Job ID = 11240741 sra ファイルのダウンロード中... Completed: 442812K bytes transferred in 18 seconds (195548K 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 27021626 spots for /home/okishinya/chipatlas/results/dm3/SRX4669025/SRR7817550.sra Written 27021626 spots for /home/okishinya/chipatlas/results/dm3/SRX4669025/SRR7817550.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:49 27021626 reads; of these: 27021626 (100.00%) were unpaired; of these: 4565016 (16.89%) aligned 0 times 20388487 (75.45%) aligned exactly 1 time 2068123 (7.65%) aligned >1 times 83.11% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 11792573 / 22456610 = 0.5251 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 20:41:37: # Command line: callpeak -t SRX4669025.bam -f BAM -g dm -n SRX4669025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669025.05 # format = BAM # ChIP-seq file = ['SRX4669025.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 20:41:37: # Command line: callpeak -t SRX4669025.bam -f BAM -g dm -n SRX4669025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669025.20 # format = BAM # ChIP-seq file = ['SRX4669025.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 20:41:37: # Command line: callpeak -t SRX4669025.bam -f BAM -g dm -n SRX4669025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669025.10 # format = BAM # ChIP-seq file = ['SRX4669025.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 20:41:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:37: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:41:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:37: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:41:44: 1000000 INFO @ Sun, 07 Oct 2018 20:41:44: 1000000 INFO @ Sun, 07 Oct 2018 20:41:44: 1000000 INFO @ Sun, 07 Oct 2018 20:41:49: 2000000 INFO @ Sun, 07 Oct 2018 20:41:50: 2000000 INFO @ Sun, 07 Oct 2018 20:41:50: 2000000 INFO @ Sun, 07 Oct 2018 20:41:55: 3000000 INFO @ Sun, 07 Oct 2018 20:41:56: 3000000 INFO @ Sun, 07 Oct 2018 20:41:56: 3000000 INFO @ Sun, 07 Oct 2018 20:42:01: 4000000 INFO @ Sun, 07 Oct 2018 20:42:02: 4000000 INFO @ Sun, 07 Oct 2018 20:42:02: 4000000 INFO @ Sun, 07 Oct 2018 20:42:07: 5000000 INFO @ Sun, 07 Oct 2018 20:42:08: 5000000 INFO @ Sun, 07 Oct 2018 20:42:08: 5000000 INFO @ Sun, 07 Oct 2018 20:42:12: 6000000 INFO @ Sun, 07 Oct 2018 20:42:14: 6000000 INFO @ Sun, 07 Oct 2018 20:42:14: 6000000 INFO @ Sun, 07 Oct 2018 20:42:18: 7000000 INFO @ Sun, 07 Oct 2018 20:42:20: 7000000 INFO @ Sun, 07 Oct 2018 20:42:20: 7000000 INFO @ Sun, 07 Oct 2018 20:42:24: 8000000 INFO @ Sun, 07 Oct 2018 20:42:26: 8000000 INFO @ Sun, 07 Oct 2018 20:42:26: 8000000 INFO @ Sun, 07 Oct 2018 20:42:29: 9000000 INFO @ Sun, 07 Oct 2018 20:42:32: 9000000 INFO @ Sun, 07 Oct 2018 20:42:33: 9000000 INFO @ Sun, 07 Oct 2018 20:42:35: 10000000 INFO @ Sun, 07 Oct 2018 20:42:39: 10000000 INFO @ Sun, 07 Oct 2018 20:42:39: 10000000 INFO @ Sun, 07 Oct 2018 20:42:39: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:42:39: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:42:39: #1 total tags in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:39: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:42:39: #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 20:42:39: #1 tags after filtering in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:42:39: #1 finished! INFO @ Sun, 07 Oct 2018 20:42:39: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:42:40: #2 number of paired peaks: 987 WARNING @ Sun, 07 Oct 2018 20:42:40: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 07 Oct 2018 20:42:40: start model_add_line... INFO @ Sun, 07 Oct 2018 20:42:40: start X-correlation... INFO @ Sun, 07 Oct 2018 20:42:41: end of X-cor INFO @ Sun, 07 Oct 2018 20:42:41: #2 finished! INFO @ Sun, 07 Oct 2018 20:42:41: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:42:41: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:42:41: #2.2 Generate R script for model : SRX4669025.10_model.r INFO @ Sun, 07 Oct 2018 20:42:41: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:42:43: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:42:43: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:42:43: #1 total tags in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:43: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:42:43: #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 20:42:43: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:42:43: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:42:43: #1 total tags in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:43: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:42:43: #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 20:42:43: #1 tags after filtering in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:42:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:42:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:42:43: #1 tags after filtering in treatment: 10664037 INFO @ Sun, 07 Oct 2018 20:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:42:43: #1 finished! INFO @ Sun, 07 Oct 2018 20:42:43: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:42:44: #2 number of paired peaks: 987 WARNING @ Sun, 07 Oct 2018 20:42:44: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 07 Oct 2018 20:42:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:42:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:42:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:42:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:42:44: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:42:44: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:42:44: #2.2 Generate R script for model : SRX4669025.20_model.r INFO @ Sun, 07 Oct 2018 20:42:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:42:44: #2 number of paired peaks: 987 WARNING @ Sun, 07 Oct 2018 20:42:44: Fewer paired peaks (987) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 987 pairs to build model! INFO @ Sun, 07 Oct 2018 20:42:44: start model_add_line... INFO @ Sun, 07 Oct 2018 20:42:44: start X-correlation... INFO @ Sun, 07 Oct 2018 20:42:44: end of X-cor INFO @ Sun, 07 Oct 2018 20:42:44: #2 finished! INFO @ Sun, 07 Oct 2018 20:42:44: #2 predicted fragment length is 118 bps INFO @ Sun, 07 Oct 2018 20:42:44: #2 alternative fragment length(s) may be 118 bps INFO @ Sun, 07 Oct 2018 20:42:44: #2.2 Generate R script for model : SRX4669025.05_model.r INFO @ Sun, 07 Oct 2018 20:42:44: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:43:05: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:08: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:11: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:43:18: #4 Write output xls file... SRX4669025.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:19: #4 Write peak in narrowPeak format file... SRX4669025.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:19: #4 Write summits bed file... SRX4669025.10_summits.bed INFO @ Sun, 07 Oct 2018 20:43:19: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6341 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write output xls file... SRX4669025.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write peak in narrowPeak format file... SRX4669025.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:22: #4 Write summits bed file... SRX4669025.20_summits.bed INFO @ Sun, 07 Oct 2018 20:43:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2824 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:43:26: #4 Write output xls file... SRX4669025.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:43:26: #4 Write peak in narrowPeak format file... SRX4669025.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:43:26: #4 Write summits bed file... SRX4669025.05_summits.bed INFO @ Sun, 07 Oct 2018 20:43:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10147 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。