Job ID = 9040701 sra ファイルのダウンロード中... Completed: 237023K bytes transferred in 4 seconds (401507K 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 --:--:-- 0 100 12695 0 12695 0 0 1623 0 --:--:-- 0:00:07 --:--:-- 9803 100 38934 0 38934 0 0 4416 0 --:--:-- 0:00:08 --:--:-- 16994 100 47110 0 47110 0 0 5149 0 --:--:-- 0:00:09 --:--:-- 17960 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 16895652 spots for /home/okishinya/chipatlas/results/dm3/SRX1149371/SRR2162779.sra Written 16895652 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:25 16895652 reads; of these: 16895652 (100.00%) were unpaired; of these: 309677 (1.83%) aligned 0 times 9575394 (56.67%) aligned exactly 1 time 7010581 (41.49%) aligned >1 times 98.17% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1470731 / 16585975 = 0.0887 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 @ Mon, 05 Jun 2017 00:18:16: # Command line: callpeak -t SRX1149371.bam -f BAM -g dm -n SRX1149371.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1149371.05 # format = BAM # ChIP-seq file = ['SRX1149371.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 00:18:16: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:18:16: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:18:16: # Command line: callpeak -t SRX1149371.bam -f BAM -g dm -n SRX1149371.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1149371.10 # format = BAM # ChIP-seq file = ['SRX1149371.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 00:18:16: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:18:16: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:18:16: # Command line: callpeak -t SRX1149371.bam -f BAM -g dm -n SRX1149371.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1149371.20 # format = BAM # ChIP-seq file = ['SRX1149371.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 00:18:16: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:18:16: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:18:22: 1000000 INFO @ Mon, 05 Jun 2017 00:18:22: 1000000 INFO @ Mon, 05 Jun 2017 00:18:22: 1000000 INFO @ Mon, 05 Jun 2017 00:18:27: 2000000 INFO @ Mon, 05 Jun 2017 00:18:27: 2000000 INFO @ Mon, 05 Jun 2017 00:18:28: 2000000 INFO @ Mon, 05 Jun 2017 00:18:33: 3000000 INFO @ Mon, 05 Jun 2017 00:18:33: 3000000 INFO @ Mon, 05 Jun 2017 00:18:33: 3000000 INFO @ Mon, 05 Jun 2017 00:18:38: 4000000 INFO @ Mon, 05 Jun 2017 00:18:38: 4000000 INFO @ Mon, 05 Jun 2017 00:18:39: 4000000 INFO @ Mon, 05 Jun 2017 00:18:44: 5000000 INFO @ Mon, 05 Jun 2017 00:18:44: 5000000 INFO @ Mon, 05 Jun 2017 00:18:44: 5000000 INFO @ Mon, 05 Jun 2017 00:18:49: 6000000 INFO @ Mon, 05 Jun 2017 00:18:49: 6000000 INFO @ Mon, 05 Jun 2017 00:18:50: 6000000 INFO @ Mon, 05 Jun 2017 00:18:55: 7000000 INFO @ Mon, 05 Jun 2017 00:18:55: 7000000 INFO @ Mon, 05 Jun 2017 00:18:55: 7000000 INFO @ Mon, 05 Jun 2017 00:19:00: 8000000 INFO @ Mon, 05 Jun 2017 00:19:00: 8000000 INFO @ Mon, 05 Jun 2017 00:19:01: 8000000 INFO @ Mon, 05 Jun 2017 00:19:05: 9000000 INFO @ Mon, 05 Jun 2017 00:19:05: 9000000 INFO @ Mon, 05 Jun 2017 00:19:06: 9000000 INFO @ Mon, 05 Jun 2017 00:19:11: 10000000 INFO @ Mon, 05 Jun 2017 00:19:11: 10000000 INFO @ Mon, 05 Jun 2017 00:19:12: 10000000 INFO @ Mon, 05 Jun 2017 00:19:16: 11000000 INFO @ Mon, 05 Jun 2017 00:19:16: 11000000 INFO @ Mon, 05 Jun 2017 00:19:17: 11000000 INFO @ Mon, 05 Jun 2017 00:19:22: 12000000 INFO @ Mon, 05 Jun 2017 00:19:22: 12000000 INFO @ Mon, 05 Jun 2017 00:19:23: 12000000 INFO @ Mon, 05 Jun 2017 00:19:27: 13000000 INFO @ Mon, 05 Jun 2017 00:19:27: 13000000 INFO @ Mon, 05 Jun 2017 00:19:28: 13000000 INFO @ Mon, 05 Jun 2017 00:19:32: 14000000 INFO @ Mon, 05 Jun 2017 00:19:32: 14000000 INFO @ Mon, 05 Jun 2017 00:19:34: 14000000 INFO @ Mon, 05 Jun 2017 00:19:38: 15000000 INFO @ Mon, 05 Jun 2017 00:19:38: 15000000 INFO @ Mon, 05 Jun 2017 00:19:38: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:19:38: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:19:38: #1 total tags in treatment: 15115244 INFO @ Mon, 05 Jun 2017 00:19:38: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:19:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:19:38: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:19:38: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:19:38: #1 total tags in treatment: 15115244 INFO @ Mon, 05 Jun 2017 00:19:38: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:19:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:19:39: 15000000 INFO @ Mon, 05 Jun 2017 00:19:40: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:19:40: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:19:40: #1 total tags in treatment: 15115244 INFO @ Mon, 05 Jun 2017 00:19:40: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:19:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 00:19:41: #1 tags after filtering in treatment: 15112349 INFO @ Mon, 05 Jun 2017 00:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:19:41: #1 finished! INFO @ Mon, 05 Jun 2017 00:19:41: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:19:41: #1 tags after filtering in treatment: 15112349 INFO @ Mon, 05 Jun 2017 00:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:19:41: #1 finished! INFO @ Mon, 05 Jun 2017 00:19:41: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:19:43: #1 tags after filtering in treatment: 15112349 INFO @ Mon, 05 Jun 2017 00:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:19:43: #1 finished! INFO @ Mon, 05 Jun 2017 00:19:43: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:19:44: #2 number of paired peaks: 743 WARNING @ Mon, 05 Jun 2017 00:19:44: Fewer paired peaks (743) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 743 pairs to build model! INFO @ Mon, 05 Jun 2017 00:19:44: start model_add_line... INFO @ Mon, 05 Jun 2017 00:19:44: #2 number of paired peaks: 743 WARNING @ Mon, 05 Jun 2017 00:19:44: Fewer paired peaks (743) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 743 pairs to build model! INFO @ Mon, 05 Jun 2017 00:19:44: start model_add_line... INFO @ Mon, 05 Jun 2017 00:19:46: #2 number of paired peaks: 743 WARNING @ Mon, 05 Jun 2017 00:19:46: Fewer paired peaks (743) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 743 pairs to build model! INFO @ Mon, 05 Jun 2017 00:19:46: start model_add_line... INFO @ Mon, 05 Jun 2017 00:19:51: start X-correlation... INFO @ Mon, 05 Jun 2017 00:19:51: end of X-cor INFO @ Mon, 05 Jun 2017 00:19:51: #2 finished! INFO @ Mon, 05 Jun 2017 00:19:51: #2 predicted fragment length is 190 bps INFO @ Mon, 05 Jun 2017 00:19:51: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 05 Jun 2017 00:19:51: #2.2 Generate R script for model : SRX1149371.20_model.r INFO @ Mon, 05 Jun 2017 00:19:51: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:19:51: start X-correlation... INFO @ Mon, 05 Jun 2017 00:19:51: end of X-cor INFO @ Mon, 05 Jun 2017 00:19:51: #2 finished! INFO @ Mon, 05 Jun 2017 00:19:51: #2 predicted fragment length is 190 bps INFO @ Mon, 05 Jun 2017 00:19:51: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 05 Jun 2017 00:19:51: #2.2 Generate R script for model : SRX1149371.10_model.r INFO @ Mon, 05 Jun 2017 00:19:51: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:19:53: start X-correlation... INFO @ Mon, 05 Jun 2017 00:19:53: end of X-cor INFO @ Mon, 05 Jun 2017 00:19:53: #2 finished! INFO @ Mon, 05 Jun 2017 00:19:53: #2 predicted fragment length is 190 bps INFO @ Mon, 05 Jun 2017 00:19:53: #2 alternative fragment length(s) may be 4,190 bps INFO @ Mon, 05 Jun 2017 00:19:53: #2.2 Generate R script for model : SRX1149371.05_model.r INFO @ Mon, 05 Jun 2017 00:19:53: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:21:13: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:21:15: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:21:24: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:22:13: #4 Write output xls file... SRX1149371.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:13: #4 Write peak in narrowPeak format file... SRX1149371.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:13: #4 Write summits bed file... SRX1149371.10_summits.bed INFO @ Mon, 05 Jun 2017 00:22:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3224 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:22:18: #4 Write output xls file... SRX1149371.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:18: #4 Write peak in narrowPeak format file... SRX1149371.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:18: #4 Write summits bed file... SRX1149371.20_summits.bed INFO @ Mon, 05 Jun 2017 00:22:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1351 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:22:37: #4 Write output xls file... SRX1149371.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:22:37: #4 Write peak in narrowPeak format file... SRX1149371.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:22:37: #4 Write summits bed file... SRX1149371.05_summits.bed INFO @ Mon, 05 Jun 2017 00:22:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6722 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。