Job ID = 9039916 sra ファイルのダウンロード中... Completed: 731388K bytes transferred in 8 seconds (691472K 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 --:--:-- 0 101 5455 0 5455 0 0 753 0 --:--:-- 0:00:07 --:--:-- 7871 100 30317 0 30317 0 0 3682 0 --:--:-- 0:00:08 --:--:-- 17960 100 72237 0 72237 0 0 7826 0 --:--:-- 0:00:09 --:--:-- 26913 100 92661 0 92661 0 0 9861 0 --:--:-- 0:00:09 --:--:-- 32501 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 33162909 spots for /home/okishinya/chipatlas/results/dm3/SRX1085381/SRR2090181.sra Written 33162909 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: 00:05:02 33162909 reads; of these: 33162909 (100.00%) were unpaired; of these: 4324100 (13.04%) aligned 0 times 25509725 (76.92%) aligned exactly 1 time 3329084 (10.04%) aligned >1 times 86.96% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 6812201 / 28838809 = 0.2362 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 @ Sun, 04 Jun 2017 23:23:44: # Command line: callpeak -t SRX1085381.bam -f BAM -g dm -n SRX1085381.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1085381.10 # format = BAM # ChIP-seq file = ['SRX1085381.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 @ Sun, 04 Jun 2017 23:23:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:23:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:23:44: # Command line: callpeak -t SRX1085381.bam -f BAM -g dm -n SRX1085381.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1085381.20 # format = BAM # ChIP-seq file = ['SRX1085381.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 @ Sun, 04 Jun 2017 23:23:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:23:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:23:44: # Command line: callpeak -t SRX1085381.bam -f BAM -g dm -n SRX1085381.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1085381.05 # format = BAM # ChIP-seq file = ['SRX1085381.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 @ Sun, 04 Jun 2017 23:23:44: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:23:44: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:23:49: 1000000 INFO @ Sun, 04 Jun 2017 23:23:49: 1000000 INFO @ Sun, 04 Jun 2017 23:23:49: 1000000 INFO @ Sun, 04 Jun 2017 23:23:54: 2000000 INFO @ Sun, 04 Jun 2017 23:23:54: 2000000 INFO @ Sun, 04 Jun 2017 23:23:54: 2000000 INFO @ Sun, 04 Jun 2017 23:23:59: 3000000 INFO @ Sun, 04 Jun 2017 23:23:59: 3000000 INFO @ Sun, 04 Jun 2017 23:23:59: 3000000 INFO @ Sun, 04 Jun 2017 23:24:04: 4000000 INFO @ Sun, 04 Jun 2017 23:24:04: 4000000 INFO @ Sun, 04 Jun 2017 23:24:04: 4000000 INFO @ Sun, 04 Jun 2017 23:24:09: 5000000 INFO @ Sun, 04 Jun 2017 23:24:09: 5000000 INFO @ Sun, 04 Jun 2017 23:24:09: 5000000 INFO @ Sun, 04 Jun 2017 23:24:14: 6000000 INFO @ Sun, 04 Jun 2017 23:24:14: 6000000 INFO @ Sun, 04 Jun 2017 23:24:14: 6000000 INFO @ Sun, 04 Jun 2017 23:24:19: 7000000 INFO @ Sun, 04 Jun 2017 23:24:19: 7000000 INFO @ Sun, 04 Jun 2017 23:24:19: 7000000 INFO @ Sun, 04 Jun 2017 23:24:24: 8000000 INFO @ Sun, 04 Jun 2017 23:24:24: 8000000 INFO @ Sun, 04 Jun 2017 23:24:24: 8000000 INFO @ Sun, 04 Jun 2017 23:24:29: 9000000 INFO @ Sun, 04 Jun 2017 23:24:29: 9000000 INFO @ Sun, 04 Jun 2017 23:24:29: 9000000 INFO @ Sun, 04 Jun 2017 23:24:34: 10000000 INFO @ Sun, 04 Jun 2017 23:24:34: 10000000 INFO @ Sun, 04 Jun 2017 23:24:34: 10000000 INFO @ Sun, 04 Jun 2017 23:24:39: 11000000 INFO @ Sun, 04 Jun 2017 23:24:39: 11000000 INFO @ Sun, 04 Jun 2017 23:24:39: 11000000 INFO @ Sun, 04 Jun 2017 23:24:44: 12000000 INFO @ Sun, 04 Jun 2017 23:24:44: 12000000 INFO @ Sun, 04 Jun 2017 23:24:44: 12000000 INFO @ Sun, 04 Jun 2017 23:24:49: 13000000 INFO @ Sun, 04 Jun 2017 23:24:49: 13000000 INFO @ Sun, 04 Jun 2017 23:24:49: 13000000 INFO @ Sun, 04 Jun 2017 23:24:54: 14000000 INFO @ Sun, 04 Jun 2017 23:24:54: 14000000 INFO @ Sun, 04 Jun 2017 23:24:54: 14000000 INFO @ Sun, 04 Jun 2017 23:24:59: 15000000 INFO @ Sun, 04 Jun 2017 23:24:59: 15000000 INFO @ Sun, 04 Jun 2017 23:24:59: 15000000 INFO @ Sun, 04 Jun 2017 23:25:04: 16000000 INFO @ Sun, 04 Jun 2017 23:25:04: 16000000 INFO @ Sun, 04 Jun 2017 23:25:04: 16000000 INFO @ Sun, 04 Jun 2017 23:25:09: 17000000 INFO @ Sun, 04 Jun 2017 23:25:09: 17000000 INFO @ Sun, 04 Jun 2017 23:25:09: 17000000 INFO @ Sun, 04 Jun 2017 23:25:14: 18000000 INFO @ Sun, 04 Jun 2017 23:25:14: 18000000 INFO @ Sun, 04 Jun 2017 23:25:15: 18000000 INFO @ Sun, 04 Jun 2017 23:25:19: 19000000 INFO @ Sun, 04 Jun 2017 23:25:20: 19000000 INFO @ Sun, 04 Jun 2017 23:25:20: 19000000 INFO @ Sun, 04 Jun 2017 23:25:24: 20000000 INFO @ Sun, 04 Jun 2017 23:25:25: 20000000 INFO @ Sun, 04 Jun 2017 23:25:25: 20000000 INFO @ Sun, 04 Jun 2017 23:25:29: 21000000 INFO @ Sun, 04 Jun 2017 23:25:30: 21000000 INFO @ Sun, 04 Jun 2017 23:25:30: 21000000 INFO @ Sun, 04 Jun 2017 23:25:34: 22000000 INFO @ Sun, 04 Jun 2017 23:25:34: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 23:25:34: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 23:25:34: #1 total tags in treatment: 22026608 INFO @ Sun, 04 Jun 2017 23:25:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:25:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:25:35: 22000000 INFO @ Sun, 04 Jun 2017 23:25:35: 22000000 INFO @ Sun, 04 Jun 2017 23:25:35: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 23:25:35: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 23:25:35: #1 total tags in treatment: 22026608 INFO @ Sun, 04 Jun 2017 23:25:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:25:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:25:35: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 23:25:35: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 23:25:35: #1 total tags in treatment: 22026608 INFO @ Sun, 04 Jun 2017 23:25:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:25:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 23:25:38: #1 tags after filtering in treatment: 22017614 INFO @ Sun, 04 Jun 2017 23:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:25:38: #1 finished! INFO @ Sun, 04 Jun 2017 23:25:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:25:39: #1 tags after filtering in treatment: 22017614 INFO @ Sun, 04 Jun 2017 23:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:25:39: #1 finished! INFO @ Sun, 04 Jun 2017 23:25:39: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:25:39: #1 tags after filtering in treatment: 22017614 INFO @ Sun, 04 Jun 2017 23:25:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:25:39: #1 finished! INFO @ Sun, 04 Jun 2017 23:25:39: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:25:42: #2 number of paired peaks: 1371 INFO @ Sun, 04 Jun 2017 23:25:42: start model_add_line... INFO @ Sun, 04 Jun 2017 23:25:43: #2 number of paired peaks: 1371 INFO @ Sun, 04 Jun 2017 23:25:43: start model_add_line... INFO @ Sun, 04 Jun 2017 23:25:43: #2 number of paired peaks: 1371 INFO @ Sun, 04 Jun 2017 23:25:43: start model_add_line... INFO @ Sun, 04 Jun 2017 23:25:58: start X-correlation... INFO @ Sun, 04 Jun 2017 23:25:58: end of X-cor INFO @ Sun, 04 Jun 2017 23:25:58: #2 finished! INFO @ Sun, 04 Jun 2017 23:25:58: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Jun 2017 23:25:58: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Jun 2017 23:25:58: #2.2 Generate R script for model : SRX1085381.10_model.r INFO @ Sun, 04 Jun 2017 23:25:58: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:25:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:25:59: start X-correlation... INFO @ Sun, 04 Jun 2017 23:25:59: end of X-cor INFO @ Sun, 04 Jun 2017 23:25:59: #2 finished! INFO @ Sun, 04 Jun 2017 23:25:59: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Jun 2017 23:25:59: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Jun 2017 23:25:59: #2.2 Generate R script for model : SRX1085381.20_model.r INFO @ Sun, 04 Jun 2017 23:25:59: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:25:59: start X-correlation... INFO @ Sun, 04 Jun 2017 23:26:00: end of X-cor INFO @ Sun, 04 Jun 2017 23:26:00: #2 finished! INFO @ Sun, 04 Jun 2017 23:26:00: #2 predicted fragment length is 177 bps INFO @ Sun, 04 Jun 2017 23:26:00: #2 alternative fragment length(s) may be 177 bps INFO @ Sun, 04 Jun 2017 23:26:00: #2.2 Generate R script for model : SRX1085381.05_model.r INFO @ Sun, 04 Jun 2017 23:26:00: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:27:57: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:28:01: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:28:02: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:29:28: #4 Write output xls file... SRX1085381.10_peaks.xls INFO @ Sun, 04 Jun 2017 23:29:28: #4 Write peak in narrowPeak format file... SRX1085381.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:29:28: #4 Write summits bed file... SRX1085381.10_summits.bed INFO @ Sun, 04 Jun 2017 23:29:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8173 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:29:36: #4 Write output xls file... SRX1085381.20_peaks.xls INFO @ Sun, 04 Jun 2017 23:29:36: #4 Write peak in narrowPeak format file... SRX1085381.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:29:36: #4 Write summits bed file... SRX1085381.20_summits.bed INFO @ Sun, 04 Jun 2017 23:29:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5906 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:29:42: #4 Write output xls file... SRX1085381.05_peaks.xls INFO @ Sun, 04 Jun 2017 23:29:42: #4 Write peak in narrowPeak format file... SRX1085381.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:29:42: #4 Write summits bed file... SRX1085381.05_summits.bed INFO @ Sun, 04 Jun 2017 23:29:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10555 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。