Job ID = 11193158 sra ファイルのダウンロード中... Completed: 482155K bytes transferred in 10 seconds (379710K 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: PAIRED fastq に変換中... Read 13285738 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337750/SRR7467853.sra Written 13285738 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337750/SRR7467853.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: 00:02:37 13285738 reads; of these: 13285738 (100.00%) were paired; of these: 13013256 (97.95%) aligned concordantly 0 times 240304 (1.81%) aligned concordantly exactly 1 time 32178 (0.24%) aligned concordantly >1 times ---- 13013256 pairs aligned concordantly 0 times; of these: 208262 (1.60%) aligned discordantly 1 time ---- 12804994 pairs aligned 0 times concordantly or discordantly; of these: 25609988 mates make up the pairs; of these: 24166855 (94.36%) aligned 0 times 1251105 (4.89%) aligned exactly 1 time 192028 (0.75%) aligned >1 times 9.05% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 195082 / 475894 = 0.4099 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, 15 Sep 2018 11:07:07: # Command line: callpeak -t SRX4337750.bam -f BAM -g 12100000 -n SRX4337750.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337750.05 # format = BAM # ChIP-seq file = ['SRX4337750.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Sep 2018 11:07:07: # Command line: callpeak -t SRX4337750.bam -f BAM -g 12100000 -n SRX4337750.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337750.10 # format = BAM # ChIP-seq file = ['SRX4337750.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Sep 2018 11:07:07: # Command line: callpeak -t SRX4337750.bam -f BAM -g 12100000 -n SRX4337750.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337750.20 # format = BAM # ChIP-seq file = ['SRX4337750.bam'] # control file = None # effective genome size = 1.21e+07 # 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, 15 Sep 2018 11:07:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:07: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:07:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:07: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:07:15: 1000000 INFO @ Sat, 15 Sep 2018 11:07:16: 1000000 INFO @ Sat, 15 Sep 2018 11:07:16: 1000000 INFO @ Sat, 15 Sep 2018 11:07:22: 2000000 INFO @ Sat, 15 Sep 2018 11:07:22: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 11:07:22: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 11:07:22: #1 total tags in treatment: 209876 INFO @ Sat, 15 Sep 2018 11:07:22: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:07:22: #1 tags after filtering in treatment: 200696 INFO @ Sat, 15 Sep 2018 11:07:22: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:07:22: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:22: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:22: #2 number of paired peaks: 214 WARNING @ Sat, 15 Sep 2018 11:07:22: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:22: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:22: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:22: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:22: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:22: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Sep 2018 11:07:22: #2 alternative fragment length(s) may be 163,184,210 bps INFO @ Sat, 15 Sep 2018 11:07:22: #2.2 Generate R script for model : SRX4337750.05_model.r INFO @ Sat, 15 Sep 2018 11:07:22: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:23: #4 Write output xls file... SRX4337750.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:23: #4 Write peak in narrowPeak format file... SRX4337750.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:23: #4 Write summits bed file... SRX4337750.05_summits.bed INFO @ Sat, 15 Sep 2018 11:07:23: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:07:26: 2000000 INFO @ Sat, 15 Sep 2018 11:07:26: 2000000 INFO @ Sat, 15 Sep 2018 11:07:26: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 11:07:26: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 11:07:26: #1 total tags in treatment: 209876 INFO @ Sat, 15 Sep 2018 11:07:26: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:07:26: #1 tags after filtering in treatment: 200696 INFO @ Sat, 15 Sep 2018 11:07:26: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:07:26: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:26: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:26: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 11:07:26: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 11:07:26: #1 total tags in treatment: 209876 INFO @ Sat, 15 Sep 2018 11:07:26: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:07:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:07:26: #1 tags after filtering in treatment: 200696 INFO @ Sat, 15 Sep 2018 11:07:26: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 11:07:26: #1 finished! INFO @ Sat, 15 Sep 2018 11:07:26: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:07:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:07:26: #2 number of paired peaks: 214 WARNING @ Sat, 15 Sep 2018 11:07:26: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:26: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:26: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:26: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:26: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:26: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Sep 2018 11:07:26: #2 alternative fragment length(s) may be 163,184,210 bps INFO @ Sat, 15 Sep 2018 11:07:26: #2.2 Generate R script for model : SRX4337750.10_model.r INFO @ Sat, 15 Sep 2018 11:07:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:26: #2 number of paired peaks: 214 WARNING @ Sat, 15 Sep 2018 11:07:26: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Sat, 15 Sep 2018 11:07:26: start model_add_line... INFO @ Sat, 15 Sep 2018 11:07:26: start X-correlation... INFO @ Sat, 15 Sep 2018 11:07:26: end of X-cor INFO @ Sat, 15 Sep 2018 11:07:26: #2 finished! INFO @ Sat, 15 Sep 2018 11:07:26: #2 predicted fragment length is 184 bps INFO @ Sat, 15 Sep 2018 11:07:26: #2 alternative fragment length(s) may be 163,184,210 bps INFO @ Sat, 15 Sep 2018 11:07:26: #2.2 Generate R script for model : SRX4337750.20_model.r INFO @ Sat, 15 Sep 2018 11:07:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:07:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write output xls file... SRX4337750.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write peak in narrowPeak format file... SRX4337750.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write summits bed file... SRX4337750.10_summits.bed INFO @ Sat, 15 Sep 2018 11:07:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write output xls file... SRX4337750.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write peak in narrowPeak format file... SRX4337750.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:07:27: #4 Write summits bed file... SRX4337750.20_summits.bed INFO @ Sat, 15 Sep 2018 11:07:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。