Job ID = 11245055 sra ファイルのダウンロード中... Completed: 137103K bytes transferred in 4 seconds (241703K 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 3986147 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554767/SRR7696439.sra Written 3986147 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554767/SRR7696439.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: 00:01:59 3986147 reads; of these: 3986147 (100.00%) were paired; of these: 2614864 (65.60%) aligned concordantly 0 times 986902 (24.76%) aligned concordantly exactly 1 time 384381 (9.64%) aligned concordantly >1 times ---- 2614864 pairs aligned concordantly 0 times; of these: 592 (0.02%) aligned discordantly 1 time ---- 2614272 pairs aligned 0 times concordantly or discordantly; of these: 5228544 mates make up the pairs; of these: 3827455 (73.20%) aligned 0 times 1040939 (19.91%) aligned exactly 1 time 360150 (6.89%) aligned >1 times 51.99% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 156678 / 1371598 = 0.1142 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 @ Tue, 09 Oct 2018 23:17:48: # Command line: callpeak -t SRX4554767.bam -f BAM -g 12100000 -n SRX4554767.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554767.10 # format = BAM # ChIP-seq file = ['SRX4554767.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 @ Tue, 09 Oct 2018 23:17:48: # Command line: callpeak -t SRX4554767.bam -f BAM -g 12100000 -n SRX4554767.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554767.05 # format = BAM # ChIP-seq file = ['SRX4554767.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 @ Tue, 09 Oct 2018 23:17:48: # Command line: callpeak -t SRX4554767.bam -f BAM -g 12100000 -n SRX4554767.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554767.20 # format = BAM # ChIP-seq file = ['SRX4554767.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 @ Tue, 09 Oct 2018 23:17:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:48: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:17:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:48: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:17:53: 1000000 INFO @ Tue, 09 Oct 2018 23:17:53: 1000000 INFO @ Tue, 09 Oct 2018 23:17:53: 1000000 INFO @ Tue, 09 Oct 2018 23:17:58: 2000000 INFO @ Tue, 09 Oct 2018 23:17:58: 2000000 INFO @ Tue, 09 Oct 2018 23:17:58: 2000000 INFO @ Tue, 09 Oct 2018 23:18:02: 3000000 INFO @ Tue, 09 Oct 2018 23:18:03: 3000000 INFO @ Tue, 09 Oct 2018 23:18:03: 3000000 INFO @ Tue, 09 Oct 2018 23:18:06: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:06: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:06: #1 total tags in treatment: 1214608 INFO @ Tue, 09 Oct 2018 23:18:06: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:06: #1 tags after filtering in treatment: 785696 INFO @ Tue, 09 Oct 2018 23:18:06: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 09 Oct 2018 23:18:06: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:06: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #2 number of paired peaks: 248 WARNING @ Tue, 09 Oct 2018 23:18:07: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:07: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:07: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:07: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:07: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:07: #2 predicted fragment length is 160 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2 alternative fragment length(s) may be 138,160,178,216,463,497,550,562 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2.2 Generate R script for model : SRX4554767.05_model.r INFO @ Tue, 09 Oct 2018 23:18:07: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:07: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:07: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:07: #1 total tags in treatment: 1214608 INFO @ Tue, 09 Oct 2018 23:18:07: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:07: #1 tags after filtering in treatment: 785696 INFO @ Tue, 09 Oct 2018 23:18:07: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 09 Oct 2018 23:18:07: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:07: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:18:07: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:18:07: #1 total tags in treatment: 1214608 INFO @ Tue, 09 Oct 2018 23:18:07: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:07: #1 tags after filtering in treatment: 785696 INFO @ Tue, 09 Oct 2018 23:18:07: #1 Redundant rate of treatment: 0.35 INFO @ Tue, 09 Oct 2018 23:18:07: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:07: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #2 number of paired peaks: 248 WARNING @ Tue, 09 Oct 2018 23:18:07: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:07: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:07: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:07: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:07: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:07: #2 predicted fragment length is 160 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2 alternative fragment length(s) may be 138,160,178,216,463,497,550,562 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2.2 Generate R script for model : SRX4554767.20_model.r INFO @ Tue, 09 Oct 2018 23:18:07: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:07: #2 number of paired peaks: 248 WARNING @ Tue, 09 Oct 2018 23:18:07: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 09 Oct 2018 23:18:07: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:07: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:07: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:07: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:07: #2 predicted fragment length is 160 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2 alternative fragment length(s) may be 138,160,178,216,463,497,550,562 bps INFO @ Tue, 09 Oct 2018 23:18:07: #2.2 Generate R script for model : SRX4554767.10_model.r INFO @ Tue, 09 Oct 2018 23:18:07: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:09: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:10: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:10: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:10: #4 Write output xls file... SRX4554767.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:10: #4 Write peak in narrowPeak format file... SRX4554767.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:10: #4 Write summits bed file... SRX4554767.05_summits.bed INFO @ Tue, 09 Oct 2018 23:18:10: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write output xls file... SRX4554767.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write peak in narrowPeak format file... SRX4554767.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write summits bed file... SRX4554767.10_summits.bed INFO @ Tue, 09 Oct 2018 23:18:11: Done! INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write output xls file... SRX4554767.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write peak in narrowPeak format file... SRX4554767.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:11: #4 Write summits bed file... SRX4554767.20_summits.bed INFO @ Tue, 09 Oct 2018 23:18:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 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。