Job ID = 10480668 sra ファイルのダウンロード中... Completed: 444612K bytes transferred in 41 seconds (88790K 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 12923525 spots for /home/okishinya/chipatlas/results/dm3/SRX2832104/SRR5573768.sra Written 12923525 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:49 12923525 reads; of these: 12923525 (100.00%) were unpaired; of these: 642118 (4.97%) aligned 0 times 8657451 (66.99%) aligned exactly 1 time 3623956 (28.04%) aligned >1 times 95.03% overall alignment rate Time searching: 00:05:49 Overall time: 00:05:49 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] 2141358 / 12281407 = 0.1744 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 @ Fri, 16 Mar 2018 07:36:15: # Command line: callpeak -t SRX2832104.bam -f BAM -g dm -n SRX2832104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832104.10 # format = BAM # ChIP-seq file = ['SRX2832104.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 @ Fri, 16 Mar 2018 07:36:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:36:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:36:15: # Command line: callpeak -t SRX2832104.bam -f BAM -g dm -n SRX2832104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832104.05 # format = BAM # ChIP-seq file = ['SRX2832104.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 @ Fri, 16 Mar 2018 07:36:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:36:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:36:15: # Command line: callpeak -t SRX2832104.bam -f BAM -g dm -n SRX2832104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832104.20 # format = BAM # ChIP-seq file = ['SRX2832104.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 @ Fri, 16 Mar 2018 07:36:15: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:36:15: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:36:22: 1000000 INFO @ Fri, 16 Mar 2018 07:36:23: 1000000 INFO @ Fri, 16 Mar 2018 07:36:23: 1000000 INFO @ Fri, 16 Mar 2018 07:36:29: 2000000 INFO @ Fri, 16 Mar 2018 07:36:30: 2000000 INFO @ Fri, 16 Mar 2018 07:36:30: 2000000 INFO @ Fri, 16 Mar 2018 07:36:36: 3000000 INFO @ Fri, 16 Mar 2018 07:36:37: 3000000 INFO @ Fri, 16 Mar 2018 07:36:37: 3000000 INFO @ Fri, 16 Mar 2018 07:36:43: 4000000 INFO @ Fri, 16 Mar 2018 07:36:44: 4000000 INFO @ Fri, 16 Mar 2018 07:36:45: 4000000 INFO @ Fri, 16 Mar 2018 07:36:50: 5000000 INFO @ Fri, 16 Mar 2018 07:36:52: 5000000 INFO @ Fri, 16 Mar 2018 07:36:52: 5000000 INFO @ Fri, 16 Mar 2018 07:36:57: 6000000 INFO @ Fri, 16 Mar 2018 07:36:59: 6000000 INFO @ Fri, 16 Mar 2018 07:37:00: 6000000 INFO @ Fri, 16 Mar 2018 07:37:04: 7000000 INFO @ Fri, 16 Mar 2018 07:37:07: 7000000 INFO @ Fri, 16 Mar 2018 07:37:07: 7000000 INFO @ Fri, 16 Mar 2018 07:37:11: 8000000 INFO @ Fri, 16 Mar 2018 07:37:14: 8000000 INFO @ Fri, 16 Mar 2018 07:37:15: 8000000 INFO @ Fri, 16 Mar 2018 07:37:18: 9000000 INFO @ Fri, 16 Mar 2018 07:37:22: 9000000 INFO @ Fri, 16 Mar 2018 07:37:22: 9000000 INFO @ Fri, 16 Mar 2018 07:37:25: 10000000 INFO @ Fri, 16 Mar 2018 07:37:26: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:37:26: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:37:26: #1 total tags in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:26: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:37:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:37:27: #1 tags after filtering in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:37:27: #1 finished! INFO @ Fri, 16 Mar 2018 07:37:27: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:37:27: #2 number of paired peaks: 828 WARNING @ Fri, 16 Mar 2018 07:37:27: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Fri, 16 Mar 2018 07:37:27: start model_add_line... INFO @ Fri, 16 Mar 2018 07:37:28: start X-correlation... INFO @ Fri, 16 Mar 2018 07:37:28: end of X-cor INFO @ Fri, 16 Mar 2018 07:37:28: #2 finished! INFO @ Fri, 16 Mar 2018 07:37:28: #2 predicted fragment length is 113 bps INFO @ Fri, 16 Mar 2018 07:37:28: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 16 Mar 2018 07:37:28: #2.2 Generate R script for model : SRX2832104.10_model.r INFO @ Fri, 16 Mar 2018 07:37:28: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:37:29: 10000000 INFO @ Fri, 16 Mar 2018 07:37:30: 10000000 INFO @ Fri, 16 Mar 2018 07:37:30: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:37:30: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:37:30: #1 total tags in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:30: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:37:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:37:30: #1 tags after filtering in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:37:30: #1 finished! INFO @ Fri, 16 Mar 2018 07:37:30: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:37:31: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:37:31: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:37:31: #1 total tags in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:31: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:37:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:37:31: #1 tags after filtering in treatment: 10140049 INFO @ Fri, 16 Mar 2018 07:37:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:37:31: #1 finished! INFO @ Fri, 16 Mar 2018 07:37:31: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:37:31: #2 number of paired peaks: 828 WARNING @ Fri, 16 Mar 2018 07:37:31: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Fri, 16 Mar 2018 07:37:31: start model_add_line... INFO @ Fri, 16 Mar 2018 07:37:31: start X-correlation... INFO @ Fri, 16 Mar 2018 07:37:31: end of X-cor INFO @ Fri, 16 Mar 2018 07:37:31: #2 finished! INFO @ Fri, 16 Mar 2018 07:37:31: #2 predicted fragment length is 113 bps INFO @ Fri, 16 Mar 2018 07:37:31: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 16 Mar 2018 07:37:31: #2.2 Generate R script for model : SRX2832104.05_model.r INFO @ Fri, 16 Mar 2018 07:37:31: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:37:32: #2 number of paired peaks: 828 WARNING @ Fri, 16 Mar 2018 07:37:32: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Fri, 16 Mar 2018 07:37:32: start model_add_line... INFO @ Fri, 16 Mar 2018 07:37:32: start X-correlation... INFO @ Fri, 16 Mar 2018 07:37:32: end of X-cor INFO @ Fri, 16 Mar 2018 07:37:32: #2 finished! INFO @ Fri, 16 Mar 2018 07:37:32: #2 predicted fragment length is 113 bps INFO @ Fri, 16 Mar 2018 07:37:32: #2 alternative fragment length(s) may be 113 bps INFO @ Fri, 16 Mar 2018 07:37:32: #2.2 Generate R script for model : SRX2832104.20_model.r INFO @ Fri, 16 Mar 2018 07:37:32: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:37:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:37:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:37:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:37:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:38:03: #4 Write output xls file... SRX2832104.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:03: #4 Write peak in narrowPeak format file... SRX2832104.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:03: #4 Write summits bed file... SRX2832104.10_summits.bed INFO @ Fri, 16 Mar 2018 07:38:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2278 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:38:08: #4 Write output xls file... SRX2832104.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:09: #4 Write peak in narrowPeak format file... SRX2832104.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:09: #4 Write summits bed file... SRX2832104.05_summits.bed INFO @ Fri, 16 Mar 2018 07:38:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4990 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:38:12: #4 Write output xls file... SRX2832104.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:38:12: #4 Write peak in narrowPeak format file... SRX2832104.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:38:12: #4 Write summits bed file... SRX2832104.20_summits.bed INFO @ Fri, 16 Mar 2018 07:38:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。