Job ID = 10043500 sra ファイルのダウンロード中... Completed: 1020885K bytes transferred in 24 seconds (340429K bits/sec), in 2 files, 3 directories. 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 17760126 spots for /home/okishinya/chipatlas/results/dm3/SRX2165282/SRR4244794.sra Written 17760126 spots total Written 9704730 spots for /home/okishinya/chipatlas/results/dm3/SRX2165282/SRR4244793.sra Written 9704730 spots total 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: 00:12:16 27464856 reads; of these: 27464856 (100.00%) were unpaired; of these: 1417244 (5.16%) aligned 0 times 18899310 (68.81%) aligned exactly 1 time 7148302 (26.03%) aligned >1 times 94.84% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 9900933 / 26047612 = 0.3801 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 @ Mon, 02 Oct 2017 03:49:58: # Command line: callpeak -t SRX2165282.bam -f BAM -g dm -n SRX2165282.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2165282.10 # format = BAM # ChIP-seq file = ['SRX2165282.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 @ Mon, 02 Oct 2017 03:49:58: # Command line: callpeak -t SRX2165282.bam -f BAM -g dm -n SRX2165282.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2165282.05 # format = BAM # ChIP-seq file = ['SRX2165282.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 @ Mon, 02 Oct 2017 03:49:58: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:58: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:58: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:49:58: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:49:58: # Command line: callpeak -t SRX2165282.bam -f BAM -g dm -n SRX2165282.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2165282.20 # format = BAM # ChIP-seq file = ['SRX2165282.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 @ Mon, 02 Oct 2017 03:49:58: #1 read tag files... INFO @ Mon, 02 Oct 2017 03:49:58: #1 read treatment tags... INFO @ Mon, 02 Oct 2017 03:50:05: 1000000 INFO @ Mon, 02 Oct 2017 03:50:05: 1000000 INFO @ Mon, 02 Oct 2017 03:50:05: 1000000 INFO @ Mon, 02 Oct 2017 03:50:11: 2000000 INFO @ Mon, 02 Oct 2017 03:50:12: 2000000 INFO @ Mon, 02 Oct 2017 03:50:13: 2000000 INFO @ Mon, 02 Oct 2017 03:50:18: 3000000 INFO @ Mon, 02 Oct 2017 03:50:19: 3000000 INFO @ Mon, 02 Oct 2017 03:50:20: 3000000 INFO @ Mon, 02 Oct 2017 03:50:24: 4000000 INFO @ Mon, 02 Oct 2017 03:50:27: 4000000 INFO @ Mon, 02 Oct 2017 03:50:27: 4000000 INFO @ Mon, 02 Oct 2017 03:50:31: 5000000 INFO @ Mon, 02 Oct 2017 03:50:34: 5000000 INFO @ Mon, 02 Oct 2017 03:50:34: 5000000 INFO @ Mon, 02 Oct 2017 03:50:37: 6000000 INFO @ Mon, 02 Oct 2017 03:50:41: 6000000 INFO @ Mon, 02 Oct 2017 03:50:41: 6000000 INFO @ Mon, 02 Oct 2017 03:50:43: 7000000 INFO @ Mon, 02 Oct 2017 03:50:48: 7000000 INFO @ Mon, 02 Oct 2017 03:50:48: 7000000 INFO @ Mon, 02 Oct 2017 03:50:50: 8000000 INFO @ Mon, 02 Oct 2017 03:50:55: 8000000 INFO @ Mon, 02 Oct 2017 03:50:55: 8000000 INFO @ Mon, 02 Oct 2017 03:50:56: 9000000 INFO @ Mon, 02 Oct 2017 03:51:02: 9000000 INFO @ Mon, 02 Oct 2017 03:51:02: 9000000 INFO @ Mon, 02 Oct 2017 03:51:02: 10000000 INFO @ Mon, 02 Oct 2017 03:51:09: 10000000 INFO @ Mon, 02 Oct 2017 03:51:09: 11000000 INFO @ Mon, 02 Oct 2017 03:51:09: 10000000 INFO @ Mon, 02 Oct 2017 03:51:15: 12000000 INFO @ Mon, 02 Oct 2017 03:51:16: 11000000 INFO @ Mon, 02 Oct 2017 03:51:16: 11000000 INFO @ Mon, 02 Oct 2017 03:51:21: 13000000 INFO @ Mon, 02 Oct 2017 03:51:23: 12000000 INFO @ Mon, 02 Oct 2017 03:51:24: 12000000 INFO @ Mon, 02 Oct 2017 03:51:28: 14000000 INFO @ Mon, 02 Oct 2017 03:51:30: 13000000 INFO @ Mon, 02 Oct 2017 03:51:31: 13000000 INFO @ Mon, 02 Oct 2017 03:51:34: 15000000 INFO @ Mon, 02 Oct 2017 03:51:37: 14000000 INFO @ Mon, 02 Oct 2017 03:51:38: 14000000 INFO @ Mon, 02 Oct 2017 03:51:40: 16000000 INFO @ Mon, 02 Oct 2017 03:51:42: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:42: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:42: #1 total tags in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:42: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:42: #1 tags after filtering in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:42: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:42: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:43: #2 number of paired peaks: 601 WARNING @ Mon, 02 Oct 2017 03:51:43: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:43: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:43: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:43: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:43: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:43: #2 predicted fragment length is 222 bps INFO @ Mon, 02 Oct 2017 03:51:43: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 02 Oct 2017 03:51:43: #2.2 Generate R script for model : SRX2165282.10_model.r INFO @ Mon, 02 Oct 2017 03:51:43: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:51:45: 15000000 INFO @ Mon, 02 Oct 2017 03:51:45: 15000000 INFO @ Mon, 02 Oct 2017 03:51:52: 16000000 INFO @ Mon, 02 Oct 2017 03:51:52: 16000000 INFO @ Mon, 02 Oct 2017 03:51:53: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:53: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:53: #1 total tags in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:53: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:53: #1 tags after filtering in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:53: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:53: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:54: #1 tag size is determined as 67 bps INFO @ Mon, 02 Oct 2017 03:51:54: #1 tag size = 67 INFO @ Mon, 02 Oct 2017 03:51:54: #1 total tags in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:54: #1 user defined the maximum tags... INFO @ Mon, 02 Oct 2017 03:51:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 02 Oct 2017 03:51:54: #1 tags after filtering in treatment: 16146679 INFO @ Mon, 02 Oct 2017 03:51:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 02 Oct 2017 03:51:54: #1 finished! INFO @ Mon, 02 Oct 2017 03:51:54: #2 Build Peak Model... INFO @ Mon, 02 Oct 2017 03:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 02 Oct 2017 03:51:55: #2 number of paired peaks: 601 WARNING @ Mon, 02 Oct 2017 03:51:55: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:55: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:55: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:55: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:55: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:55: #2 predicted fragment length is 222 bps INFO @ Mon, 02 Oct 2017 03:51:55: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 02 Oct 2017 03:51:55: #2.2 Generate R script for model : SRX2165282.05_model.r INFO @ Mon, 02 Oct 2017 03:51:55: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:51:55: #2 number of paired peaks: 601 WARNING @ Mon, 02 Oct 2017 03:51:55: Fewer paired peaks (601) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 601 pairs to build model! INFO @ Mon, 02 Oct 2017 03:51:55: start model_add_line... INFO @ Mon, 02 Oct 2017 03:51:55: start X-correlation... INFO @ Mon, 02 Oct 2017 03:51:55: end of X-cor INFO @ Mon, 02 Oct 2017 03:51:55: #2 finished! INFO @ Mon, 02 Oct 2017 03:51:55: #2 predicted fragment length is 222 bps INFO @ Mon, 02 Oct 2017 03:51:55: #2 alternative fragment length(s) may be 222 bps INFO @ Mon, 02 Oct 2017 03:51:55: #2.2 Generate R script for model : SRX2165282.20_model.r INFO @ Mon, 02 Oct 2017 03:51:55: #3 Call peaks... INFO @ Mon, 02 Oct 2017 03:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 02 Oct 2017 03:52:23: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:52:34: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:52:35: #3 Call peaks for each chromosome... INFO @ Mon, 02 Oct 2017 03:52:44: #4 Write output xls file... SRX2165282.10_peaks.xls INFO @ Mon, 02 Oct 2017 03:52:44: #4 Write peak in narrowPeak format file... SRX2165282.10_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:52:44: #4 Write summits bed file... SRX2165282.10_summits.bed INFO @ Mon, 02 Oct 2017 03:52:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4349 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:52:53: #4 Write output xls file... SRX2165282.05_peaks.xls INFO @ Mon, 02 Oct 2017 03:52:53: #4 Write peak in narrowPeak format file... SRX2165282.05_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:52:53: #4 Write summits bed file... SRX2165282.05_summits.bed INFO @ Mon, 02 Oct 2017 03:52:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7143 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 02 Oct 2017 03:52:56: #4 Write output xls file... SRX2165282.20_peaks.xls INFO @ Mon, 02 Oct 2017 03:52:56: #4 Write peak in narrowPeak format file... SRX2165282.20_peaks.narrowPeak INFO @ Mon, 02 Oct 2017 03:52:56: #4 Write summits bed file... SRX2165282.20_summits.bed INFO @ Mon, 02 Oct 2017 03:52:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2352 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。