Job ID = 11171223 sra ファイルのダウンロード中... Completed: 307842K bytes transferred in 14 seconds (170740K 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 14834287 spots for /home/okishinya/chipatlas/results/dm3/SRX2618531/SRR5319085.sra Written 14834287 spots for /home/okishinya/chipatlas/results/dm3/SRX2618531/SRR5319085.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: 00:05:40 14834287 reads; of these: 14834287 (100.00%) were unpaired; of these: 786733 (5.30%) aligned 0 times 10544326 (71.08%) aligned exactly 1 time 3503228 (23.62%) aligned >1 times 94.70% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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 8 files... [bam_rmdupse_core] 1371958 / 14047554 = 0.0977 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, 08 Sep 2018 13:13:15: # Command line: callpeak -t SRX2618531.bam -f BAM -g dm -n SRX2618531.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618531.20 # format = BAM # ChIP-seq file = ['SRX2618531.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 @ Sat, 08 Sep 2018 13:13:15: # Command line: callpeak -t SRX2618531.bam -f BAM -g dm -n SRX2618531.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618531.10 # format = BAM # ChIP-seq file = ['SRX2618531.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 @ Sat, 08 Sep 2018 13:13:15: # Command line: callpeak -t SRX2618531.bam -f BAM -g dm -n SRX2618531.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618531.05 # format = BAM # ChIP-seq file = ['SRX2618531.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 @ Sat, 08 Sep 2018 13:13:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:13:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:13:15: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:13:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:13:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:13:15: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:13:21: 1000000 INFO @ Sat, 08 Sep 2018 13:13:21: 1000000 INFO @ Sat, 08 Sep 2018 13:13:21: 1000000 INFO @ Sat, 08 Sep 2018 13:13:28: 2000000 INFO @ Sat, 08 Sep 2018 13:13:28: 2000000 INFO @ Sat, 08 Sep 2018 13:13:28: 2000000 INFO @ Sat, 08 Sep 2018 13:13:34: 3000000 INFO @ Sat, 08 Sep 2018 13:13:35: 3000000 INFO @ Sat, 08 Sep 2018 13:13:36: 3000000 INFO @ Sat, 08 Sep 2018 13:13:41: 4000000 INFO @ Sat, 08 Sep 2018 13:13:41: 4000000 INFO @ Sat, 08 Sep 2018 13:13:43: 4000000 INFO @ Sat, 08 Sep 2018 13:13:47: 5000000 INFO @ Sat, 08 Sep 2018 13:13:48: 5000000 INFO @ Sat, 08 Sep 2018 13:13:50: 5000000 INFO @ Sat, 08 Sep 2018 13:13:53: 6000000 INFO @ Sat, 08 Sep 2018 13:13:55: 6000000 INFO @ Sat, 08 Sep 2018 13:13:57: 6000000 INFO @ Sat, 08 Sep 2018 13:14:00: 7000000 INFO @ Sat, 08 Sep 2018 13:14:01: 7000000 INFO @ Sat, 08 Sep 2018 13:14:04: 7000000 INFO @ Sat, 08 Sep 2018 13:14:07: 8000000 INFO @ Sat, 08 Sep 2018 13:14:07: 8000000 INFO @ Sat, 08 Sep 2018 13:14:11: 8000000 INFO @ Sat, 08 Sep 2018 13:14:14: 9000000 INFO @ Sat, 08 Sep 2018 13:14:14: 9000000 INFO @ Sat, 08 Sep 2018 13:14:18: 9000000 INFO @ Sat, 08 Sep 2018 13:14:20: 10000000 INFO @ Sat, 08 Sep 2018 13:14:21: 10000000 INFO @ Sat, 08 Sep 2018 13:14:25: 10000000 INFO @ Sat, 08 Sep 2018 13:14:26: 11000000 INFO @ Sat, 08 Sep 2018 13:14:28: 11000000 INFO @ Sat, 08 Sep 2018 13:14:32: 11000000 INFO @ Sat, 08 Sep 2018 13:14:33: 12000000 INFO @ Sat, 08 Sep 2018 13:14:35: 12000000 INFO @ Sat, 08 Sep 2018 13:14:37: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:14:37: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:14:37: #1 total tags in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:37: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:14:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:14:37: #1 tags after filtering in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:14:37: #1 finished! INFO @ Sat, 08 Sep 2018 13:14:37: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:14:38: #2 number of paired peaks: 250 WARNING @ Sat, 08 Sep 2018 13:14:38: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 08 Sep 2018 13:14:38: start model_add_line... INFO @ Sat, 08 Sep 2018 13:14:39: start X-correlation... INFO @ Sat, 08 Sep 2018 13:14:39: end of X-cor INFO @ Sat, 08 Sep 2018 13:14:39: #2 finished! INFO @ Sat, 08 Sep 2018 13:14:39: #2 predicted fragment length is 137 bps INFO @ Sat, 08 Sep 2018 13:14:39: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 08 Sep 2018 13:14:39: #2.2 Generate R script for model : SRX2618531.05_model.r INFO @ Sat, 08 Sep 2018 13:14:39: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:14:39: 12000000 INFO @ Sat, 08 Sep 2018 13:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:14:40: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:14:40: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:14:40: #1 total tags in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:40: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:14:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:14:40: #1 tags after filtering in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:14:40: #1 finished! INFO @ Sat, 08 Sep 2018 13:14:40: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:14:41: #2 number of paired peaks: 250 WARNING @ Sat, 08 Sep 2018 13:14:41: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 08 Sep 2018 13:14:41: start model_add_line... INFO @ Sat, 08 Sep 2018 13:14:41: start X-correlation... INFO @ Sat, 08 Sep 2018 13:14:41: end of X-cor INFO @ Sat, 08 Sep 2018 13:14:41: #2 finished! INFO @ Sat, 08 Sep 2018 13:14:41: #2 predicted fragment length is 137 bps INFO @ Sat, 08 Sep 2018 13:14:41: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 08 Sep 2018 13:14:41: #2.2 Generate R script for model : SRX2618531.20_model.r INFO @ Sat, 08 Sep 2018 13:14:41: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:14:43: #1 tag size is determined as 49 bps INFO @ Sat, 08 Sep 2018 13:14:43: #1 tag size = 49 INFO @ Sat, 08 Sep 2018 13:14:43: #1 total tags in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:43: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:14:44: #1 tags after filtering in treatment: 12675596 INFO @ Sat, 08 Sep 2018 13:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:14:44: #1 finished! INFO @ Sat, 08 Sep 2018 13:14:44: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:14:44: #2 number of paired peaks: 250 WARNING @ Sat, 08 Sep 2018 13:14:44: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 08 Sep 2018 13:14:44: start model_add_line... INFO @ Sat, 08 Sep 2018 13:14:45: start X-correlation... INFO @ Sat, 08 Sep 2018 13:14:45: end of X-cor INFO @ Sat, 08 Sep 2018 13:14:45: #2 finished! INFO @ Sat, 08 Sep 2018 13:14:45: #2 predicted fragment length is 137 bps INFO @ Sat, 08 Sep 2018 13:14:45: #2 alternative fragment length(s) may be 137 bps INFO @ Sat, 08 Sep 2018 13:14:45: #2.2 Generate R script for model : SRX2618531.10_model.r INFO @ Sat, 08 Sep 2018 13:14:45: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:15:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:15:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:15:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:15:24: #4 Write output xls file... SRX2618531.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:15:24: #4 Write peak in narrowPeak format file... SRX2618531.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:15:24: #4 Write summits bed file... SRX2618531.05_summits.bed INFO @ Sat, 08 Sep 2018 13:15:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5187 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:15:27: #4 Write output xls file... SRX2618531.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:15:27: #4 Write peak in narrowPeak format file... SRX2618531.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:15:27: #4 Write summits bed file... SRX2618531.20_summits.bed INFO @ Sat, 08 Sep 2018 13:15:27: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1003 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:15:30: #4 Write output xls file... SRX2618531.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:15:30: #4 Write peak in narrowPeak format file... SRX2618531.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:15:30: #4 Write summits bed file... SRX2618531.10_summits.bed INFO @ Sat, 08 Sep 2018 13:15:30: Done! pass1 - making usageList (12 chroms): 212 millis pass2 - checking and writing primary data (2623 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。