Job ID = 9025553 sra ファイルのダウンロード中... Completed: 1338615K bytes transferred in 14 seconds (758272K 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 --:--:-- 0:00:23 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:23 --:--:-- 0 100 7663 0 7663 0 0 311 0 --:--:-- 0:00:24 --:--:-- 6265 100 22318 0 22318 0 0 873 0 --:--:-- 0:00:25 --:--:-- 10053 100 70571 0 70571 0 0 2670 0 --:--:-- 0:00:26 --:--:-- 22838 100 70571 0 70571 0 0 2670 0 --:--:-- 0:00:26 --:--:-- 22831 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 57625311 spots for /home/okishinya/chipatlas/results/ce10/SRX1674100/SRR3320146.sra Written 57625311 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: 00:17:12 57625311 reads; of these: 57625311 (100.00%) were unpaired; of these: 2028607 (3.52%) aligned 0 times 49468916 (85.85%) aligned exactly 1 time 6127788 (10.63%) aligned >1 times 96.48% overall alignment rate Time searching: 00:17:12 Overall time: 00:17:12 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 24 files... [bam_rmdupse_core] 24645417 / 55596704 = 0.4433 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 04:50:29: # Command line: callpeak -t SRX1674100.bam -f BAM -g ce -n SRX1674100.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674100.20 # format = BAM # ChIP-seq file = ['SRX1674100.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 04:50:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:29: # Command line: callpeak -t SRX1674100.bam -f BAM -g ce -n SRX1674100.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674100.10 # format = BAM # ChIP-seq file = ['SRX1674100.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 04:50:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:29: # Command line: callpeak -t SRX1674100.bam -f BAM -g ce -n SRX1674100.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674100.05 # format = BAM # ChIP-seq file = ['SRX1674100.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 04:50:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:50:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:50:36: 1000000 INFO @ Sat, 03 Jun 2017 04:50:36: 1000000 INFO @ Sat, 03 Jun 2017 04:50:36: 1000000 INFO @ Sat, 03 Jun 2017 04:50:42: 2000000 INFO @ Sat, 03 Jun 2017 04:50:44: 2000000 INFO @ Sat, 03 Jun 2017 04:50:44: 2000000 INFO @ Sat, 03 Jun 2017 04:50:48: 3000000 INFO @ Sat, 03 Jun 2017 04:50:51: 3000000 INFO @ Sat, 03 Jun 2017 04:50:51: 3000000 INFO @ Sat, 03 Jun 2017 04:50:55: 4000000 INFO @ Sat, 03 Jun 2017 04:50:59: 4000000 INFO @ Sat, 03 Jun 2017 04:50:59: 4000000 INFO @ Sat, 03 Jun 2017 04:51:01: 5000000 INFO @ Sat, 03 Jun 2017 04:51:06: 5000000 INFO @ Sat, 03 Jun 2017 04:51:06: 5000000 INFO @ Sat, 03 Jun 2017 04:51:07: 6000000 INFO @ Sat, 03 Jun 2017 04:51:14: 7000000 INFO @ Sat, 03 Jun 2017 04:51:14: 6000000 INFO @ Sat, 03 Jun 2017 04:51:14: 6000000 INFO @ Sat, 03 Jun 2017 04:51:20: 8000000 INFO @ Sat, 03 Jun 2017 04:51:22: 7000000 INFO @ Sat, 03 Jun 2017 04:51:22: 7000000 INFO @ Sat, 03 Jun 2017 04:51:26: 9000000 INFO @ Sat, 03 Jun 2017 04:51:30: 8000000 INFO @ Sat, 03 Jun 2017 04:51:30: 8000000 INFO @ Sat, 03 Jun 2017 04:51:31: 10000000 INFO @ Sat, 03 Jun 2017 04:51:37: 11000000 INFO @ Sat, 03 Jun 2017 04:51:38: 9000000 INFO @ Sat, 03 Jun 2017 04:51:38: 9000000 INFO @ Sat, 03 Jun 2017 04:51:43: 12000000 INFO @ Sat, 03 Jun 2017 04:51:46: 10000000 INFO @ Sat, 03 Jun 2017 04:51:46: 10000000 INFO @ Sat, 03 Jun 2017 04:51:48: 13000000 INFO @ Sat, 03 Jun 2017 04:51:51: 11000000 INFO @ Sat, 03 Jun 2017 04:51:51: 11000000 INFO @ Sat, 03 Jun 2017 04:51:54: 14000000 INFO @ Sat, 03 Jun 2017 04:51:57: 12000000 INFO @ Sat, 03 Jun 2017 04:51:57: 12000000 INFO @ Sat, 03 Jun 2017 04:51:59: 15000000 INFO @ Sat, 03 Jun 2017 04:52:02: 13000000 INFO @ Sat, 03 Jun 2017 04:52:03: 13000000 INFO @ Sat, 03 Jun 2017 04:52:05: 16000000 INFO @ Sat, 03 Jun 2017 04:52:08: 14000000 INFO @ Sat, 03 Jun 2017 04:52:09: 14000000 INFO @ Sat, 03 Jun 2017 04:52:13: 17000000 INFO @ Sat, 03 Jun 2017 04:52:16: 15000000 INFO @ Sat, 03 Jun 2017 04:52:17: 15000000 INFO @ Sat, 03 Jun 2017 04:52:21: 18000000 INFO @ Sat, 03 Jun 2017 04:52:23: 16000000 INFO @ Sat, 03 Jun 2017 04:52:24: 16000000 INFO @ Sat, 03 Jun 2017 04:52:30: 19000000 INFO @ Sat, 03 Jun 2017 04:52:30: 17000000 INFO @ Sat, 03 Jun 2017 04:52:32: 17000000 INFO @ Sat, 03 Jun 2017 04:52:38: 18000000 INFO @ Sat, 03 Jun 2017 04:52:38: 20000000 INFO @ Sat, 03 Jun 2017 04:52:39: 18000000 INFO @ Sat, 03 Jun 2017 04:52:45: 19000000 INFO @ Sat, 03 Jun 2017 04:52:46: 21000000 INFO @ Sat, 03 Jun 2017 04:52:47: 19000000 INFO @ Sat, 03 Jun 2017 04:52:52: 20000000 INFO @ Sat, 03 Jun 2017 04:52:54: 20000000 INFO @ Sat, 03 Jun 2017 04:52:55: 22000000 INFO @ Sat, 03 Jun 2017 04:52:59: 21000000 INFO @ Sat, 03 Jun 2017 04:53:02: 21000000 INFO @ Sat, 03 Jun 2017 04:53:03: 23000000 INFO @ Sat, 03 Jun 2017 04:53:07: 22000000 INFO @ Sat, 03 Jun 2017 04:53:09: 22000000 INFO @ Sat, 03 Jun 2017 04:53:11: 24000000 INFO @ Sat, 03 Jun 2017 04:53:14: 23000000 INFO @ Sat, 03 Jun 2017 04:53:17: 23000000 INFO @ Sat, 03 Jun 2017 04:53:19: 25000000 INFO @ Sat, 03 Jun 2017 04:53:21: 24000000 INFO @ Sat, 03 Jun 2017 04:53:24: 24000000 INFO @ Sat, 03 Jun 2017 04:53:27: 26000000 INFO @ Sat, 03 Jun 2017 04:53:28: 25000000 INFO @ Sat, 03 Jun 2017 04:53:32: 25000000 INFO @ Sat, 03 Jun 2017 04:53:36: 26000000 INFO @ Sat, 03 Jun 2017 04:53:36: 27000000 INFO @ Sat, 03 Jun 2017 04:53:39: 26000000 INFO @ Sat, 03 Jun 2017 04:53:43: 27000000 INFO @ Sat, 03 Jun 2017 04:53:44: 28000000 INFO @ Sat, 03 Jun 2017 04:53:47: 27000000 INFO @ Sat, 03 Jun 2017 04:53:50: 28000000 INFO @ Sat, 03 Jun 2017 04:53:52: 29000000 INFO @ Sat, 03 Jun 2017 04:53:54: 28000000 INFO @ Sat, 03 Jun 2017 04:53:57: 29000000 INFO @ Sat, 03 Jun 2017 04:54:01: 30000000 INFO @ Sat, 03 Jun 2017 04:54:02: 29000000 INFO @ Sat, 03 Jun 2017 04:54:05: 30000000 INFO @ Sat, 03 Jun 2017 04:54:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:54:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:54:09: #1 total tags in treatment: 30951287 INFO @ Sat, 03 Jun 2017 04:54:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:54:09: #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 04:54:09: 30000000 INFO @ Sat, 03 Jun 2017 04:54:12: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:54:12: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:54:12: #1 total tags in treatment: 30951287 INFO @ Sat, 03 Jun 2017 04:54:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:54:12: #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 04:54:15: #1 tags after filtering in treatment: 30910272 INFO @ Sat, 03 Jun 2017 04:54:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:54:15: #1 finished! INFO @ Sat, 03 Jun 2017 04:54:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:54:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:54:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:54:16: #1 total tags in treatment: 30951287 INFO @ Sat, 03 Jun 2017 04:54:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:54:16: #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 04:54:18: #1 tags after filtering in treatment: 30910272 INFO @ Sat, 03 Jun 2017 04:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:54:18: #1 finished! INFO @ Sat, 03 Jun 2017 04:54:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:54:20: #2 number of paired peaks: 711 WARNING @ Sat, 03 Jun 2017 04:54:20: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 03 Jun 2017 04:54:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:54:21: #1 tags after filtering in treatment: 30910272 INFO @ Sat, 03 Jun 2017 04:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:54:21: #1 finished! INFO @ Sat, 03 Jun 2017 04:54:21: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:54:23: #2 number of paired peaks: 711 WARNING @ Sat, 03 Jun 2017 04:54:23: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 03 Jun 2017 04:54:23: start model_add_line... INFO @ Sat, 03 Jun 2017 04:54:27: #2 number of paired peaks: 711 WARNING @ Sat, 03 Jun 2017 04:54:27: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Sat, 03 Jun 2017 04:54:27: start model_add_line... INFO @ Sat, 03 Jun 2017 04:54:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:54:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:54:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:54:37: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 04:54:37: #2 alternative fragment length(s) may be 2,141,160,193,213 bps INFO @ Sat, 03 Jun 2017 04:54:37: #2.2 Generate R script for model : SRX1674100.20_model.r INFO @ Sat, 03 Jun 2017 04:54:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:54:41: start X-correlation... INFO @ Sat, 03 Jun 2017 04:54:41: end of X-cor INFO @ Sat, 03 Jun 2017 04:54:41: #2 finished! INFO @ Sat, 03 Jun 2017 04:54:41: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 04:54:41: #2 alternative fragment length(s) may be 2,141,160,193,213 bps INFO @ Sat, 03 Jun 2017 04:54:41: #2.2 Generate R script for model : SRX1674100.10_model.r INFO @ Sat, 03 Jun 2017 04:54:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:54:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:54:44: start X-correlation... INFO @ Sat, 03 Jun 2017 04:54:44: end of X-cor INFO @ Sat, 03 Jun 2017 04:54:44: #2 finished! INFO @ Sat, 03 Jun 2017 04:54:44: #2 predicted fragment length is 141 bps INFO @ Sat, 03 Jun 2017 04:54:44: #2 alternative fragment length(s) may be 2,141,160,193,213 bps INFO @ Sat, 03 Jun 2017 04:54:44: #2.2 Generate R script for model : SRX1674100.05_model.r INFO @ Sat, 03 Jun 2017 04:54:44: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:56:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:57:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:57:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:58:25: #4 Write output xls file... SRX1674100.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:58:25: #4 Write peak in narrowPeak format file... SRX1674100.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:58:25: #4 Write summits bed file... SRX1674100.20_summits.bed INFO @ Sat, 03 Jun 2017 04:58:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2921 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:58:50: #4 Write output xls file... SRX1674100.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:58:50: #4 Write peak in narrowPeak format file... SRX1674100.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:58:50: #4 Write summits bed file... SRX1674100.10_summits.bed INFO @ Sat, 03 Jun 2017 04:58:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6847 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:59:10: #4 Write output xls file... SRX1674100.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:59:10: #4 Write peak in narrowPeak format file... SRX1674100.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:59:10: #4 Write summits bed file... SRX1674100.05_summits.bed INFO @ Sat, 03 Jun 2017 04:59:10: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (11876 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。