Job ID = 9025622 sra ファイルのダウンロード中... Completed: 296127K bytes transferred in 6 seconds (392791K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:13 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:14 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:15 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:16 --:--:-- 0 100 14323 0 14323 0 0 823 0 --:--:-- 0:00:17 --:--:-- 2998 100 47621 0 47621 0 0 2614 0 --:--:-- 0:00:18 --:--:-- 10341 100 55643 0 55643 0 0 3054 0 --:--:-- 0:00:18 --:--:-- 15434 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 14746480 spots for /home/okishinya/chipatlas/results/ce10/SRX208764/SRR628898.sra Written 14746480 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: 00:03:23 14746480 reads; of these: 14746480 (100.00%) were unpaired; of these: 2022976 (13.72%) aligned 0 times 10132194 (68.71%) aligned exactly 1 time 2591310 (17.57%) aligned >1 times 86.28% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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_rmdupse_core] 3138280 / 12723504 = 0.2467 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 04:44:48: # Command line: callpeak -t SRX208764.bam -f BAM -g ce -n SRX208764.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208764.20 # format = BAM # ChIP-seq file = ['SRX208764.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 04:44:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:44:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:44:48: # Command line: callpeak -t SRX208764.bam -f BAM -g ce -n SRX208764.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208764.10 # format = BAM # ChIP-seq file = ['SRX208764.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 04:44:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:44:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:44:48: # Command line: callpeak -t SRX208764.bam -f BAM -g ce -n SRX208764.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208764.05 # format = BAM # ChIP-seq file = ['SRX208764.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 04:44:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:44:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:44:54: 1000000 INFO @ Sat, 03 Jun 2017 04:44:54: 1000000 INFO @ Sat, 03 Jun 2017 04:44:55: 1000000 INFO @ Sat, 03 Jun 2017 04:45:00: 2000000 INFO @ Sat, 03 Jun 2017 04:45:01: 2000000 INFO @ Sat, 03 Jun 2017 04:45:02: 2000000 INFO @ Sat, 03 Jun 2017 04:45:06: 3000000 INFO @ Sat, 03 Jun 2017 04:45:07: 3000000 INFO @ Sat, 03 Jun 2017 04:45:09: 3000000 INFO @ Sat, 03 Jun 2017 04:45:11: 4000000 INFO @ Sat, 03 Jun 2017 04:45:13: 4000000 INFO @ Sat, 03 Jun 2017 04:45:16: 4000000 INFO @ Sat, 03 Jun 2017 04:45:16: 5000000 INFO @ Sat, 03 Jun 2017 04:45:19: 5000000 INFO @ Sat, 03 Jun 2017 04:45:21: 6000000 INFO @ Sat, 03 Jun 2017 04:45:23: 5000000 INFO @ Sat, 03 Jun 2017 04:45:26: 6000000 INFO @ Sat, 03 Jun 2017 04:45:26: 7000000 INFO @ Sat, 03 Jun 2017 04:45:30: 6000000 INFO @ Sat, 03 Jun 2017 04:45:32: 8000000 INFO @ Sat, 03 Jun 2017 04:45:32: 7000000 INFO @ Sat, 03 Jun 2017 04:45:36: 7000000 INFO @ Sat, 03 Jun 2017 04:45:37: 9000000 INFO @ Sat, 03 Jun 2017 04:45:38: 8000000 INFO @ Sat, 03 Jun 2017 04:45:40: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 04:45:40: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 04:45:40: #1 total tags in treatment: 9585224 INFO @ Sat, 03 Jun 2017 04:45:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:45:40: #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 04:45:41: #1 tags after filtering in treatment: 9584732 INFO @ Sat, 03 Jun 2017 04:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:45:41: #1 finished! INFO @ Sat, 03 Jun 2017 04:45:41: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:45:42: 8000000 INFO @ Sat, 03 Jun 2017 04:45:43: 9000000 INFO @ Sat, 03 Jun 2017 04:45:43: #2 number of paired peaks: 599 WARNING @ Sat, 03 Jun 2017 04:45:43: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Jun 2017 04:45:43: start model_add_line... INFO @ Sat, 03 Jun 2017 04:45:47: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 04:45:47: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 04:45:47: #1 total tags in treatment: 9585224 INFO @ Sat, 03 Jun 2017 04:45:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:45:47: #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 04:45:48: 9000000 INFO @ Sat, 03 Jun 2017 04:45:48: #1 tags after filtering in treatment: 9584732 INFO @ Sat, 03 Jun 2017 04:45:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:45:48: #1 finished! INFO @ Sat, 03 Jun 2017 04:45:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:45:50: #2 number of paired peaks: 599 WARNING @ Sat, 03 Jun 2017 04:45:50: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Jun 2017 04:45:50: start model_add_line... INFO @ Sat, 03 Jun 2017 04:45:50: start X-correlation... INFO @ Sat, 03 Jun 2017 04:45:50: end of X-cor INFO @ Sat, 03 Jun 2017 04:45:50: #2 finished! INFO @ Sat, 03 Jun 2017 04:45:50: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Jun 2017 04:45:50: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Jun 2017 04:45:50: #2.2 Generate R script for model : SRX208764.20_model.r INFO @ Sat, 03 Jun 2017 04:45:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:45:51: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 04:45:51: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 04:45:51: #1 total tags in treatment: 9585224 INFO @ Sat, 03 Jun 2017 04:45:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:45:51: #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 04:45:54: #1 tags after filtering in treatment: 9584732 INFO @ Sat, 03 Jun 2017 04:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:45:54: #1 finished! INFO @ Sat, 03 Jun 2017 04:45:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:45:55: #2 number of paired peaks: 599 WARNING @ Sat, 03 Jun 2017 04:45:55: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Jun 2017 04:45:55: start model_add_line... INFO @ Sat, 03 Jun 2017 04:45:57: start X-correlation... INFO @ Sat, 03 Jun 2017 04:45:57: end of X-cor INFO @ Sat, 03 Jun 2017 04:45:57: #2 finished! INFO @ Sat, 03 Jun 2017 04:45:57: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Jun 2017 04:45:57: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Jun 2017 04:45:57: #2.2 Generate R script for model : SRX208764.05_model.r INFO @ Sat, 03 Jun 2017 04:45:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:02: start X-correlation... INFO @ Sat, 03 Jun 2017 04:46:02: end of X-cor INFO @ Sat, 03 Jun 2017 04:46:02: #2 finished! INFO @ Sat, 03 Jun 2017 04:46:02: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Jun 2017 04:46:02: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Jun 2017 04:46:02: #2.2 Generate R script for model : SRX208764.10_model.r INFO @ Sat, 03 Jun 2017 04:46:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:46:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:46:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:46:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:47:19: #4 Write output xls file... SRX208764.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:47:19: #4 Write peak in narrowPeak format file... SRX208764.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:47:19: #4 Write summits bed file... SRX208764.20_summits.bed INFO @ Sat, 03 Jun 2017 04:47:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (761 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:47:30: #4 Write output xls file... SRX208764.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:47:30: #4 Write peak in narrowPeak format file... SRX208764.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:47:30: #4 Write summits bed file... SRX208764.05_summits.bed INFO @ Sat, 03 Jun 2017 04:47:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1478 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:47:36: #4 Write output xls file... SRX208764.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:47:36: #4 Write peak in narrowPeak format file... SRX208764.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:47:36: #4 Write summits bed file... SRX208764.10_summits.bed INFO @ Sat, 03 Jun 2017 04:47:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1116 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。