Job ID = 10450722 sra ファイルのダウンロード中... Completed: 519453K bytes transferred in 32 seconds (131668K 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 27442936 spots for /home/okishinya/chipatlas/results/dm3/SRX3404014/SRR6303491.sra Written 27442936 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:43 27442936 reads; of these: 27442936 (100.00%) were unpaired; of these: 710173 (2.59%) aligned 0 times 19134586 (69.72%) aligned exactly 1 time 7598177 (27.69%) aligned >1 times 97.41% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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] 3222838 / 26732763 = 0.1206 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 @ Wed, 07 Feb 2018 12:01:31: # Command line: callpeak -t SRX3404014.bam -f BAM -g dm -n SRX3404014.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404014.05 # format = BAM # ChIP-seq file = ['SRX3404014.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 @ Wed, 07 Feb 2018 12:01:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:01:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:01:31: # Command line: callpeak -t SRX3404014.bam -f BAM -g dm -n SRX3404014.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404014.20 # format = BAM # ChIP-seq file = ['SRX3404014.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 @ Wed, 07 Feb 2018 12:01:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:01:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:01:31: # Command line: callpeak -t SRX3404014.bam -f BAM -g dm -n SRX3404014.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404014.10 # format = BAM # ChIP-seq file = ['SRX3404014.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 @ Wed, 07 Feb 2018 12:01:31: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:01:31: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:01:37: 1000000 INFO @ Wed, 07 Feb 2018 12:01:37: 1000000 INFO @ Wed, 07 Feb 2018 12:01:38: 1000000 INFO @ Wed, 07 Feb 2018 12:01:44: 2000000 INFO @ Wed, 07 Feb 2018 12:01:44: 2000000 INFO @ Wed, 07 Feb 2018 12:01:45: 2000000 INFO @ Wed, 07 Feb 2018 12:01:51: 3000000 INFO @ Wed, 07 Feb 2018 12:01:52: 3000000 INFO @ Wed, 07 Feb 2018 12:01:52: 3000000 INFO @ Wed, 07 Feb 2018 12:01:58: 4000000 INFO @ Wed, 07 Feb 2018 12:01:59: 4000000 INFO @ Wed, 07 Feb 2018 12:01:59: 4000000 INFO @ Wed, 07 Feb 2018 12:02:06: 5000000 INFO @ Wed, 07 Feb 2018 12:02:06: 5000000 INFO @ Wed, 07 Feb 2018 12:02:07: 5000000 INFO @ Wed, 07 Feb 2018 12:02:13: 6000000 INFO @ Wed, 07 Feb 2018 12:02:13: 6000000 INFO @ Wed, 07 Feb 2018 12:02:15: 6000000 INFO @ Wed, 07 Feb 2018 12:02:20: 7000000 INFO @ Wed, 07 Feb 2018 12:02:21: 7000000 INFO @ Wed, 07 Feb 2018 12:02:22: 7000000 INFO @ Wed, 07 Feb 2018 12:02:28: 8000000 INFO @ Wed, 07 Feb 2018 12:02:28: 8000000 INFO @ Wed, 07 Feb 2018 12:02:30: 8000000 INFO @ Wed, 07 Feb 2018 12:02:35: 9000000 INFO @ Wed, 07 Feb 2018 12:02:36: 9000000 INFO @ Wed, 07 Feb 2018 12:02:37: 9000000 INFO @ Wed, 07 Feb 2018 12:02:42: 10000000 INFO @ Wed, 07 Feb 2018 12:02:43: 10000000 INFO @ Wed, 07 Feb 2018 12:02:45: 10000000 INFO @ Wed, 07 Feb 2018 12:02:50: 11000000 INFO @ Wed, 07 Feb 2018 12:02:51: 11000000 INFO @ Wed, 07 Feb 2018 12:02:53: 11000000 INFO @ Wed, 07 Feb 2018 12:02:57: 12000000 INFO @ Wed, 07 Feb 2018 12:02:58: 12000000 INFO @ Wed, 07 Feb 2018 12:03:00: 12000000 INFO @ Wed, 07 Feb 2018 12:03:04: 13000000 INFO @ Wed, 07 Feb 2018 12:03:06: 13000000 INFO @ Wed, 07 Feb 2018 12:03:08: 13000000 INFO @ Wed, 07 Feb 2018 12:03:12: 14000000 INFO @ Wed, 07 Feb 2018 12:03:13: 14000000 INFO @ Wed, 07 Feb 2018 12:03:15: 14000000 INFO @ Wed, 07 Feb 2018 12:03:19: 15000000 INFO @ Wed, 07 Feb 2018 12:03:21: 15000000 INFO @ Wed, 07 Feb 2018 12:03:23: 15000000 INFO @ Wed, 07 Feb 2018 12:03:26: 16000000 INFO @ Wed, 07 Feb 2018 12:03:28: 16000000 INFO @ Wed, 07 Feb 2018 12:03:30: 16000000 INFO @ Wed, 07 Feb 2018 12:03:33: 17000000 INFO @ Wed, 07 Feb 2018 12:03:35: 17000000 INFO @ Wed, 07 Feb 2018 12:03:38: 17000000 INFO @ Wed, 07 Feb 2018 12:03:41: 18000000 INFO @ Wed, 07 Feb 2018 12:03:43: 18000000 INFO @ Wed, 07 Feb 2018 12:03:45: 18000000 INFO @ Wed, 07 Feb 2018 12:03:48: 19000000 INFO @ Wed, 07 Feb 2018 12:03:50: 19000000 INFO @ Wed, 07 Feb 2018 12:03:53: 19000000 INFO @ Wed, 07 Feb 2018 12:03:55: 20000000 INFO @ Wed, 07 Feb 2018 12:03:58: 20000000 INFO @ Wed, 07 Feb 2018 12:04:00: 20000000 INFO @ Wed, 07 Feb 2018 12:04:02: 21000000 INFO @ Wed, 07 Feb 2018 12:04:05: 21000000 INFO @ Wed, 07 Feb 2018 12:04:08: 21000000 INFO @ Wed, 07 Feb 2018 12:04:10: 22000000 INFO @ Wed, 07 Feb 2018 12:04:13: 22000000 INFO @ Wed, 07 Feb 2018 12:04:16: 22000000 INFO @ Wed, 07 Feb 2018 12:04:17: 23000000 INFO @ Wed, 07 Feb 2018 12:04:20: 23000000 INFO @ Wed, 07 Feb 2018 12:04:21: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:04:21: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:04:21: #1 total tags in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:21: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:04:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:04:21: #1 tags after filtering in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:21: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:04:21: #1 finished! INFO @ Wed, 07 Feb 2018 12:04:21: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:04:23: 23000000 INFO @ Wed, 07 Feb 2018 12:04:23: #2 number of paired peaks: 323 WARNING @ Wed, 07 Feb 2018 12:04:23: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Wed, 07 Feb 2018 12:04:23: start model_add_line... INFO @ Wed, 07 Feb 2018 12:04:23: start X-correlation... INFO @ Wed, 07 Feb 2018 12:04:23: end of X-cor INFO @ Wed, 07 Feb 2018 12:04:23: #2 finished! INFO @ Wed, 07 Feb 2018 12:04:23: #2 predicted fragment length is 113 bps INFO @ Wed, 07 Feb 2018 12:04:23: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 07 Feb 2018 12:04:23: #2.2 Generate R script for model : SRX3404014.20_model.r INFO @ Wed, 07 Feb 2018 12:04:23: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:04:24: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:04:24: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:04:24: #1 total tags in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:24: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:04:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:04:24: #1 tags after filtering in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:04:24: #1 finished! INFO @ Wed, 07 Feb 2018 12:04:24: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:04:26: #2 number of paired peaks: 323 WARNING @ Wed, 07 Feb 2018 12:04:26: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Wed, 07 Feb 2018 12:04:26: start model_add_line... INFO @ Wed, 07 Feb 2018 12:04:26: start X-correlation... INFO @ Wed, 07 Feb 2018 12:04:26: end of X-cor INFO @ Wed, 07 Feb 2018 12:04:26: #2 finished! INFO @ Wed, 07 Feb 2018 12:04:26: #2 predicted fragment length is 113 bps INFO @ Wed, 07 Feb 2018 12:04:26: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 07 Feb 2018 12:04:26: #2.2 Generate R script for model : SRX3404014.05_model.r INFO @ Wed, 07 Feb 2018 12:04:26: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:04:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:04:26: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:04:26: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:04:26: #1 total tags in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:26: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:04:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 12:04:27: #1 tags after filtering in treatment: 23509925 INFO @ Wed, 07 Feb 2018 12:04:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:04:27: #1 finished! INFO @ Wed, 07 Feb 2018 12:04:27: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:04:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:04:28: #2 number of paired peaks: 323 WARNING @ Wed, 07 Feb 2018 12:04:28: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Wed, 07 Feb 2018 12:04:28: start model_add_line... INFO @ Wed, 07 Feb 2018 12:04:29: start X-correlation... INFO @ Wed, 07 Feb 2018 12:04:29: end of X-cor INFO @ Wed, 07 Feb 2018 12:04:29: #2 finished! INFO @ Wed, 07 Feb 2018 12:04:29: #2 predicted fragment length is 113 bps INFO @ Wed, 07 Feb 2018 12:04:29: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 07 Feb 2018 12:04:29: #2.2 Generate R script for model : SRX3404014.10_model.r INFO @ Wed, 07 Feb 2018 12:04:29: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:05:14: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:05:17: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:05:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:05:38: #4 Write output xls file... SRX3404014.20_peaks.xls INFO @ Wed, 07 Feb 2018 12:05:38: #4 Write peak in narrowPeak format file... SRX3404014.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:05:38: #4 Write summits bed file... SRX3404014.20_summits.bed INFO @ Wed, 07 Feb 2018 12:05:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2494 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write output xls file... SRX3404014.10_peaks.xls INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write peak in narrowPeak format file... SRX3404014.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write summits bed file... SRX3404014.10_summits.bed INFO @ Wed, 07 Feb 2018 12:05:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3873 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write output xls file... SRX3404014.05_peaks.xls INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write peak in narrowPeak format file... SRX3404014.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:05:44: #4 Write summits bed file... SRX3404014.05_summits.bed INFO @ Wed, 07 Feb 2018 12:05:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5593 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。