Job ID = 11192913 sra ファイルのダウンロード中... Completed: 626741K bytes transferred in 7 seconds (669573K 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 15670905 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242028/SRR6129634.sra Written 15670905 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242028/SRR6129634.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: 00:11:11 15670905 reads; of these: 15670905 (100.00%) were paired; of these: 12694399 (81.01%) aligned concordantly 0 times 1933129 (12.34%) aligned concordantly exactly 1 time 1043377 (6.66%) aligned concordantly >1 times ---- 12694399 pairs aligned concordantly 0 times; of these: 1289831 (10.16%) aligned discordantly 1 time ---- 11404568 pairs aligned 0 times concordantly or discordantly; of these: 22809136 mates make up the pairs; of these: 15653156 (68.63%) aligned 0 times 5916210 (25.94%) aligned exactly 1 time 1239770 (5.44%) aligned >1 times 50.06% overall alignment rate Time searching: 00:11:11 Overall time: 00:11:11 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 8 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] 997573 / 3862463 = 0.2583 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 10:41:53: # Command line: callpeak -t SRX3242028.bam -f BAM -g 12100000 -n SRX3242028.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242028.10 # format = BAM # ChIP-seq file = ['SRX3242028.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 10:41:53: # Command line: callpeak -t SRX3242028.bam -f BAM -g 12100000 -n SRX3242028.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242028.05 # format = BAM # ChIP-seq file = ['SRX3242028.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 10:41:53: # Command line: callpeak -t SRX3242028.bam -f BAM -g 12100000 -n SRX3242028.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242028.20 # format = BAM # ChIP-seq file = ['SRX3242028.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 10:41:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:53: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:41:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:53: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:41:59: 1000000 INFO @ Sat, 15 Sep 2018 10:41:59: 1000000 INFO @ Sat, 15 Sep 2018 10:41:59: 1000000 INFO @ Sat, 15 Sep 2018 10:42:05: 2000000 INFO @ Sat, 15 Sep 2018 10:42:05: 2000000 INFO @ Sat, 15 Sep 2018 10:42:05: 2000000 INFO @ Sat, 15 Sep 2018 10:42:10: 3000000 INFO @ Sat, 15 Sep 2018 10:42:10: 3000000 INFO @ Sat, 15 Sep 2018 10:42:10: 3000000 INFO @ Sat, 15 Sep 2018 10:42:16: 4000000 INFO @ Sat, 15 Sep 2018 10:42:16: 4000000 INFO @ Sat, 15 Sep 2018 10:42:16: 4000000 INFO @ Sat, 15 Sep 2018 10:42:21: 5000000 INFO @ Sat, 15 Sep 2018 10:42:21: 5000000 INFO @ Sat, 15 Sep 2018 10:42:21: 5000000 INFO @ Sat, 15 Sep 2018 10:42:27: 6000000 INFO @ Sat, 15 Sep 2018 10:42:27: 6000000 INFO @ Sat, 15 Sep 2018 10:42:27: 6000000 INFO @ Sat, 15 Sep 2018 10:42:32: 7000000 INFO @ Sat, 15 Sep 2018 10:42:32: 7000000 INFO @ Sat, 15 Sep 2018 10:42:32: 7000000 INFO @ Sat, 15 Sep 2018 10:42:38: 8000000 INFO @ Sat, 15 Sep 2018 10:42:38: 8000000 INFO @ Sat, 15 Sep 2018 10:42:38: 8000000 INFO @ Sat, 15 Sep 2018 10:42:44: 9000000 INFO @ Sat, 15 Sep 2018 10:42:44: 9000000 INFO @ Sat, 15 Sep 2018 10:42:44: 9000000 INFO @ Sat, 15 Sep 2018 10:42:50: 10000000 INFO @ Sat, 15 Sep 2018 10:42:50: 10000000 INFO @ Sat, 15 Sep 2018 10:42:50: 10000000 INFO @ Sat, 15 Sep 2018 10:42:56: 11000000 INFO @ Sat, 15 Sep 2018 10:42:56: 11000000 INFO @ Sat, 15 Sep 2018 10:42:56: 11000000 INFO @ Sat, 15 Sep 2018 10:43:02: 12000000 INFO @ Sat, 15 Sep 2018 10:43:02: 12000000 INFO @ Sat, 15 Sep 2018 10:43:02: 12000000 INFO @ Sat, 15 Sep 2018 10:43:07: 13000000 INFO @ Sat, 15 Sep 2018 10:43:07: 13000000 INFO @ Sat, 15 Sep 2018 10:43:07: 13000000 INFO @ Sat, 15 Sep 2018 10:43:11: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:43:11: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:43:11: #1 total tags in treatment: 2517952 INFO @ Sat, 15 Sep 2018 10:43:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:11: #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 10:43:11: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:43:11: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:43:11: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:43:11: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:43:11: #1 total tags in treatment: 2517952 INFO @ Sat, 15 Sep 2018 10:43:11: #1 total tags in treatment: 2517952 INFO @ Sat, 15 Sep 2018 10:43:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:11: #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 10:43:11: #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 10:43:11: #1 tags after filtering in treatment: 1564094 INFO @ Sat, 15 Sep 2018 10:43:11: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:43:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:11: #1 tags after filtering in treatment: 1564094 INFO @ Sat, 15 Sep 2018 10:43:11: #1 tags after filtering in treatment: 1564094 INFO @ Sat, 15 Sep 2018 10:43:11: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:43:11: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Sep 2018 10:43:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:12: #2 number of paired peaks: 647 WARNING @ Sat, 15 Sep 2018 10:43:12: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:12: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:12: #2 number of paired peaks: 647 WARNING @ Sat, 15 Sep 2018 10:43:12: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:12: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:12: #2 number of paired peaks: 647 WARNING @ Sat, 15 Sep 2018 10:43:12: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:12: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:12: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:12: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:12: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:12: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:12: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:12: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:12: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:12: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:12: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:12: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2 alternative fragment length(s) may be 4,170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2 alternative fragment length(s) may be 4,170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2 alternative fragment length(s) may be 4,170 bps INFO @ Sat, 15 Sep 2018 10:43:12: #2.2 Generate R script for model : SRX3242028.20_model.r INFO @ Sat, 15 Sep 2018 10:43:12: #2.2 Generate R script for model : SRX3242028.10_model.r INFO @ Sat, 15 Sep 2018 10:43:12: #2.2 Generate R script for model : SRX3242028.05_model.r INFO @ Sat, 15 Sep 2018 10:43:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:12: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write output xls file... SRX3242028.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write peak in narrowPeak format file... SRX3242028.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write summits bed file... SRX3242028.20_summits.bed INFO @ Sat, 15 Sep 2018 10:43:20: Done! INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write output xls file... SRX3242028.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write peak in narrowPeak format file... SRX3242028.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write summits bed file... SRX3242028.10_summits.bed INFO @ Sat, 15 Sep 2018 10:43:20: Done! INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write output xls file... SRX3242028.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write peak in narrowPeak format file... SRX3242028.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:20: #4 Write summits bed file... SRX3242028.05_summits.bed INFO @ Sat, 15 Sep 2018 10:43:20: Done! pass1 - making usageList (17 chroms): 20 millis pass1 - making usageList (17 chroms): 20 millis pass1 - making usageList (17 chroms): 20 millis pass2 - checking and writing primary data (250 records, 4 fields): 6 millis pass2 - checking and writing primary data (355 records, 4 fields): 6 millis pass2 - checking and writing primary data (422 records, 4 fields): 6 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。