Job ID = 9028827 sra ファイルのダウンロード中... Completed: 727456K bytes transferred in 7 seconds (773566K 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 14324 0 14324 0 0 1913 0 --:--:-- 0:00:07 --:--:-- 13287 100 38318 0 38318 0 0 4517 0 --:--:-- 0:00:08 --:--:-- 18475 100 70274 0 70274 0 0 7682 0 --:--:-- 0:00:09 --:--:-- 25666 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 20608259 spots for /home/okishinya/chipatlas/results/ce10/SRX982065/SRR1956541.sra Written 20608259 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: 00:05:14 20608259 reads; of these: 20608259 (100.00%) were unpaired; of these: 1441998 (7.00%) aligned 0 times 16363675 (79.40%) aligned exactly 1 time 2802586 (13.60%) aligned >1 times 93.00% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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 8 files... [bam_rmdupse_core] 2799622 / 19166261 = 0.1461 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 12:05:15: # Command line: callpeak -t SRX982065.bam -f BAM -g ce -n SRX982065.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982065.10 # format = BAM # ChIP-seq file = ['SRX982065.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 12:05:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:15: # Command line: callpeak -t SRX982065.bam -f BAM -g ce -n SRX982065.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982065.20 # format = BAM # ChIP-seq file = ['SRX982065.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 12:05:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:15: # Command line: callpeak -t SRX982065.bam -f BAM -g ce -n SRX982065.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982065.05 # format = BAM # ChIP-seq file = ['SRX982065.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 12:05:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:05:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:05:21: 1000000 INFO @ Sat, 03 Jun 2017 12:05:21: 1000000 INFO @ Sat, 03 Jun 2017 12:05:22: 1000000 INFO @ Sat, 03 Jun 2017 12:05:27: 2000000 INFO @ Sat, 03 Jun 2017 12:05:27: 2000000 INFO @ Sat, 03 Jun 2017 12:05:28: 2000000 INFO @ Sat, 03 Jun 2017 12:05:33: 3000000 INFO @ Sat, 03 Jun 2017 12:05:33: 3000000 INFO @ Sat, 03 Jun 2017 12:05:34: 3000000 INFO @ Sat, 03 Jun 2017 12:05:39: 4000000 INFO @ Sat, 03 Jun 2017 12:05:39: 4000000 INFO @ Sat, 03 Jun 2017 12:05:40: 4000000 INFO @ Sat, 03 Jun 2017 12:05:45: 5000000 INFO @ Sat, 03 Jun 2017 12:05:45: 5000000 INFO @ Sat, 03 Jun 2017 12:05:46: 5000000 INFO @ Sat, 03 Jun 2017 12:05:51: 6000000 INFO @ Sat, 03 Jun 2017 12:05:51: 6000000 INFO @ Sat, 03 Jun 2017 12:05:52: 6000000 INFO @ Sat, 03 Jun 2017 12:05:57: 7000000 INFO @ Sat, 03 Jun 2017 12:05:57: 7000000 INFO @ Sat, 03 Jun 2017 12:05:58: 7000000 INFO @ Sat, 03 Jun 2017 12:06:03: 8000000 INFO @ Sat, 03 Jun 2017 12:06:03: 8000000 INFO @ Sat, 03 Jun 2017 12:06:04: 8000000 INFO @ Sat, 03 Jun 2017 12:06:09: 9000000 INFO @ Sat, 03 Jun 2017 12:06:10: 9000000 INFO @ Sat, 03 Jun 2017 12:06:11: 9000000 INFO @ Sat, 03 Jun 2017 12:06:14: 10000000 INFO @ Sat, 03 Jun 2017 12:06:17: 10000000 INFO @ Sat, 03 Jun 2017 12:06:18: 10000000 INFO @ Sat, 03 Jun 2017 12:06:20: 11000000 INFO @ Sat, 03 Jun 2017 12:06:25: 11000000 INFO @ Sat, 03 Jun 2017 12:06:25: 11000000 INFO @ Sat, 03 Jun 2017 12:06:26: 12000000 INFO @ Sat, 03 Jun 2017 12:06:32: 12000000 INFO @ Sat, 03 Jun 2017 12:06:32: 13000000 INFO @ Sat, 03 Jun 2017 12:06:32: 12000000 INFO @ Sat, 03 Jun 2017 12:06:37: 14000000 INFO @ Sat, 03 Jun 2017 12:06:39: 13000000 INFO @ Sat, 03 Jun 2017 12:06:39: 13000000 INFO @ Sat, 03 Jun 2017 12:06:43: 15000000 INFO @ Sat, 03 Jun 2017 12:06:45: 14000000 INFO @ Sat, 03 Jun 2017 12:06:45: 14000000 INFO @ Sat, 03 Jun 2017 12:06:49: 16000000 INFO @ Sat, 03 Jun 2017 12:06:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:06:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:06:51: #1 total tags in treatment: 16366639 INFO @ Sat, 03 Jun 2017 12:06:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:06:51: #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 12:06:52: 15000000 INFO @ Sat, 03 Jun 2017 12:06:52: 15000000 INFO @ Sat, 03 Jun 2017 12:06:54: #1 tags after filtering in treatment: 16364648 INFO @ Sat, 03 Jun 2017 12:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:06:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:06:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:06:57: #2 number of paired peaks: 515 WARNING @ Sat, 03 Jun 2017 12:06:57: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Jun 2017 12:06:57: start model_add_line... INFO @ Sat, 03 Jun 2017 12:06:58: 16000000 INFO @ Sat, 03 Jun 2017 12:06:58: 16000000 INFO @ Sat, 03 Jun 2017 12:07:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:07:01: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:07:01: #1 total tags in treatment: 16366639 INFO @ Sat, 03 Jun 2017 12:07:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:07:01: #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 12:07:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:07:01: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:07:01: #1 total tags in treatment: 16366639 INFO @ Sat, 03 Jun 2017 12:07:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:07:01: #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 12:07:04: #1 tags after filtering in treatment: 16364648 INFO @ Sat, 03 Jun 2017 12:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:07:04: #1 finished! INFO @ Sat, 03 Jun 2017 12:07:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:07:05: #1 tags after filtering in treatment: 16364648 INFO @ Sat, 03 Jun 2017 12:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:07:05: #1 finished! INFO @ Sat, 03 Jun 2017 12:07:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:07:06: start X-correlation... INFO @ Sat, 03 Jun 2017 12:07:06: end of X-cor INFO @ Sat, 03 Jun 2017 12:07:06: #2 finished! INFO @ Sat, 03 Jun 2017 12:07:06: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 12:07:06: #2 alternative fragment length(s) may be 4,132 bps INFO @ Sat, 03 Jun 2017 12:07:06: #2.2 Generate R script for model : SRX982065.20_model.r INFO @ Sat, 03 Jun 2017 12:07:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:07:07: #2 number of paired peaks: 515 WARNING @ Sat, 03 Jun 2017 12:07:07: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Jun 2017 12:07:07: start model_add_line... INFO @ Sat, 03 Jun 2017 12:07:08: #2 number of paired peaks: 515 WARNING @ Sat, 03 Jun 2017 12:07:08: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Jun 2017 12:07:08: start model_add_line... INFO @ Sat, 03 Jun 2017 12:07:15: start X-correlation... INFO @ Sat, 03 Jun 2017 12:07:15: end of X-cor INFO @ Sat, 03 Jun 2017 12:07:15: #2 finished! INFO @ Sat, 03 Jun 2017 12:07:15: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 12:07:15: #2 alternative fragment length(s) may be 4,132 bps INFO @ Sat, 03 Jun 2017 12:07:15: #2.2 Generate R script for model : SRX982065.05_model.r INFO @ Sat, 03 Jun 2017 12:07:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:07:16: start X-correlation... INFO @ Sat, 03 Jun 2017 12:07:16: end of X-cor INFO @ Sat, 03 Jun 2017 12:07:16: #2 finished! INFO @ Sat, 03 Jun 2017 12:07:16: #2 predicted fragment length is 132 bps INFO @ Sat, 03 Jun 2017 12:07:16: #2 alternative fragment length(s) may be 4,132 bps INFO @ Sat, 03 Jun 2017 12:07:16: #2.2 Generate R script for model : SRX982065.10_model.r INFO @ Sat, 03 Jun 2017 12:07:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:08:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:08:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write output xls file... SRX982065.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write peak in narrowPeak format file... SRX982065.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:23: #4 Write summits bed file... SRX982065.20_summits.bed INFO @ Sat, 03 Jun 2017 12:09:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:34: #4 Write output xls file... SRX982065.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:34: #4 Write peak in narrowPeak format file... SRX982065.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:34: #4 Write summits bed file... SRX982065.05_summits.bed INFO @ Sat, 03 Jun 2017 12:09:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1765 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:09:36: #4 Write output xls file... SRX982065.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:09:36: #4 Write peak in narrowPeak format file... SRX982065.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:09:36: #4 Write summits bed file... SRX982065.10_summits.bed INFO @ Sat, 03 Jun 2017 12:09:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1089 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。