Job ID = 9025543 sra ファイルのダウンロード中... Completed: 1128702K bytes transferred in 11 seconds (828918K 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 --:--:-- 0 100 7663 0 7663 0 0 999 0 --:--:-- 0:00:07 --:--:-- 6101 100 30318 0 30318 0 0 3500 0 --:--:-- 0:00:08 --:--:-- 13456 100 54862 0 54862 0 0 5780 0 --:--:-- 0:00:09 --:--:-- 17783 100 81258 0 81258 0 0 8270 0 --:--:-- 0:00:09 --:--:-- 23773 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 50879695 spots for /home/okishinya/chipatlas/results/ce10/SRX1674090/SRR3320136.sra Written 50879695 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: 00:13:16 50879695 reads; of these: 50879695 (100.00%) were unpaired; of these: 1507210 (2.96%) aligned 0 times 43370558 (85.24%) aligned exactly 1 time 6001927 (11.80%) aligned >1 times 97.04% overall alignment rate Time searching: 00:13:16 Overall time: 00:13:16 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] 21981863 / 49372485 = 0.4452 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 04:42:38: # Command line: callpeak -t SRX1674090.bam -f BAM -g ce -n SRX1674090.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674090.20 # format = BAM # ChIP-seq file = ['SRX1674090.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 04:42:38: # Command line: callpeak -t SRX1674090.bam -f BAM -g ce -n SRX1674090.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674090.10 # format = BAM # ChIP-seq file = ['SRX1674090.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 04:42:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:38: # Command line: callpeak -t SRX1674090.bam -f BAM -g ce -n SRX1674090.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674090.05 # format = BAM # ChIP-seq file = ['SRX1674090.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 04:42:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:42:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:42:45: 1000000 INFO @ Sat, 03 Jun 2017 04:42:45: 1000000 INFO @ Sat, 03 Jun 2017 04:42:45: 1000000 INFO @ Sat, 03 Jun 2017 04:42:50: 2000000 INFO @ Sat, 03 Jun 2017 04:42:52: 2000000 INFO @ Sat, 03 Jun 2017 04:42:52: 2000000 INFO @ Sat, 03 Jun 2017 04:42:56: 3000000 INFO @ Sat, 03 Jun 2017 04:42:59: 3000000 INFO @ Sat, 03 Jun 2017 04:42:59: 3000000 INFO @ Sat, 03 Jun 2017 04:43:02: 4000000 INFO @ Sat, 03 Jun 2017 04:43:06: 4000000 INFO @ Sat, 03 Jun 2017 04:43:06: 4000000 INFO @ Sat, 03 Jun 2017 04:43:08: 5000000 INFO @ Sat, 03 Jun 2017 04:43:14: 6000000 INFO @ Sat, 03 Jun 2017 04:43:14: 5000000 INFO @ Sat, 03 Jun 2017 04:43:14: 5000000 INFO @ Sat, 03 Jun 2017 04:43:19: 7000000 INFO @ Sat, 03 Jun 2017 04:43:21: 6000000 INFO @ Sat, 03 Jun 2017 04:43:21: 6000000 INFO @ Sat, 03 Jun 2017 04:43:25: 8000000 INFO @ Sat, 03 Jun 2017 04:43:28: 7000000 INFO @ Sat, 03 Jun 2017 04:43:28: 7000000 INFO @ Sat, 03 Jun 2017 04:43:32: 9000000 INFO @ Sat, 03 Jun 2017 04:43:35: 8000000 INFO @ Sat, 03 Jun 2017 04:43:35: 8000000 INFO @ Sat, 03 Jun 2017 04:43:41: 10000000 INFO @ Sat, 03 Jun 2017 04:43:43: 9000000 INFO @ Sat, 03 Jun 2017 04:43:43: 9000000 INFO @ Sat, 03 Jun 2017 04:43:49: 11000000 INFO @ Sat, 03 Jun 2017 04:43:51: 10000000 INFO @ Sat, 03 Jun 2017 04:43:52: 10000000 INFO @ Sat, 03 Jun 2017 04:43:58: 12000000 INFO @ Sat, 03 Jun 2017 04:44:00: 11000000 INFO @ Sat, 03 Jun 2017 04:44:00: 11000000 INFO @ Sat, 03 Jun 2017 04:44:06: 13000000 INFO @ Sat, 03 Jun 2017 04:44:08: 12000000 INFO @ Sat, 03 Jun 2017 04:44:08: 12000000 INFO @ Sat, 03 Jun 2017 04:44:15: 14000000 INFO @ Sat, 03 Jun 2017 04:44:16: 13000000 INFO @ Sat, 03 Jun 2017 04:44:16: 13000000 INFO @ Sat, 03 Jun 2017 04:44:24: 15000000 INFO @ Sat, 03 Jun 2017 04:44:24: 14000000 INFO @ Sat, 03 Jun 2017 04:44:24: 14000000 INFO @ Sat, 03 Jun 2017 04:44:32: 15000000 INFO @ Sat, 03 Jun 2017 04:44:32: 16000000 INFO @ Sat, 03 Jun 2017 04:44:32: 15000000 INFO @ Sat, 03 Jun 2017 04:44:40: 16000000 INFO @ Sat, 03 Jun 2017 04:44:41: 16000000 INFO @ Sat, 03 Jun 2017 04:44:41: 17000000 INFO @ Sat, 03 Jun 2017 04:44:49: 17000000 INFO @ Sat, 03 Jun 2017 04:44:49: 17000000 INFO @ Sat, 03 Jun 2017 04:44:50: 18000000 INFO @ Sat, 03 Jun 2017 04:44:57: 18000000 INFO @ Sat, 03 Jun 2017 04:44:57: 18000000 INFO @ Sat, 03 Jun 2017 04:44:58: 19000000 INFO @ Sat, 03 Jun 2017 04:45:05: 19000000 INFO @ Sat, 03 Jun 2017 04:45:05: 19000000 INFO @ Sat, 03 Jun 2017 04:45:07: 20000000 INFO @ Sat, 03 Jun 2017 04:45:13: 20000000 INFO @ Sat, 03 Jun 2017 04:45:13: 20000000 INFO @ Sat, 03 Jun 2017 04:45:16: 21000000 INFO @ Sat, 03 Jun 2017 04:45:22: 21000000 INFO @ Sat, 03 Jun 2017 04:45:22: 21000000 INFO @ Sat, 03 Jun 2017 04:45:24: 22000000 INFO @ Sat, 03 Jun 2017 04:45:30: 22000000 INFO @ Sat, 03 Jun 2017 04:45:30: 22000000 INFO @ Sat, 03 Jun 2017 04:45:33: 23000000 INFO @ Sat, 03 Jun 2017 04:45:38: 23000000 INFO @ Sat, 03 Jun 2017 04:45:38: 23000000 INFO @ Sat, 03 Jun 2017 04:45:42: 24000000 INFO @ Sat, 03 Jun 2017 04:45:46: 24000000 INFO @ Sat, 03 Jun 2017 04:45:46: 24000000 INFO @ Sat, 03 Jun 2017 04:45:50: 25000000 INFO @ Sat, 03 Jun 2017 04:45:54: 25000000 INFO @ Sat, 03 Jun 2017 04:45:55: 25000000 INFO @ Sat, 03 Jun 2017 04:45:59: 26000000 INFO @ Sat, 03 Jun 2017 04:46:03: 26000000 INFO @ Sat, 03 Jun 2017 04:46:03: 26000000 INFO @ Sat, 03 Jun 2017 04:46:08: 27000000 INFO @ Sat, 03 Jun 2017 04:46:11: 27000000 INFO @ Sat, 03 Jun 2017 04:46:11: 27000000 INFO @ Sat, 03 Jun 2017 04:46:11: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:46:11: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:46:11: #1 total tags in treatment: 27390622 INFO @ Sat, 03 Jun 2017 04:46:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:11: #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 04:46:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:46:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:46:14: #1 total tags in treatment: 27390622 INFO @ Sat, 03 Jun 2017 04:46:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:14: #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 04:46:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:46:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:46:14: #1 total tags in treatment: 27390622 INFO @ Sat, 03 Jun 2017 04:46:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:46:14: #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 04:46:16: #1 tags after filtering in treatment: 27340180 INFO @ Sat, 03 Jun 2017 04:46:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:16: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:16: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:19: #1 tags after filtering in treatment: 27340180 INFO @ Sat, 03 Jun 2017 04:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:19: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:19: #1 tags after filtering in treatment: 27340180 INFO @ Sat, 03 Jun 2017 04:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:46:19: #1 finished! INFO @ Sat, 03 Jun 2017 04:46:19: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:46:20: #2 number of paired peaks: 588 WARNING @ Sat, 03 Jun 2017 04:46:20: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:24: #2 number of paired peaks: 588 WARNING @ Sat, 03 Jun 2017 04:46:24: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:24: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:24: #2 number of paired peaks: 588 WARNING @ Sat, 03 Jun 2017 04:46:24: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Sat, 03 Jun 2017 04:46:24: start model_add_line... INFO @ Sat, 03 Jun 2017 04:46:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:34: #2 predicted fragment length is 260 bps INFO @ Sat, 03 Jun 2017 04:46:34: #2 alternative fragment length(s) may be 2,200,229,240,260,291,337 bps INFO @ Sat, 03 Jun 2017 04:46:34: #2.2 Generate R script for model : SRX1674090.10_model.r INFO @ Sat, 03 Jun 2017 04:46:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:37: #2 predicted fragment length is 260 bps INFO @ Sat, 03 Jun 2017 04:46:37: #2 alternative fragment length(s) may be 2,200,229,240,260,291,337 bps INFO @ Sat, 03 Jun 2017 04:46:37: #2.2 Generate R script for model : SRX1674090.05_model.r INFO @ Sat, 03 Jun 2017 04:46:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:37: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:37: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:37: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:37: #2 predicted fragment length is 260 bps INFO @ Sat, 03 Jun 2017 04:46:37: #2 alternative fragment length(s) may be 2,200,229,240,260,291,337 bps INFO @ Sat, 03 Jun 2017 04:46:37: #2.2 Generate R script for model : SRX1674090.20_model.r INFO @ Sat, 03 Jun 2017 04:46:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:23: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:50:43: #4 Write output xls file... SRX1674090.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:50:43: #4 Write peak in narrowPeak format file... SRX1674090.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:50:43: #4 Write summits bed file... SRX1674090.20_summits.bed INFO @ Sat, 03 Jun 2017 04:50:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3916 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:51:08: #4 Write output xls file... SRX1674090.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:08: #4 Write peak in narrowPeak format file... SRX1674090.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:09: #4 Write summits bed file... SRX1674090.10_summits.bed INFO @ Sat, 03 Jun 2017 04:51:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7299 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 04:51:30: #4 Write output xls file... SRX1674090.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:51:30: #4 Write peak in narrowPeak format file... SRX1674090.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:51:30: #4 Write summits bed file... SRX1674090.05_summits.bed INFO @ Sat, 03 Jun 2017 04:51:30: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10473 records, 4 fields): 14 millis CompletedMACS2peakCalling