Job ID = 10201957 sra ファイルのダウンロード中... Completed: 417993K bytes transferred in 11 seconds (300047K 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... Written 17606297 spots for /home/okishinya/chipatlas/results/ce10/SRX2576626/SRR5272583.sra Written 17606297 spots total 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 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: 00:03:21 17606297 reads; of these: 17606297 (100.00%) were unpaired; of these: 657416 (3.73%) aligned 0 times 13984149 (79.43%) aligned exactly 1 time 2964732 (16.84%) aligned >1 times 96.27% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2561963 / 16948881 = 0.1512 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, 13 Nov 2017 13:15:32: # Command line: callpeak -t SRX2576626.bam -f BAM -g ce -n SRX2576626.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2576626.20 # format = BAM # ChIP-seq file = ['SRX2576626.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 # Paired-End mode is off INFO @ Mon, 13 Nov 2017 13:15:32: # Command line: callpeak -t SRX2576626.bam -f BAM -g ce -n SRX2576626.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2576626.05 # format = BAM # ChIP-seq file = ['SRX2576626.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 # Paired-End mode is off INFO @ Mon, 13 Nov 2017 13:15:32: # Command line: callpeak -t SRX2576626.bam -f BAM -g ce -n SRX2576626.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2576626.10 # format = BAM # ChIP-seq file = ['SRX2576626.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 # Paired-End mode is off INFO @ Mon, 13 Nov 2017 13:15:32: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:32: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:32: #1 read tag files... INFO @ Mon, 13 Nov 2017 13:15:32: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:32: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:32: #1 read treatment tags... INFO @ Mon, 13 Nov 2017 13:15:39: 1000000 INFO @ Mon, 13 Nov 2017 13:15:39: 1000000 INFO @ Mon, 13 Nov 2017 13:15:39: 1000000 INFO @ Mon, 13 Nov 2017 13:15:46: 2000000 INFO @ Mon, 13 Nov 2017 13:15:46: 2000000 INFO @ Mon, 13 Nov 2017 13:15:46: 2000000 INFO @ Mon, 13 Nov 2017 13:15:53: 3000000 INFO @ Mon, 13 Nov 2017 13:15:54: 3000000 INFO @ Mon, 13 Nov 2017 13:15:54: 3000000 INFO @ Mon, 13 Nov 2017 13:16:01: 4000000 INFO @ Mon, 13 Nov 2017 13:16:02: 4000000 INFO @ Mon, 13 Nov 2017 13:16:02: 4000000 INFO @ Mon, 13 Nov 2017 13:16:08: 5000000 INFO @ Mon, 13 Nov 2017 13:16:10: 5000000 INFO @ Mon, 13 Nov 2017 13:16:10: 5000000 INFO @ Mon, 13 Nov 2017 13:16:15: 6000000 INFO @ Mon, 13 Nov 2017 13:16:18: 6000000 INFO @ Mon, 13 Nov 2017 13:16:18: 6000000 INFO @ Mon, 13 Nov 2017 13:16:22: 7000000 INFO @ Mon, 13 Nov 2017 13:16:26: 7000000 INFO @ Mon, 13 Nov 2017 13:16:26: 7000000 INFO @ Mon, 13 Nov 2017 13:16:30: 8000000 INFO @ Mon, 13 Nov 2017 13:16:34: 8000000 INFO @ Mon, 13 Nov 2017 13:16:34: 8000000 INFO @ Mon, 13 Nov 2017 13:16:37: 9000000 INFO @ Mon, 13 Nov 2017 13:16:42: 9000000 INFO @ Mon, 13 Nov 2017 13:16:42: 9000000 INFO @ Mon, 13 Nov 2017 13:16:45: 10000000 INFO @ Mon, 13 Nov 2017 13:16:50: 10000000 INFO @ Mon, 13 Nov 2017 13:16:50: 10000000 INFO @ Mon, 13 Nov 2017 13:16:52: 11000000 INFO @ Mon, 13 Nov 2017 13:16:58: 11000000 INFO @ Mon, 13 Nov 2017 13:16:58: 11000000 INFO @ Mon, 13 Nov 2017 13:16:59: 12000000 INFO @ Mon, 13 Nov 2017 13:17:05: 12000000 INFO @ Mon, 13 Nov 2017 13:17:06: 12000000 INFO @ Mon, 13 Nov 2017 13:17:07: 13000000 INFO @ Mon, 13 Nov 2017 13:17:13: 13000000 INFO @ Mon, 13 Nov 2017 13:17:14: 13000000 INFO @ Mon, 13 Nov 2017 13:17:15: 14000000 INFO @ Mon, 13 Nov 2017 13:17:18: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:18: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:18: #1 total tags in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:18: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:18: #1 tags after filtering in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:18: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:18: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:19: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:17:19: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:19: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:20: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:20: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:20: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:20: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:17:20: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:17:20: #2.2 Generate R script for model : SRX2576626.10_model.r INFO @ Mon, 13 Nov 2017 13:17:20: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:20: 14000000 INFO @ Mon, 13 Nov 2017 13:17:22: 14000000 INFO @ Mon, 13 Nov 2017 13:17:23: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:23: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:23: #1 total tags in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:23: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:23: #1 tags after filtering in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:23: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:23: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:24: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:17:24: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:24: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:24: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:24: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:24: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:24: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:17:24: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:17:24: #2.2 Generate R script for model : SRX2576626.05_model.r INFO @ Mon, 13 Nov 2017 13:17:24: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:25: #1 tag size is determined as 35 bps INFO @ Mon, 13 Nov 2017 13:17:25: #1 tag size = 35 INFO @ Mon, 13 Nov 2017 13:17:25: #1 total tags in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:25: #1 user defined the maximum tags... INFO @ Mon, 13 Nov 2017 13:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 13 Nov 2017 13:17:25: #1 tags after filtering in treatment: 14386918 INFO @ Mon, 13 Nov 2017 13:17:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 13 Nov 2017 13:17:25: #1 finished! INFO @ Mon, 13 Nov 2017 13:17:25: #2 Build Peak Model... INFO @ Mon, 13 Nov 2017 13:17:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 13 Nov 2017 13:17:26: #2 number of paired peaks: 487 WARNING @ Mon, 13 Nov 2017 13:17:26: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Mon, 13 Nov 2017 13:17:26: start model_add_line... INFO @ Mon, 13 Nov 2017 13:17:26: start X-correlation... INFO @ Mon, 13 Nov 2017 13:17:26: end of X-cor INFO @ Mon, 13 Nov 2017 13:17:26: #2 finished! INFO @ Mon, 13 Nov 2017 13:17:26: #2 predicted fragment length is 132 bps INFO @ Mon, 13 Nov 2017 13:17:26: #2 alternative fragment length(s) may be 132 bps INFO @ Mon, 13 Nov 2017 13:17:26: #2.2 Generate R script for model : SRX2576626.20_model.r INFO @ Mon, 13 Nov 2017 13:17:26: #3 Call peaks... INFO @ Mon, 13 Nov 2017 13:17:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 13 Nov 2017 13:17:50: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:58: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:17:58: #3 Call peaks for each chromosome... INFO @ Mon, 13 Nov 2017 13:18:08: #4 Write output xls file... SRX2576626.10_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:08: #4 Write peak in narrowPeak format file... SRX2576626.10_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:08: #4 Write summits bed file... SRX2576626.10_summits.bed INFO @ Mon, 13 Nov 2017 13:18:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1804 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:15: #4 Write output xls file... SRX2576626.05_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:15: #4 Write peak in narrowPeak format file... SRX2576626.05_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:15: #4 Write summits bed file... SRX2576626.05_summits.bed INFO @ Mon, 13 Nov 2017 13:18:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2512 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 13 Nov 2017 13:18:16: #4 Write output xls file... SRX2576626.20_peaks.xls INFO @ Mon, 13 Nov 2017 13:18:16: #4 Write peak in narrowPeak format file... SRX2576626.20_peaks.narrowPeak INFO @ Mon, 13 Nov 2017 13:18:16: #4 Write summits bed file... SRX2576626.20_summits.bed INFO @ Mon, 13 Nov 2017 13:18:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1245 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。