Job ID = 11171212 sra ファイルのダウンロード中... Completed: 321819K bytes transferred in 9 seconds (280492K 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 15535946 spots for /home/okishinya/chipatlas/results/dm3/SRX2618521/SRR5319075.sra Written 15535946 spots for /home/okishinya/chipatlas/results/dm3/SRX2618521/SRR5319075.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: 00:06:01 15535946 reads; of these: 15535946 (100.00%) were unpaired; of these: 795154 (5.12%) aligned 0 times 11035148 (71.03%) aligned exactly 1 time 3705644 (23.85%) aligned >1 times 94.88% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 1542295 / 14740792 = 0.1046 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 13:08:22: # Command line: callpeak -t SRX2618521.bam -f BAM -g dm -n SRX2618521.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618521.05 # format = BAM # ChIP-seq file = ['SRX2618521.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 13:08:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:22: # Command line: callpeak -t SRX2618521.bam -f BAM -g dm -n SRX2618521.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618521.20 # format = BAM # ChIP-seq file = ['SRX2618521.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 13:08:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:22: # Command line: callpeak -t SRX2618521.bam -f BAM -g dm -n SRX2618521.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618521.10 # format = BAM # ChIP-seq file = ['SRX2618521.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 13:08:22: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:22: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:29: 1000000 INFO @ Sat, 08 Sep 2018 13:08:29: 1000000 INFO @ Sat, 08 Sep 2018 13:08:29: 1000000 INFO @ Sat, 08 Sep 2018 13:08:35: 2000000 INFO @ Sat, 08 Sep 2018 13:08:36: 2000000 INFO @ Sat, 08 Sep 2018 13:08:37: 2000000 INFO @ Sat, 08 Sep 2018 13:08:41: 3000000 INFO @ Sat, 08 Sep 2018 13:08:44: 3000000 INFO @ Sat, 08 Sep 2018 13:08:44: 3000000 INFO @ Sat, 08 Sep 2018 13:08:47: 4000000 INFO @ Sat, 08 Sep 2018 13:08:51: 4000000 INFO @ Sat, 08 Sep 2018 13:08:51: 4000000 INFO @ Sat, 08 Sep 2018 13:08:53: 5000000 INFO @ Sat, 08 Sep 2018 13:08:58: 5000000 INFO @ Sat, 08 Sep 2018 13:08:59: 6000000 INFO @ Sat, 08 Sep 2018 13:08:59: 5000000 INFO @ Sat, 08 Sep 2018 13:09:05: 7000000 INFO @ Sat, 08 Sep 2018 13:09:06: 6000000 INFO @ Sat, 08 Sep 2018 13:09:06: 6000000 INFO @ Sat, 08 Sep 2018 13:09:11: 8000000 INFO @ Sat, 08 Sep 2018 13:09:13: 7000000 INFO @ Sat, 08 Sep 2018 13:09:14: 7000000 INFO @ Sat, 08 Sep 2018 13:09:17: 9000000 INFO @ Sat, 08 Sep 2018 13:09:20: 8000000 INFO @ Sat, 08 Sep 2018 13:09:22: 8000000 INFO @ Sat, 08 Sep 2018 13:09:23: 10000000 INFO @ Sat, 08 Sep 2018 13:09:28: 9000000 INFO @ Sat, 08 Sep 2018 13:09:29: 11000000 INFO @ Sat, 08 Sep 2018 13:09:29: 9000000 INFO @ Sat, 08 Sep 2018 13:09:35: 12000000 INFO @ Sat, 08 Sep 2018 13:09:35: 10000000 INFO @ Sat, 08 Sep 2018 13:09:37: 10000000 INFO @ Sat, 08 Sep 2018 13:09:41: 13000000 INFO @ Sat, 08 Sep 2018 13:09:42: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:09:42: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:09:42: #1 total tags in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:09:42: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:09:42: #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 13:09:42: #1 tags after filtering in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:09:42: #1 finished! INFO @ Sat, 08 Sep 2018 13:09:42: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:09:43: 11000000 INFO @ Sat, 08 Sep 2018 13:09:43: #2 number of paired peaks: 157 WARNING @ Sat, 08 Sep 2018 13:09:43: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 08 Sep 2018 13:09:43: start model_add_line... INFO @ Sat, 08 Sep 2018 13:09:43: start X-correlation... INFO @ Sat, 08 Sep 2018 13:09:43: end of X-cor INFO @ Sat, 08 Sep 2018 13:09:43: #2 finished! INFO @ Sat, 08 Sep 2018 13:09:43: #2 predicted fragment length is 140 bps INFO @ Sat, 08 Sep 2018 13:09:43: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 08 Sep 2018 13:09:43: #2.2 Generate R script for model : SRX2618521.05_model.r INFO @ Sat, 08 Sep 2018 13:09:43: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:09:45: 11000000 INFO @ Sat, 08 Sep 2018 13:09:50: 12000000 INFO @ Sat, 08 Sep 2018 13:09:52: 12000000 INFO @ Sat, 08 Sep 2018 13:09:58: 13000000 INFO @ Sat, 08 Sep 2018 13:09:59: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:09:59: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:09:59: #1 total tags in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:09:59: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:09:59: #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 13:10:00: #1 tags after filtering in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:00: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:00: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:00: 13000000 INFO @ Sat, 08 Sep 2018 13:10:00: #2 number of paired peaks: 157 WARNING @ Sat, 08 Sep 2018 13:10:00: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:00: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:01: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:01: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:01: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:01: #2 predicted fragment length is 140 bps INFO @ Sat, 08 Sep 2018 13:10:01: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 08 Sep 2018 13:10:01: #2.2 Generate R script for model : SRX2618521.20_model.r INFO @ Sat, 08 Sep 2018 13:10:01: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:01: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:01: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:01: #1 total tags in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:10:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:01: #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 13:10:02: #1 tags after filtering in treatment: 13198497 INFO @ Sat, 08 Sep 2018 13:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:02: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:02: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:03: #2 number of paired peaks: 157 WARNING @ Sat, 08 Sep 2018 13:10:03: Fewer paired peaks (157) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 157 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:03: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:03: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:03: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:03: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:03: #2 predicted fragment length is 140 bps INFO @ Sat, 08 Sep 2018 13:10:03: #2 alternative fragment length(s) may be 140 bps INFO @ Sat, 08 Sep 2018 13:10:03: #2.2 Generate R script for model : SRX2618521.10_model.r INFO @ Sat, 08 Sep 2018 13:10:03: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:28: #4 Write output xls file... SRX2618521.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:10:28: #4 Write peak in narrowPeak format file... SRX2618521.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:10:29: #4 Write summits bed file... SRX2618521.05_summits.bed INFO @ Sat, 08 Sep 2018 13:10:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6165 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:31: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write output xls file... SRX2618521.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write peak in narrowPeak format file... SRX2618521.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write summits bed file... SRX2618521.10_summits.bed INFO @ Sat, 08 Sep 2018 13:10:48: Done! INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write output xls file... SRX2618521.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write peak in narrowPeak format file... SRX2618521.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:10:48: #4 Write summits bed file... SRX2618521.20_summits.bed pass1 - making usageList (14 chroms): 2 millis INFO @ Sat, 08 Sep 2018 13:10:48: Done! pass2 - checking and writing primary data (3865 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1723 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。