Job ID = 10450771 sra ファイルのダウンロード中... Completed: 342835K bytes transferred in 9 seconds (286947K 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 17869683 spots for /home/okishinya/chipatlas/results/dm3/SRX3404026/SRR6303503.sra Written 17869683 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': No such file or directory 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: 00:14:09 17869683 reads; of these: 17869683 (100.00%) were unpaired; of these: 530455 (2.97%) aligned 0 times 12402856 (69.41%) aligned exactly 1 time 4936372 (27.62%) aligned >1 times 97.03% overall alignment rate Time searching: 00:14:09 Overall time: 00:14:09 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] 1518164 / 17339228 = 0.0876 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 12:44:45: # Command line: callpeak -t SRX3404026.bam -f BAM -g dm -n SRX3404026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404026.10 # format = BAM # ChIP-seq file = ['SRX3404026.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 12:44:45: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:44:45: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:44:45: # Command line: callpeak -t SRX3404026.bam -f BAM -g dm -n SRX3404026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404026.20 # format = BAM # ChIP-seq file = ['SRX3404026.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 12:44:45: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:44:45: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:44:45: # Command line: callpeak -t SRX3404026.bam -f BAM -g dm -n SRX3404026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404026.05 # format = BAM # ChIP-seq file = ['SRX3404026.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 12:44:45: #1 read tag files... INFO @ Wed, 07 Feb 2018 12:44:45: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 12:44:54: 1000000 INFO @ Wed, 07 Feb 2018 12:45:01: 1000000 INFO @ Wed, 07 Feb 2018 12:45:04: 2000000 INFO @ Wed, 07 Feb 2018 12:45:06: 1000000 INFO @ Wed, 07 Feb 2018 12:45:14: 3000000 INFO @ Wed, 07 Feb 2018 12:45:16: 2000000 INFO @ Wed, 07 Feb 2018 12:45:23: 4000000 INFO @ Wed, 07 Feb 2018 12:45:29: 3000000 INFO @ Wed, 07 Feb 2018 12:45:29: 2000000 INFO @ Wed, 07 Feb 2018 12:45:33: 5000000 INFO @ Wed, 07 Feb 2018 12:45:43: 6000000 INFO @ Wed, 07 Feb 2018 12:45:43: 4000000 INFO @ Wed, 07 Feb 2018 12:45:53: 7000000 INFO @ Wed, 07 Feb 2018 12:45:53: 3000000 INFO @ Wed, 07 Feb 2018 12:45:57: 5000000 INFO @ Wed, 07 Feb 2018 12:46:02: 8000000 INFO @ Wed, 07 Feb 2018 12:46:12: 6000000 INFO @ Wed, 07 Feb 2018 12:46:12: 9000000 INFO @ Wed, 07 Feb 2018 12:46:17: 4000000 INFO @ Wed, 07 Feb 2018 12:46:22: 10000000 INFO @ Wed, 07 Feb 2018 12:46:26: 7000000 INFO @ Wed, 07 Feb 2018 12:46:32: 11000000 INFO @ Wed, 07 Feb 2018 12:46:39: 8000000 INFO @ Wed, 07 Feb 2018 12:46:40: 5000000 INFO @ Wed, 07 Feb 2018 12:46:42: 12000000 INFO @ Wed, 07 Feb 2018 12:46:51: 13000000 INFO @ Wed, 07 Feb 2018 12:46:54: 9000000 INFO @ Wed, 07 Feb 2018 12:47:01: 6000000 INFO @ Wed, 07 Feb 2018 12:47:03: 14000000 INFO @ Wed, 07 Feb 2018 12:47:07: 10000000 INFO @ Wed, 07 Feb 2018 12:47:14: 15000000 INFO @ Wed, 07 Feb 2018 12:47:22: 7000000 INFO @ Wed, 07 Feb 2018 12:47:23: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:47:23: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:47:23: #1 total tags in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:47:23: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:47:23: #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 12:47:23: #1 tags after filtering in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:47:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:47:23: #1 finished! INFO @ Wed, 07 Feb 2018 12:47:23: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:47:24: 11000000 INFO @ Wed, 07 Feb 2018 12:47:25: #2 number of paired peaks: 495 WARNING @ Wed, 07 Feb 2018 12:47:25: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Wed, 07 Feb 2018 12:47:25: start model_add_line... INFO @ Wed, 07 Feb 2018 12:47:25: start X-correlation... INFO @ Wed, 07 Feb 2018 12:47:25: end of X-cor INFO @ Wed, 07 Feb 2018 12:47:25: #2 finished! INFO @ Wed, 07 Feb 2018 12:47:25: #2 predicted fragment length is 138 bps INFO @ Wed, 07 Feb 2018 12:47:25: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 07 Feb 2018 12:47:25: #2.2 Generate R script for model : SRX3404026.20_model.r INFO @ Wed, 07 Feb 2018 12:47:25: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:47:37: 12000000 INFO @ Wed, 07 Feb 2018 12:47:42: 8000000 INFO @ Wed, 07 Feb 2018 12:47:51: 13000000 INFO @ Wed, 07 Feb 2018 12:48:02: 9000000 INFO @ Wed, 07 Feb 2018 12:48:05: 14000000 INFO @ Wed, 07 Feb 2018 12:48:12: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:48:19: 15000000 INFO @ Wed, 07 Feb 2018 12:48:22: 10000000 INFO @ Wed, 07 Feb 2018 12:48:29: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:48:29: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:48:29: #1 total tags in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:48:29: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:48:29: #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 12:48:29: #1 tags after filtering in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:48:29: #1 finished! INFO @ Wed, 07 Feb 2018 12:48:29: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:48:31: #2 number of paired peaks: 495 WARNING @ Wed, 07 Feb 2018 12:48:31: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Wed, 07 Feb 2018 12:48:31: start model_add_line... INFO @ Wed, 07 Feb 2018 12:48:31: start X-correlation... INFO @ Wed, 07 Feb 2018 12:48:31: end of X-cor INFO @ Wed, 07 Feb 2018 12:48:31: #2 finished! INFO @ Wed, 07 Feb 2018 12:48:31: #2 predicted fragment length is 138 bps INFO @ Wed, 07 Feb 2018 12:48:31: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 07 Feb 2018 12:48:31: #2.2 Generate R script for model : SRX3404026.05_model.r INFO @ Wed, 07 Feb 2018 12:48:31: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:48:40: #4 Write output xls file... SRX3404026.20_peaks.xls INFO @ Wed, 07 Feb 2018 12:48:40: #4 Write peak in narrowPeak format file... SRX3404026.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:48:40: #4 Write summits bed file... SRX3404026.20_summits.bed INFO @ Wed, 07 Feb 2018 12:48:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1649 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:48:42: 11000000 INFO @ Wed, 07 Feb 2018 12:49:02: 12000000 INFO @ Wed, 07 Feb 2018 12:49:18: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:49:22: 13000000 INFO @ Wed, 07 Feb 2018 12:49:42: 14000000 INFO @ Wed, 07 Feb 2018 12:49:45: #4 Write output xls file... SRX3404026.05_peaks.xls INFO @ Wed, 07 Feb 2018 12:49:45: #4 Write peak in narrowPeak format file... SRX3404026.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:49:45: #4 Write summits bed file... SRX3404026.05_summits.bed INFO @ Wed, 07 Feb 2018 12:49:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3992 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 12:50:03: 15000000 INFO @ Wed, 07 Feb 2018 12:50:20: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 12:50:20: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 12:50:20: #1 total tags in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:50:20: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 12:50:20: #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 12:50:20: #1 tags after filtering in treatment: 15821064 INFO @ Wed, 07 Feb 2018 12:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 12:50:20: #1 finished! INFO @ Wed, 07 Feb 2018 12:50:20: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 12:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 12:50:22: #2 number of paired peaks: 495 WARNING @ Wed, 07 Feb 2018 12:50:22: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Wed, 07 Feb 2018 12:50:22: start model_add_line... INFO @ Wed, 07 Feb 2018 12:50:22: start X-correlation... INFO @ Wed, 07 Feb 2018 12:50:22: end of X-cor INFO @ Wed, 07 Feb 2018 12:50:22: #2 finished! INFO @ Wed, 07 Feb 2018 12:50:22: #2 predicted fragment length is 138 bps INFO @ Wed, 07 Feb 2018 12:50:22: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 07 Feb 2018 12:50:22: #2.2 Generate R script for model : SRX3404026.10_model.r INFO @ Wed, 07 Feb 2018 12:50:22: #3 Call peaks... INFO @ Wed, 07 Feb 2018 12:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 12:51:09: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 12:51:36: #4 Write output xls file... SRX3404026.10_peaks.xls INFO @ Wed, 07 Feb 2018 12:51:36: #4 Write peak in narrowPeak format file... SRX3404026.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 12:51:36: #4 Write summits bed file... SRX3404026.10_summits.bed INFO @ Wed, 07 Feb 2018 12:51:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2721 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。