Job ID = 10254413 sra ファイルのダウンロード中... Completed: 784035K bytes transferred in 10 seconds (594400K 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... Written 17372460 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2658707/SRR5363223.sra Written 17372460 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: 00:08:49 17372460 reads; of these: 17372460 (100.00%) were paired; of these: 7576370 (43.61%) aligned concordantly 0 times 8100594 (46.63%) aligned concordantly exactly 1 time 1695496 (9.76%) aligned concordantly >1 times ---- 7576370 pairs aligned concordantly 0 times; of these: 136386 (1.80%) aligned discordantly 1 time ---- 7439984 pairs aligned 0 times concordantly or discordantly; of these: 14879968 mates make up the pairs; of these: 14608218 (98.17%) aligned 0 times 144897 (0.97%) aligned exactly 1 time 126853 (0.85%) aligned >1 times 57.96% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [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] 8596507 / 9926968 = 0.8660 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, 06 Dec 2017 18:02:05: # Command line: callpeak -t SRX2658707.bam -f BAM -g 12100000 -n SRX2658707.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2658707.20 # format = BAM # ChIP-seq file = ['SRX2658707.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 @ Wed, 06 Dec 2017 18:02:05: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:02:05: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:02:05: # Command line: callpeak -t SRX2658707.bam -f BAM -g 12100000 -n SRX2658707.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2658707.05 # format = BAM # ChIP-seq file = ['SRX2658707.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 @ Wed, 06 Dec 2017 18:02:05: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:02:05: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:02:05: # Command line: callpeak -t SRX2658707.bam -f BAM -g 12100000 -n SRX2658707.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2658707.10 # format = BAM # ChIP-seq file = ['SRX2658707.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 @ Wed, 06 Dec 2017 18:02:05: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:02:05: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:02:11: 1000000 INFO @ Wed, 06 Dec 2017 18:02:11: 1000000 INFO @ Wed, 06 Dec 2017 18:02:11: 1000000 INFO @ Wed, 06 Dec 2017 18:02:17: 2000000 INFO @ Wed, 06 Dec 2017 18:02:17: 2000000 INFO @ Wed, 06 Dec 2017 18:02:17: 2000000 INFO @ Wed, 06 Dec 2017 18:02:22: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:02:22: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:02:22: #1 total tags in treatment: 1296009 INFO @ Wed, 06 Dec 2017 18:02:22: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:02:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:02:22: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:02:22: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:02:22: #1 total tags in treatment: 1296009 INFO @ Wed, 06 Dec 2017 18:02:22: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:02:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:02:22: #1 tags after filtering in treatment: 987057 INFO @ Wed, 06 Dec 2017 18:02:22: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 06 Dec 2017 18:02:22: #1 finished! INFO @ Wed, 06 Dec 2017 18:02:22: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:02:22: #1 tags after filtering in treatment: 987057 INFO @ Wed, 06 Dec 2017 18:02:22: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 06 Dec 2017 18:02:22: #1 finished! INFO @ Wed, 06 Dec 2017 18:02:22: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:02:23: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 18:02:23: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 18:02:23: #1 total tags in treatment: 1296009 INFO @ Wed, 06 Dec 2017 18:02:23: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:02:23: #2 number of paired peaks: 166 WARNING @ Wed, 06 Dec 2017 18:02:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 06 Dec 2017 18:02:23: start model_add_line... INFO @ Wed, 06 Dec 2017 18:02:23: #2 number of paired peaks: 166 WARNING @ Wed, 06 Dec 2017 18:02:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 06 Dec 2017 18:02:23: start model_add_line... INFO @ Wed, 06 Dec 2017 18:02:23: start X-correlation... INFO @ Wed, 06 Dec 2017 18:02:23: end of X-cor INFO @ Wed, 06 Dec 2017 18:02:23: #2 finished! INFO @ Wed, 06 Dec 2017 18:02:23: #2 predicted fragment length is 178 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2 alternative fragment length(s) may be 3,130,164,178,194,225 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2.2 Generate R script for model : SRX2658707.05_model.r INFO @ Wed, 06 Dec 2017 18:02:23: #1 tags after filtering in treatment: 987057 INFO @ Wed, 06 Dec 2017 18:02:23: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 06 Dec 2017 18:02:23: #1 finished! INFO @ Wed, 06 Dec 2017 18:02:23: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:02:23: start X-correlation... INFO @ Wed, 06 Dec 2017 18:02:23: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:02:23: end of X-cor INFO @ Wed, 06 Dec 2017 18:02:23: #2 finished! INFO @ Wed, 06 Dec 2017 18:02:23: #2 predicted fragment length is 178 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2 alternative fragment length(s) may be 3,130,164,178,194,225 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2.2 Generate R script for model : SRX2658707.10_model.r INFO @ Wed, 06 Dec 2017 18:02:23: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:02:23: #2 number of paired peaks: 166 WARNING @ Wed, 06 Dec 2017 18:02:23: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Wed, 06 Dec 2017 18:02:23: start model_add_line... INFO @ Wed, 06 Dec 2017 18:02:23: start X-correlation... INFO @ Wed, 06 Dec 2017 18:02:23: end of X-cor INFO @ Wed, 06 Dec 2017 18:02:23: #2 finished! INFO @ Wed, 06 Dec 2017 18:02:23: #2 predicted fragment length is 178 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2 alternative fragment length(s) may be 3,130,164,178,194,225 bps INFO @ Wed, 06 Dec 2017 18:02:23: #2.2 Generate R script for model : SRX2658707.20_model.r INFO @ Wed, 06 Dec 2017 18:02:23: #3 Call peaks... INFO @ Wed, 06 Dec 2017 18:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 06 Dec 2017 18:02:26: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:02:26: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:02:26: #3 Call peaks for each chromosome... INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write output xls file... SRX2658707.05_peaks.xls INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write peak in narrowPeak format file... SRX2658707.05_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write summits bed file... SRX2658707.05_summits.bed INFO @ Wed, 06 Dec 2017 18:02:27: Done! INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write output xls file... SRX2658707.20_peaks.xls INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write peak in narrowPeak format file... SRX2658707.20_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write summits bed file... SRX2658707.20_summits.bed INFO @ Wed, 06 Dec 2017 18:02:27: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (502 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write output xls file... SRX2658707.10_peaks.xls INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write peak in narrowPeak format file... SRX2658707.10_peaks.narrowPeak INFO @ Wed, 06 Dec 2017 18:02:27: #4 Write summits bed file... SRX2658707.10_summits.bed INFO @ Wed, 06 Dec 2017 18:02:27: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。