Job ID = 11240733 sra ファイルのダウンロード中... Completed: 670054K bytes transferred in 20 seconds (268537K 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 37549684 spots for /home/okishinya/chipatlas/results/dm3/SRX4669017/SRR7817542.sra Written 37549684 spots for /home/okishinya/chipatlas/results/dm3/SRX4669017/SRR7817542.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: 00:10:05 37549684 reads; of these: 37549684 (100.00%) were unpaired; of these: 4304830 (11.46%) aligned 0 times 26550894 (70.71%) aligned exactly 1 time 6693960 (17.83%) aligned >1 times 88.54% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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 16 files... [bam_rmdupse_core] 21853919 / 33244854 = 0.6574 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 20:46:47: # Command line: callpeak -t SRX4669017.bam -f BAM -g dm -n SRX4669017.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669017.05 # format = BAM # ChIP-seq file = ['SRX4669017.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 20:46:47: # Command line: callpeak -t SRX4669017.bam -f BAM -g dm -n SRX4669017.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669017.10 # format = BAM # ChIP-seq file = ['SRX4669017.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 20:46:47: # Command line: callpeak -t SRX4669017.bam -f BAM -g dm -n SRX4669017.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669017.20 # format = BAM # ChIP-seq file = ['SRX4669017.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 20:46:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:46:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:46:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:46:53: 1000000 INFO @ Sun, 07 Oct 2018 20:46:53: 1000000 INFO @ Sun, 07 Oct 2018 20:46:53: 1000000 INFO @ Sun, 07 Oct 2018 20:46:59: 2000000 INFO @ Sun, 07 Oct 2018 20:46:59: 2000000 INFO @ Sun, 07 Oct 2018 20:46:59: 2000000 INFO @ Sun, 07 Oct 2018 20:47:05: 3000000 INFO @ Sun, 07 Oct 2018 20:47:05: 3000000 INFO @ Sun, 07 Oct 2018 20:47:05: 3000000 INFO @ Sun, 07 Oct 2018 20:47:10: 4000000 INFO @ Sun, 07 Oct 2018 20:47:11: 4000000 INFO @ Sun, 07 Oct 2018 20:47:11: 4000000 INFO @ Sun, 07 Oct 2018 20:47:16: 5000000 INFO @ Sun, 07 Oct 2018 20:47:17: 5000000 INFO @ Sun, 07 Oct 2018 20:47:17: 5000000 INFO @ Sun, 07 Oct 2018 20:47:22: 6000000 INFO @ Sun, 07 Oct 2018 20:47:23: 6000000 INFO @ Sun, 07 Oct 2018 20:47:23: 6000000 INFO @ Sun, 07 Oct 2018 20:47:28: 7000000 INFO @ Sun, 07 Oct 2018 20:47:28: 7000000 INFO @ Sun, 07 Oct 2018 20:47:29: 7000000 INFO @ Sun, 07 Oct 2018 20:47:34: 8000000 INFO @ Sun, 07 Oct 2018 20:47:34: 8000000 INFO @ Sun, 07 Oct 2018 20:47:35: 8000000 INFO @ Sun, 07 Oct 2018 20:47:39: 9000000 INFO @ Sun, 07 Oct 2018 20:47:40: 9000000 INFO @ Sun, 07 Oct 2018 20:47:41: 9000000 INFO @ Sun, 07 Oct 2018 20:47:45: 10000000 INFO @ Sun, 07 Oct 2018 20:47:46: 10000000 INFO @ Sun, 07 Oct 2018 20:47:47: 10000000 INFO @ Sun, 07 Oct 2018 20:47:51: 11000000 INFO @ Sun, 07 Oct 2018 20:47:52: 11000000 INFO @ Sun, 07 Oct 2018 20:47:53: 11000000 INFO @ Sun, 07 Oct 2018 20:47:53: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:53: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:53: #1 total tags in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:53: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:53: #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 20:47:54: #1 tags after filtering in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:54: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:54: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:55: #2 number of paired peaks: 938 WARNING @ Sun, 07 Oct 2018 20:47:55: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:55: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:55: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:55: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:55: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:55: #2 predicted fragment length is 145 bps INFO @ Sun, 07 Oct 2018 20:47:55: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 07 Oct 2018 20:47:55: #2.2 Generate R script for model : SRX4669017.20_model.r INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:55: #1 total tags in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:55: #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 20:47:55: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:55: #1 tags after filtering in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:55: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:55: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:55: #1 total tags in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:55: #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 20:47:56: #1 tags after filtering in treatment: 11390935 INFO @ Sun, 07 Oct 2018 20:47:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:56: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:56: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:56: #2 number of paired peaks: 938 WARNING @ Sun, 07 Oct 2018 20:47:56: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:56: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:56: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:56: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:56: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:56: #2 predicted fragment length is 145 bps INFO @ Sun, 07 Oct 2018 20:47:56: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 07 Oct 2018 20:47:56: #2.2 Generate R script for model : SRX4669017.10_model.r INFO @ Sun, 07 Oct 2018 20:47:56: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:56: #2 number of paired peaks: 938 WARNING @ Sun, 07 Oct 2018 20:47:56: Fewer paired peaks (938) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 938 pairs to build model! INFO @ Sun, 07 Oct 2018 20:47:56: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:57: #2 predicted fragment length is 145 bps INFO @ Sun, 07 Oct 2018 20:47:57: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 07 Oct 2018 20:47:57: #2.2 Generate R script for model : SRX4669017.05_model.r INFO @ Sun, 07 Oct 2018 20:47:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:24: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:25: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:39: #4 Write output xls file... SRX4669017.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:39: #4 Write peak in narrowPeak format file... SRX4669017.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:39: #4 Write summits bed file... SRX4669017.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4627 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write output xls file... SRX4669017.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write peak in narrowPeak format file... SRX4669017.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:40: #4 Write summits bed file... SRX4669017.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1414 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:43: #4 Write output xls file... SRX4669017.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:43: #4 Write peak in narrowPeak format file... SRX4669017.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:44: #4 Write summits bed file... SRX4669017.05_summits.bed INFO @ Sun, 07 Oct 2018 20:48:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11014 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。