Job ID = 11240739 sra ファイルのダウンロード中... Completed: 455977K bytes transferred in 18 seconds (196860K 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 24654445 spots for /home/okishinya/chipatlas/results/dm3/SRX4669023/SRR7817548.sra Written 24654445 spots for /home/okishinya/chipatlas/results/dm3/SRX4669023/SRR7817548.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 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: 00:07:28 24654445 reads; of these: 24654445 (100.00%) were unpaired; of these: 2465103 (10.00%) aligned 0 times 15856175 (64.31%) aligned exactly 1 time 6333167 (25.69%) aligned >1 times 90.00% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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 12 files... [bam_rmdupse_core] 10646136 / 22189342 = 0.4798 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, 07 Oct 2018 20:42:09: # Command line: callpeak -t SRX4669023.bam -f BAM -g dm -n SRX4669023.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669023.10 # format = BAM # ChIP-seq file = ['SRX4669023.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 @ Sun, 07 Oct 2018 20:42:09: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:09: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:42:09: # Command line: callpeak -t SRX4669023.bam -f BAM -g dm -n SRX4669023.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669023.05 # format = BAM # ChIP-seq file = ['SRX4669023.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 @ Sun, 07 Oct 2018 20:42:09: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:09: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:42:09: # Command line: callpeak -t SRX4669023.bam -f BAM -g dm -n SRX4669023.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669023.20 # format = BAM # ChIP-seq file = ['SRX4669023.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 @ Sun, 07 Oct 2018 20:42:09: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:42:09: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:42:16: 1000000 INFO @ Sun, 07 Oct 2018 20:42:16: 1000000 INFO @ Sun, 07 Oct 2018 20:42:16: 1000000 INFO @ Sun, 07 Oct 2018 20:42:22: 2000000 INFO @ Sun, 07 Oct 2018 20:42:22: 2000000 INFO @ Sun, 07 Oct 2018 20:42:23: 2000000 INFO @ Sun, 07 Oct 2018 20:42:28: 3000000 INFO @ Sun, 07 Oct 2018 20:42:28: 3000000 INFO @ Sun, 07 Oct 2018 20:42:30: 3000000 INFO @ Sun, 07 Oct 2018 20:42:35: 4000000 INFO @ Sun, 07 Oct 2018 20:42:35: 4000000 INFO @ Sun, 07 Oct 2018 20:42:37: 4000000 INFO @ Sun, 07 Oct 2018 20:42:41: 5000000 INFO @ Sun, 07 Oct 2018 20:42:41: 5000000 INFO @ Sun, 07 Oct 2018 20:42:44: 5000000 INFO @ Sun, 07 Oct 2018 20:42:47: 6000000 INFO @ Sun, 07 Oct 2018 20:42:47: 6000000 INFO @ Sun, 07 Oct 2018 20:42:51: 6000000 INFO @ Sun, 07 Oct 2018 20:42:53: 7000000 INFO @ Sun, 07 Oct 2018 20:42:53: 7000000 INFO @ Sun, 07 Oct 2018 20:42:58: 7000000 INFO @ Sun, 07 Oct 2018 20:42:58: 8000000 INFO @ Sun, 07 Oct 2018 20:42:59: 8000000 INFO @ Sun, 07 Oct 2018 20:43:04: 9000000 INFO @ Sun, 07 Oct 2018 20:43:05: 9000000 INFO @ Sun, 07 Oct 2018 20:43:05: 8000000 INFO @ Sun, 07 Oct 2018 20:43:10: 10000000 INFO @ Sun, 07 Oct 2018 20:43:11: 10000000 INFO @ Sun, 07 Oct 2018 20:43:11: 9000000 INFO @ Sun, 07 Oct 2018 20:43:16: 11000000 INFO @ Sun, 07 Oct 2018 20:43:16: 11000000 INFO @ Sun, 07 Oct 2018 20:43:17: 10000000 INFO @ Sun, 07 Oct 2018 20:43:19: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:43:19: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:43:19: #1 total tags in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:19: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:19: #1 tags after filtering in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:19: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:19: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:20: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:43:20: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:43:20: #1 total tags in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:20: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:20: #1 tags after filtering in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:20: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:20: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:20: #2 number of paired peaks: 963 WARNING @ Sun, 07 Oct 2018 20:43:20: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 07 Oct 2018 20:43:20: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:21: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:21: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:21: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:21: #2 predicted fragment length is 107 bps INFO @ Sun, 07 Oct 2018 20:43:21: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 07 Oct 2018 20:43:21: #2.2 Generate R script for model : SRX4669023.10_model.r INFO @ Sun, 07 Oct 2018 20:43:21: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:21: #2 number of paired peaks: 963 WARNING @ Sun, 07 Oct 2018 20:43:21: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 07 Oct 2018 20:43:21: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:21: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:21: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:21: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:21: #2 predicted fragment length is 107 bps INFO @ Sun, 07 Oct 2018 20:43:21: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 07 Oct 2018 20:43:21: #2.2 Generate R script for model : SRX4669023.05_model.r INFO @ Sun, 07 Oct 2018 20:43:21: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:22: 11000000 INFO @ Sun, 07 Oct 2018 20:43:25: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:43:25: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:43:25: #1 total tags in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:25: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:43:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:43:26: #1 tags after filtering in treatment: 11543206 INFO @ Sun, 07 Oct 2018 20:43:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:43:26: #1 finished! INFO @ Sun, 07 Oct 2018 20:43:26: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:43:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:43:27: #2 number of paired peaks: 963 WARNING @ Sun, 07 Oct 2018 20:43:27: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sun, 07 Oct 2018 20:43:27: start model_add_line... INFO @ Sun, 07 Oct 2018 20:43:27: start X-correlation... INFO @ Sun, 07 Oct 2018 20:43:27: end of X-cor INFO @ Sun, 07 Oct 2018 20:43:27: #2 finished! INFO @ Sun, 07 Oct 2018 20:43:27: #2 predicted fragment length is 107 bps INFO @ Sun, 07 Oct 2018 20:43:27: #2 alternative fragment length(s) may be 4,107 bps INFO @ Sun, 07 Oct 2018 20:43:27: #2.2 Generate R script for model : SRX4669023.20_model.r INFO @ Sun, 07 Oct 2018 20:43:27: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:47: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:50: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:57: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:44:04: #4 Write output xls file... SRX4669023.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:04: #4 Write peak in narrowPeak format file... SRX4669023.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:04: #4 Write summits bed file... SRX4669023.05_summits.bed INFO @ Sun, 07 Oct 2018 20:44:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6305 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:44:07: #4 Write output xls file... SRX4669023.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:07: #4 Write peak in narrowPeak format file... SRX4669023.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:07: #4 Write summits bed file... SRX4669023.10_summits.bed INFO @ Sun, 07 Oct 2018 20:44:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3076 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:44:13: #4 Write output xls file... SRX4669023.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:44:13: #4 Write peak in narrowPeak format file... SRX4669023.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:44:13: #4 Write summits bed file... SRX4669023.20_summits.bed INFO @ Sun, 07 Oct 2018 20:44:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。