Job ID = 11171278 sra ファイルのダウンロード中... Completed: 112222K bytes transferred in 6 seconds (137154K bits/sec), in 1 file. Completed: 111574K bytes transferred in 6 seconds (139265K bits/sec), in 1 file. Completed: 112177K bytes transferred in 5 seconds (180549K bits/sec), in 1 file. Completed: 111095K bytes transferred in 17 seconds (52903K bits/sec), in 1 file. 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... Read 5857319 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850439.sra Written 5857319 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850439.sra Read 5931218 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850438.sra Written 5931218 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850438.sra Read 5887872 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850437.sra Written 5887872 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850437.sra Read 5938595 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850436.sra Written 5938595 spots for /home/okishinya/chipatlas/results/dm3/SRX3020544/SRR5850436.sra rm: cannot remove `[DSE]RX*': 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: 00:06:55 23615004 reads; of these: 23615004 (100.00%) were unpaired; of these: 6619707 (28.03%) aligned 0 times 12982880 (54.98%) aligned exactly 1 time 4012417 (16.99%) aligned >1 times 71.97% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2492397 / 16995297 = 0.1467 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, 08 Sep 2018 13:36:46: # Command line: callpeak -t SRX3020544.bam -f BAM -g dm -n SRX3020544.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3020544.20 # format = BAM # ChIP-seq file = ['SRX3020544.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:36:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:46: # Command line: callpeak -t SRX3020544.bam -f BAM -g dm -n SRX3020544.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3020544.10 # format = BAM # ChIP-seq file = ['SRX3020544.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:36:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:46: # Command line: callpeak -t SRX3020544.bam -f BAM -g dm -n SRX3020544.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3020544.05 # format = BAM # ChIP-seq file = ['SRX3020544.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 13:36:46: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:36:46: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:36:52: 1000000 INFO @ Sat, 08 Sep 2018 13:36:52: 1000000 INFO @ Sat, 08 Sep 2018 13:36:53: 1000000 INFO @ Sat, 08 Sep 2018 13:36:59: 2000000 INFO @ Sat, 08 Sep 2018 13:36:59: 2000000 INFO @ Sat, 08 Sep 2018 13:36:59: 2000000 INFO @ Sat, 08 Sep 2018 13:37:06: 3000000 INFO @ Sat, 08 Sep 2018 13:37:06: 3000000 INFO @ Sat, 08 Sep 2018 13:37:06: 3000000 INFO @ Sat, 08 Sep 2018 13:37:13: 4000000 INFO @ Sat, 08 Sep 2018 13:37:13: 4000000 INFO @ Sat, 08 Sep 2018 13:37:14: 4000000 INFO @ Sat, 08 Sep 2018 13:37:20: 5000000 INFO @ Sat, 08 Sep 2018 13:37:20: 5000000 INFO @ Sat, 08 Sep 2018 13:37:21: 5000000 INFO @ Sat, 08 Sep 2018 13:37:27: 6000000 INFO @ Sat, 08 Sep 2018 13:37:27: 6000000 INFO @ Sat, 08 Sep 2018 13:37:28: 6000000 INFO @ Sat, 08 Sep 2018 13:37:34: 7000000 INFO @ Sat, 08 Sep 2018 13:37:34: 7000000 INFO @ Sat, 08 Sep 2018 13:37:35: 7000000 INFO @ Sat, 08 Sep 2018 13:37:41: 8000000 INFO @ Sat, 08 Sep 2018 13:37:41: 8000000 INFO @ Sat, 08 Sep 2018 13:37:42: 8000000 INFO @ Sat, 08 Sep 2018 13:37:48: 9000000 INFO @ Sat, 08 Sep 2018 13:37:48: 9000000 INFO @ Sat, 08 Sep 2018 13:37:49: 9000000 INFO @ Sat, 08 Sep 2018 13:37:55: 10000000 INFO @ Sat, 08 Sep 2018 13:37:55: 10000000 INFO @ Sat, 08 Sep 2018 13:37:56: 10000000 INFO @ Sat, 08 Sep 2018 13:38:02: 11000000 INFO @ Sat, 08 Sep 2018 13:38:02: 11000000 INFO @ Sat, 08 Sep 2018 13:38:03: 11000000 INFO @ Sat, 08 Sep 2018 13:38:09: 12000000 INFO @ Sat, 08 Sep 2018 13:38:09: 12000000 INFO @ Sat, 08 Sep 2018 13:38:10: 12000000 INFO @ Sat, 08 Sep 2018 13:38:16: 13000000 INFO @ Sat, 08 Sep 2018 13:38:16: 13000000 INFO @ Sat, 08 Sep 2018 13:38:17: 13000000 INFO @ Sat, 08 Sep 2018 13:38:23: 14000000 INFO @ Sat, 08 Sep 2018 13:38:23: 14000000 INFO @ Sat, 08 Sep 2018 13:38:24: 14000000 INFO @ Sat, 08 Sep 2018 13:38:26: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:26: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:26: #1 total tags in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:27: #1 tags after filtering in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:27: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:27: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:27: #1 total tags in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:27: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:27: #1 tags after filtering in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:27: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:28: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:38:28: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:38:28: #1 total tags in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:38:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:38:28: #1 tags after filtering in treatment: 14502900 INFO @ Sat, 08 Sep 2018 13:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:38:28: #1 finished! INFO @ Sat, 08 Sep 2018 13:38:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:38:28: #2 number of paired peaks: 1448 INFO @ Sat, 08 Sep 2018 13:38:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:28: #2 predicted fragment length is 106 bps INFO @ Sat, 08 Sep 2018 13:38:28: #2 alternative fragment length(s) may be 3,106 bps INFO @ Sat, 08 Sep 2018 13:38:28: #2.2 Generate R script for model : SRX3020544.10_model.r INFO @ Sat, 08 Sep 2018 13:38:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:28: #2 number of paired peaks: 1448 INFO @ Sat, 08 Sep 2018 13:38:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:29: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:29: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:29: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:29: #2 predicted fragment length is 106 bps INFO @ Sat, 08 Sep 2018 13:38:29: #2 alternative fragment length(s) may be 3,106 bps INFO @ Sat, 08 Sep 2018 13:38:29: #2.2 Generate R script for model : SRX3020544.05_model.r INFO @ Sat, 08 Sep 2018 13:38:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:38:29: #2 number of paired peaks: 1448 INFO @ Sat, 08 Sep 2018 13:38:29: start model_add_line... INFO @ Sat, 08 Sep 2018 13:38:29: start X-correlation... INFO @ Sat, 08 Sep 2018 13:38:29: end of X-cor INFO @ Sat, 08 Sep 2018 13:38:29: #2 finished! INFO @ Sat, 08 Sep 2018 13:38:29: #2 predicted fragment length is 106 bps INFO @ Sat, 08 Sep 2018 13:38:29: #2 alternative fragment length(s) may be 3,106 bps INFO @ Sat, 08 Sep 2018 13:38:29: #2.2 Generate R script for model : SRX3020544.20_model.r INFO @ Sat, 08 Sep 2018 13:38:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:39:01: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:04: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:39:18: #4 Write output xls file... SRX3020544.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:18: #4 Write peak in narrowPeak format file... SRX3020544.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:18: #4 Write summits bed file... SRX3020544.10_summits.bed INFO @ Sat, 08 Sep 2018 13:39:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2921 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:39:19: #4 Write output xls file... SRX3020544.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:19: #4 Write peak in narrowPeak format file... SRX3020544.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:19: #4 Write summits bed file... SRX3020544.05_summits.bed INFO @ Sat, 08 Sep 2018 13:39:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8175 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:39:21: #4 Write output xls file... SRX3020544.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:39:21: #4 Write peak in narrowPeak format file... SRX3020544.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:39:21: #4 Write summits bed file... SRX3020544.20_summits.bed INFO @ Sat, 08 Sep 2018 13:39:21: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (807 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。