Job ID = 11171213 sra ファイルのダウンロード中... Completed: 303343K bytes transferred in 18 seconds (133808K 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 14638335 spots for /home/okishinya/chipatlas/results/dm3/SRX2618522/SRR5319076.sra Written 14638335 spots for /home/okishinya/chipatlas/results/dm3/SRX2618522/SRR5319076.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: 00:05:32 14638335 reads; of these: 14638335 (100.00%) were unpaired; of these: 643681 (4.40%) aligned 0 times 10298299 (70.35%) aligned exactly 1 time 3696355 (25.25%) aligned >1 times 95.60% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 1401315 / 13994654 = 0.1001 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 13:08:51: # Command line: callpeak -t SRX2618522.bam -f BAM -g dm -n SRX2618522.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2618522.05 # format = BAM # ChIP-seq file = ['SRX2618522.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 13:08:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:51: # Command line: callpeak -t SRX2618522.bam -f BAM -g dm -n SRX2618522.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2618522.10 # format = BAM # ChIP-seq file = ['SRX2618522.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 13:08:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:51: # Command line: callpeak -t SRX2618522.bam -f BAM -g dm -n SRX2618522.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2618522.20 # format = BAM # ChIP-seq file = ['SRX2618522.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 13:08:51: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:08:51: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:08:57: 1000000 INFO @ Sat, 08 Sep 2018 13:09:04: 2000000 INFO @ Sat, 08 Sep 2018 13:09:04: 2000000 INFO @ Sat, 08 Sep 2018 13:09:05: 2000000 INFO @ Sat, 08 Sep 2018 13:09:11: 3000000 INFO @ Sat, 08 Sep 2018 13:09:11: 3000000 INFO @ Sat, 08 Sep 2018 13:09:12: 3000000 INFO @ Sat, 08 Sep 2018 13:09:18: 4000000 INFO @ Sat, 08 Sep 2018 13:09:18: 4000000 INFO @ Sat, 08 Sep 2018 13:09:19: 4000000 INFO @ Sat, 08 Sep 2018 13:09:25: 5000000 INFO @ Sat, 08 Sep 2018 13:09:25: 5000000 INFO @ Sat, 08 Sep 2018 13:09:26: 5000000 INFO @ Sat, 08 Sep 2018 13:09:31: 6000000 INFO @ Sat, 08 Sep 2018 13:09:32: 6000000 INFO @ Sat, 08 Sep 2018 13:09:33: 6000000 INFO @ Sat, 08 Sep 2018 13:09:38: 7000000 INFO @ Sat, 08 Sep 2018 13:09:39: 7000000 INFO @ Sat, 08 Sep 2018 13:09:40: 7000000 INFO @ Sat, 08 Sep 2018 13:09:45: 8000000 INFO @ Sat, 08 Sep 2018 13:09:46: 8000000 INFO @ Sat, 08 Sep 2018 13:09:47: 8000000 INFO @ Sat, 08 Sep 2018 13:09:51: 9000000 INFO @ Sat, 08 Sep 2018 13:09:53: 9000000 INFO @ Sat, 08 Sep 2018 13:09:54: 9000000 INFO @ Sat, 08 Sep 2018 13:09:58: 10000000 INFO @ Sat, 08 Sep 2018 13:10:00: 10000000 INFO @ Sat, 08 Sep 2018 13:10:01: 10000000 INFO @ Sat, 08 Sep 2018 13:10:05: 11000000 INFO @ Sat, 08 Sep 2018 13:10:07: 11000000 INFO @ Sat, 08 Sep 2018 13:10:08: 11000000 INFO @ Sat, 08 Sep 2018 13:10:12: 12000000 INFO @ Sat, 08 Sep 2018 13:10:15: 12000000 INFO @ Sat, 08 Sep 2018 13:10:16: 12000000 INFO @ Sat, 08 Sep 2018 13:10:16: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:16: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:16: #1 total tags in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:16: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:16: #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 13:10:16: #1 tags after filtering in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:16: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:16: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:17: #2 number of paired peaks: 156 WARNING @ Sat, 08 Sep 2018 13:10:17: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:17: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:17: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:17: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:17: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:17: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:10:17: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 08 Sep 2018 13:10:17: #2.2 Generate R script for model : SRX2618522.20_model.r INFO @ Sat, 08 Sep 2018 13:10:17: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:19: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:19: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:19: #1 total tags in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:19: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:19: #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 13:10:19: #1 tags after filtering in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:19: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:19: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:20: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 13:10:20: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 13:10:20: #1 total tags in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:10:20: #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 13:10:20: #2 number of paired peaks: 156 WARNING @ Sat, 08 Sep 2018 13:10:20: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:20: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:20: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:20: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:20: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:20: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:10:20: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 08 Sep 2018 13:10:20: #2.2 Generate R script for model : SRX2618522.05_model.r INFO @ Sat, 08 Sep 2018 13:10:20: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:20: #1 tags after filtering in treatment: 12593339 INFO @ Sat, 08 Sep 2018 13:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:10:20: #1 finished! INFO @ Sat, 08 Sep 2018 13:10:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:10:21: #2 number of paired peaks: 156 WARNING @ Sat, 08 Sep 2018 13:10:21: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 08 Sep 2018 13:10:21: start model_add_line... INFO @ Sat, 08 Sep 2018 13:10:21: start X-correlation... INFO @ Sat, 08 Sep 2018 13:10:21: end of X-cor INFO @ Sat, 08 Sep 2018 13:10:21: #2 finished! INFO @ Sat, 08 Sep 2018 13:10:21: #2 predicted fragment length is 133 bps INFO @ Sat, 08 Sep 2018 13:10:21: #2 alternative fragment length(s) may be 133 bps INFO @ Sat, 08 Sep 2018 13:10:21: #2.2 Generate R script for model : SRX2618522.10_model.r INFO @ Sat, 08 Sep 2018 13:10:21: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:10:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:49: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:11:00: #4 Write output xls file... SRX2618522.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:00: #4 Write peak in narrowPeak format file... SRX2618522.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:00: #4 Write summits bed file... SRX2618522.20_summits.bed INFO @ Sat, 08 Sep 2018 13:11:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1190 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:02: #4 Write output xls file... SRX2618522.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:02: #4 Write peak in narrowPeak format file... SRX2618522.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:02: #4 Write summits bed file... SRX2618522.10_summits.bed INFO @ Sat, 08 Sep 2018 13:11:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2886 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:05: #4 Write output xls file... SRX2618522.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:05: #4 Write peak in narrowPeak format file... SRX2618522.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:05: #4 Write summits bed file... SRX2618522.05_summits.bed INFO @ Sat, 08 Sep 2018 13:11:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5188 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。