, 03 Jun 2017 11:58:46: 16000000 INFO @ Sat, 03 Jun 2017 11:58:47: 14000000 INFO @ Sat, 03 Jun 2017 11:58:47: 16000000 INFO @ Sat, 03 Jun 2017 11:58:53: 17000000 INFO @ Sat, 03 Jun 2017 11:58:54: 17000000 INFO @ Sat, 03 Jun 2017 11:58:55: 15000000 INFO @ Sat, 03 Jun 2017 11:59:00: 18000000 INFO @ Sat, 03 Jun 2017 11:59:02: 18000000 INFO @ Sat, 03 Jun 2017 11:59:04: 16000000 INFO @ Sat, 03 Jun 2017 11:59:07: 19000000 INFO @ Sat, 03 Jun 2017 11:59:09: 19000000 INFO @ Sat, 03 Jun 2017 11:59:12: 17000000 INFO @ Sat, 03 Jun 2017 11:59:14: 20000000 INFO @ Sat, 03 Jun 2017 11:59:16: 20000000 INFO @ Sat, 03 Jun 2017 11:59:20: 18000000 INFO @ Sat, 03 Jun 2017 11:59:21: 21000000 INFO @ Sat, 03 Jun 2017 11:59:23: 21000000 INFO @ Sat, 03 Jun 2017 11:59:28: 19000000 INFO @ Sat, 03 Jun 2017 11:59:28: 22000000 INFO @ Sat, 03 Jun 2017 11:59:30: 22000000 INFO @ Sat, 03 Jun 2017 11:59:35: 23000000 INFO @ Sat, 03 Jun 2017 11:59:36: 20000000 INFO @ Sat, 03 Jun 2017 11:59:37: 23000000 INFO @ Sat, 03 Jun 2017 11:59:42: 24000000 INFO @ Sat, 03 Jun 2017 11:59:44: 21000000 INFO @ Sat, 03 Jun 2017 11:59:44: 24000000 INFO @ Sat, 03 Jun 2017 11:59:50: 25000000 INFO @ Sat, 03 Jun 2017 11:59:52: 25000000 INFO @ Sat, 03 Jun 2017 11:59:52: 22000000 INFO @ Sat, 03 Jun 2017 11:59:52: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:59:52: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:59:52: #1 total tags in treatment: 25337388 INFO @ Sat, 03 Jun 2017 11:59:52: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:59:52: #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 11:59:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 11:59:54: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 11:59:54: #1 total tags in treatment: 25337388 INFO @ Sat, 03 Jun 2017 11:59:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 11:59:54: #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 11:59:57: #1 tags after filtering in treatment: 25045547 INFO @ Sat, 03 Jun 2017 11:59:57: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 11:59:57: #1 finished! INFO @ Sat, 03 Jun 2017 11:59:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 11:59:58: 23000000 INFO @ Sat, 03 Jun 2017 11:59:59: #1 tags after filtering in treatment: 25045547 INFO @ Sat, 03 Jun 2017 11:59:59: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 11:59:59: #1 finished! INFO @ Sat, 03 Jun 2017 11:59:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:00:01: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 12:00:01: 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 12:00:01: start model_add_line... INFO @ Sat, 03 Jun 2017 12:00:03: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 12:00:03: 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 12:00:03: start model_add_line... INFO @ Sat, 03 Jun 2017 12:00:04: 24000000 INFO @ Sat, 03 Jun 2017 12:00:06: start X-correlation... INFO @ Sat, 03 Jun 2017 12:00:06: end of X-cor INFO @ Sat, 03 Jun 2017 12:00:06: #2 finished! INFO @ Sat, 03 Jun 2017 12:00:06: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 12:00:06: #2 alternative fragment length(s) may be 1,61,93,121,141,162,181 bps INFO @ Sat, 03 Jun 2017 12:00:06: #2.2 Generate R script for model : SRX707298.20_model.r INFO @ Sat, 03 Jun 2017 12:00:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:00:08: start X-correlation... INFO @ Sat, 03 Jun 2017 12:00:08: end of X-cor INFO @ Sat, 03 Jun 2017 12:00:08: #2 finished! INFO @ Sat, 03 Jun 2017 12:00:08: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 12:00:08: #2 alternative fragment length(s) may be 1,61,93,121,141,162,181 bps INFO @ Sat, 03 Jun 2017 12:00:08: #2.2 Generate R script for model : SRX707298.10_model.r INFO @ Sat, 03 Jun 2017 12:00:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:00:10: 25000000 INFO @ Sat, 03 Jun 2017 12:00:12: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:00:12: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:00:12: #1 total tags in treatment: 25337388 INFO @ Sat, 03 Jun 2017 12:00:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:00:12: #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 12:00:17: #1 tags after filtering in treatment: 25045547 INFO @ Sat, 03 Jun 2017 12:00:17: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 03 Jun 2017 12:00:17: #1 finished! INFO @ Sat, 03 Jun 2017 12:00:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:00:21: #2 number of paired peaks: 148 WARNING @ Sat, 03 Jun 2017 12:00:21: 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 12:00:21: start model_add_line... INFO @ Sat, 03 Jun 2017 12:00:25: start X-correlation... INFO @ Sat, 03 Jun 2017 12:00:25: end of X-cor INFO @ Sat, 03 Jun 2017 12:00:25: #2 finished! INFO @ Sat, 03 Jun 2017 12:00:25: #2 predicted fragment length is 121 bps INFO @ Sat, 03 Jun 2017 12:00:25: #2 alternative fragment length(s) may be 1,61,93,121,141,162,181 bps INFO @ Sat, 03 Jun 2017 12:00:25: #2.2 Generate R script for model : SRX707298.05_model.r INFO @ Sat, 03 Jun 2017 12:00:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:02:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:02:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:02:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:03:23: #4 Write output xls file... SRX707298.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:03:23: #4 Write peak in narrowPeak format file... SRX707298.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:03:23: #4 Write summits bed file... SRX707298.10_summits.bed INFO @ Sat, 03 Jun 2017 12:03:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:03:26: #4 Write output xls file... SRX707298.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:03:26: #4 Write peak in narrowPeak format file... SRX707298.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:03:26: #4 Write summits bed file... SRX707298.20_summits.bed INFO @ Sat, 03 Jun 2017 12:03:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:03:45: #4 Write output xls file... SRX707298.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:03:45: #4 Write peak in narrowPeak format file... SRX707298.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:03:45: #4 Write summits bed file... SRX707298.05_summits.bed INFO @ Sat, 03 Jun 2017 12:03:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1973 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。