Job ID = 9025657 sra ファイルのダウンロード中... Completed: 191210K bytes transferred in 5 seconds (287648K 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 --:--:-- 0 100 7663 0 7663 0 0 905 0 --:--:-- 0:00:08 --:--:-- 3673 100 30246 0 30246 0 0 3196 0 --:--:-- 0:00:09 --:--:-- 9813 100 49660 0 49660 0 0 4985 0 --:--:-- 0:00:09 --:--:-- 13867 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 6715360 spots for /home/okishinya/chipatlas/results/ce10/SRX2144183/SRR4188787.sra Written 6715360 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: 00:01:43 6715360 reads; of these: 6715360 (100.00%) were unpaired; of these: 1188497 (17.70%) aligned 0 times 4685742 (69.78%) aligned exactly 1 time 841121 (12.53%) aligned >1 times 82.30% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 1402022 / 5526863 = 0.2537 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 04:51:15: # Command line: callpeak -t SRX2144183.bam -f BAM -g ce -n SRX2144183.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144183.05 # format = BAM # ChIP-seq file = ['SRX2144183.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 04:51:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:15: # Command line: callpeak -t SRX2144183.bam -f BAM -g ce -n SRX2144183.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144183.10 # format = BAM # ChIP-seq file = ['SRX2144183.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 04:51:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:15: # Command line: callpeak -t SRX2144183.bam -f BAM -g ce -n SRX2144183.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144183.20 # format = BAM # ChIP-seq file = ['SRX2144183.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 04:51:15: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:15: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:21: 1000000 INFO @ Sat, 03 Jun 2017 04:51:21: 1000000 INFO @ Sat, 03 Jun 2017 04:51:22: 1000000 INFO @ Sat, 03 Jun 2017 04:51:26: 2000000 INFO @ Sat, 03 Jun 2017 04:51:28: 2000000 INFO @ Sat, 03 Jun 2017 04:51:28: 2000000 INFO @ Sat, 03 Jun 2017 04:51:31: 3000000 INFO @ Sat, 03 Jun 2017 04:51:34: 3000000 INFO @ Sat, 03 Jun 2017 04:51:35: 3000000 INFO @ Sat, 03 Jun 2017 04:51:37: 4000000 INFO @ Sat, 03 Jun 2017 04:51:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:38: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:38: #1 total tags in treatment: 4124841 INFO @ Sat, 03 Jun 2017 04:51:38: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:38: #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 04:51:38: #1 tags after filtering in treatment: 4124145 INFO @ Sat, 03 Jun 2017 04:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:38: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:39: #2 number of paired peaks: 1539 INFO @ Sat, 03 Jun 2017 04:51:39: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:41: 4000000 INFO @ Sat, 03 Jun 2017 04:51:41: 4000000 INFO @ Sat, 03 Jun 2017 04:51:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:41: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:41: #1 total tags in treatment: 4124841 INFO @ Sat, 03 Jun 2017 04:51:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:41: #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 04:51:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:51:42: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:51:42: #1 total tags in treatment: 4124841 INFO @ Sat, 03 Jun 2017 04:51:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:51:42: #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 04:51:42: #1 tags after filtering in treatment: 4124145 INFO @ Sat, 03 Jun 2017 04:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:42: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:43: #1 tags after filtering in treatment: 4124145 INFO @ Sat, 03 Jun 2017 04:51:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:51:43: #1 finished! INFO @ Sat, 03 Jun 2017 04:51:43: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:51:43: #2 number of paired peaks: 1539 INFO @ Sat, 03 Jun 2017 04:51:43: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:44: #2 number of paired peaks: 1539 INFO @ Sat, 03 Jun 2017 04:51:44: start model_add_line... INFO @ Sat, 03 Jun 2017 04:51:46: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:46: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:46: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:46: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 04:51:46: #2 alternative fragment length(s) may be 4,123 bps INFO @ Sat, 03 Jun 2017 04:51:46: #2.2 Generate R script for model : SRX2144183.10_model.r INFO @ Sat, 03 Jun 2017 04:51:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:50: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:50: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:50: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:50: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 04:51:50: #2 alternative fragment length(s) may be 4,123 bps INFO @ Sat, 03 Jun 2017 04:51:50: #2.2 Generate R script for model : SRX2144183.05_model.r INFO @ Sat, 03 Jun 2017 04:51:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:51:51: start X-correlation... INFO @ Sat, 03 Jun 2017 04:51:51: end of X-cor INFO @ Sat, 03 Jun 2017 04:51:51: #2 finished! INFO @ Sat, 03 Jun 2017 04:51:51: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 04:51:51: #2 alternative fragment length(s) may be 4,123 bps INFO @ Sat, 03 Jun 2017 04:51:51: #2.2 Generate R script for model : SRX2144183.20_model.r INFO @ Sat, 03 Jun 2017 04:51:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:52:28: #4 Write output xls file... SRX2144183.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:28: #4 Write peak in narrowPeak format file... SRX2144183.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:28: #4 Write summits bed file... SRX2144183.10_summits.bed INFO @ Sat, 03 Jun 2017 04:52:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (628 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:52:33: #4 Write output xls file... SRX2144183.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:33: #4 Write peak in narrowPeak format file... SRX2144183.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:33: #4 Write summits bed file... SRX2144183.05_summits.bed INFO @ Sat, 03 Jun 2017 04:52:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1604 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:52:37: #4 Write output xls file... SRX2144183.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:52:37: #4 Write peak in narrowPeak format file... SRX2144183.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:52:37: #4 Write summits bed file... SRX2144183.20_summits.bed INFO @ Sat, 03 Jun 2017 04:52:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。