Job ID = 9029464 sra ファイルのダウンロード中... Completed: 256815K bytes transferred in 5 seconds (386481K 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 --:--:-- 0 100 7663 0 7663 0 0 1045 0 --:--:-- 0:00:07 --:--:-- 10082 100 30246 0 30246 0 0 3707 0 --:--:-- 0:00:08 --:--:-- 19022 100 66243 0 66243 0 0 7508 0 --:--:-- 0:00:08 --:--:-- 29402 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 9989575 spots for /home/okishinya/chipatlas/results/dm3/SRX1794215/SRR3575246.sra Written 9989575 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: 00:03:32 9989575 reads; of these: 9989575 (100.00%) were unpaired; of these: 613207 (6.14%) aligned 0 times 7452648 (74.60%) aligned exactly 1 time 1923720 (19.26%) aligned >1 times 93.86% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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] 1145684 / 9376368 = 0.1222 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 13:55:50: # Command line: callpeak -t SRX1794215.bam -f BAM -g dm -n SRX1794215.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794215.20 # format = BAM # ChIP-seq file = ['SRX1794215.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 @ Sat, 03 Jun 2017 13:55:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:50: # Command line: callpeak -t SRX1794215.bam -f BAM -g dm -n SRX1794215.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794215.10 # format = BAM # ChIP-seq file = ['SRX1794215.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 @ Sat, 03 Jun 2017 13:55:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:50: # Command line: callpeak -t SRX1794215.bam -f BAM -g dm -n SRX1794215.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794215.05 # format = BAM # ChIP-seq file = ['SRX1794215.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 @ Sat, 03 Jun 2017 13:55:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:58: 1000000 INFO @ Sat, 03 Jun 2017 13:55:58: 1000000 INFO @ Sat, 03 Jun 2017 13:55:58: 1000000 INFO @ Sat, 03 Jun 2017 13:56:06: 2000000 INFO @ Sat, 03 Jun 2017 13:56:06: 2000000 INFO @ Sat, 03 Jun 2017 13:56:06: 2000000 INFO @ Sat, 03 Jun 2017 13:56:14: 3000000 INFO @ Sat, 03 Jun 2017 13:56:14: 3000000 INFO @ Sat, 03 Jun 2017 13:56:14: 3000000 INFO @ Sat, 03 Jun 2017 13:56:22: 4000000 INFO @ Sat, 03 Jun 2017 13:56:22: 4000000 INFO @ Sat, 03 Jun 2017 13:56:22: 4000000 INFO @ Sat, 03 Jun 2017 13:56:30: 5000000 INFO @ Sat, 03 Jun 2017 13:56:30: 5000000 INFO @ Sat, 03 Jun 2017 13:56:30: 5000000 INFO @ Sat, 03 Jun 2017 13:56:37: 6000000 INFO @ Sat, 03 Jun 2017 13:56:37: 6000000 INFO @ Sat, 03 Jun 2017 13:56:37: 6000000 INFO @ Sat, 03 Jun 2017 13:56:45: 7000000 INFO @ Sat, 03 Jun 2017 13:56:45: 7000000 INFO @ Sat, 03 Jun 2017 13:56:45: 7000000 INFO @ Sat, 03 Jun 2017 13:56:53: 8000000 INFO @ Sat, 03 Jun 2017 13:56:53: 8000000 INFO @ Sat, 03 Jun 2017 13:56:53: 8000000 INFO @ Sat, 03 Jun 2017 13:56:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:55: #1 total tags in treatment: 8230684 INFO @ Sat, 03 Jun 2017 13:56:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:55: #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 13:56:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:55: #1 total tags in treatment: 8230684 INFO @ Sat, 03 Jun 2017 13:56:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:55: #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 13:56:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:56:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:56:55: #1 total tags in treatment: 8230684 INFO @ Sat, 03 Jun 2017 13:56:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:56:55: #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 13:56:56: #1 tags after filtering in treatment: 8228632 INFO @ Sat, 03 Jun 2017 13:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:56: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:56: #1 tags after filtering in treatment: 8228632 INFO @ Sat, 03 Jun 2017 13:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:56: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:56: #1 tags after filtering in treatment: 8228632 INFO @ Sat, 03 Jun 2017 13:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:56:56: #1 finished! INFO @ Sat, 03 Jun 2017 13:56:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:58: #2 number of paired peaks: 4984 INFO @ Sat, 03 Jun 2017 13:56:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:58: #2 number of paired peaks: 4984 INFO @ Sat, 03 Jun 2017 13:56:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:59: #2 number of paired peaks: 4984 INFO @ Sat, 03 Jun 2017 13:56:59: start model_add_line... INFO @ Sat, 03 Jun 2017 13:57:27: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:27: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:27: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:27: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:57:27: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:57:27: #2.2 Generate R script for model : SRX1794215.20_model.r INFO @ Sat, 03 Jun 2017 13:57:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:27: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:27: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:27: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:27: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:57:27: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:57:27: #2.2 Generate R script for model : SRX1794215.10_model.r INFO @ Sat, 03 Jun 2017 13:57:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:28: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:28: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:28: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:28: #2 predicted fragment length is 137 bps INFO @ Sat, 03 Jun 2017 13:57:28: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 03 Jun 2017 13:57:28: #2.2 Generate R script for model : SRX1794215.05_model.r INFO @ Sat, 03 Jun 2017 13:57:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:58:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:58:51: #4 Write output xls file... SRX1794215.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:51: #4 Write peak in narrowPeak format file... SRX1794215.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:51: #4 Write summits bed file... SRX1794215.20_summits.bed INFO @ Sat, 03 Jun 2017 13:58:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3084 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:58:59: #4 Write output xls file... SRX1794215.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:59: #4 Write peak in narrowPeak format file... SRX1794215.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:59: #4 Write summits bed file... SRX1794215.10_summits.bed INFO @ Sat, 03 Jun 2017 13:58:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6499 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:59:06: #4 Write output xls file... SRX1794215.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:59:06: #4 Write peak in narrowPeak format file... SRX1794215.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:59:06: #4 Write summits bed file... SRX1794215.05_summits.bed INFO @ Sat, 03 Jun 2017 13:59:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10227 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。