Job ID = 11193132 sra ファイルのダウンロード中... Completed: 273570K bytes transferred in 9 seconds (237479K 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 7775715 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337724/SRR7467879.sra Written 7775715 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4337724/SRR7467879.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: 00:03:38 7775715 reads; of these: 7775715 (100.00%) were paired; of these: 6566456 (84.45%) aligned concordantly 0 times 743781 (9.57%) aligned concordantly exactly 1 time 465478 (5.99%) aligned concordantly >1 times ---- 6566456 pairs aligned concordantly 0 times; of these: 589621 (8.98%) aligned discordantly 1 time ---- 5976835 pairs aligned 0 times concordantly or discordantly; of these: 11953670 mates make up the pairs; of these: 9197032 (76.94%) aligned 0 times 2309179 (19.32%) aligned exactly 1 time 447459 (3.74%) aligned >1 times 40.86% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 988870 / 1791429 = 0.5520 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 11:05:01: # Command line: callpeak -t SRX4337724.bam -f BAM -g 12100000 -n SRX4337724.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4337724.05 # format = BAM # ChIP-seq file = ['SRX4337724.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 11:05:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:01: # Command line: callpeak -t SRX4337724.bam -f BAM -g 12100000 -n SRX4337724.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4337724.10 # format = BAM # ChIP-seq file = ['SRX4337724.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 11:05:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:01: # Command line: callpeak -t SRX4337724.bam -f BAM -g 12100000 -n SRX4337724.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4337724.20 # format = BAM # ChIP-seq file = ['SRX4337724.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 11:05:01: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:05:01: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:05:09: 1000000 INFO @ Sat, 15 Sep 2018 11:05:09: 1000000 INFO @ Sat, 15 Sep 2018 11:05:09: 1000000 INFO @ Sat, 15 Sep 2018 11:05:15: 2000000 INFO @ Sat, 15 Sep 2018 11:05:15: 2000000 INFO @ Sat, 15 Sep 2018 11:05:16: 2000000 INFO @ Sat, 15 Sep 2018 11:05:22: 3000000 INFO @ Sat, 15 Sep 2018 11:05:22: 3000000 INFO @ Sat, 15 Sep 2018 11:05:25: 3000000 INFO @ Sat, 15 Sep 2018 11:05:29: 4000000 INFO @ Sat, 15 Sep 2018 11:05:29: 4000000 INFO @ Sat, 15 Sep 2018 11:05:31: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:05:31: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:05:31: #1 total tags in treatment: 649932 INFO @ Sat, 15 Sep 2018 11:05:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:31: #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 11:05:31: #1 tags after filtering in treatment: 446210 INFO @ Sat, 15 Sep 2018 11:05:31: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:05:31: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:31: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:05:31: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:05:31: #1 total tags in treatment: 649932 INFO @ Sat, 15 Sep 2018 11:05:31: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:31: #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 11:05:31: #1 tags after filtering in treatment: 446210 INFO @ Sat, 15 Sep 2018 11:05:31: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:05:31: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:31: #2 number of paired peaks: 153 WARNING @ Sat, 15 Sep 2018 11:05:31: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:31: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:31: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:31: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:31: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:31: #2 predicted fragment length is 200 bps INFO @ Sat, 15 Sep 2018 11:05:31: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 15 Sep 2018 11:05:31: #2.2 Generate R script for model : SRX4337724.10_model.r INFO @ Sat, 15 Sep 2018 11:05:31: #2 number of paired peaks: 153 WARNING @ Sat, 15 Sep 2018 11:05:31: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:31: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:31: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:31: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:31: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:31: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:31: #2 predicted fragment length is 200 bps INFO @ Sat, 15 Sep 2018 11:05:31: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 15 Sep 2018 11:05:31: #2.2 Generate R script for model : SRX4337724.20_model.r INFO @ Sat, 15 Sep 2018 11:05:31: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:33: 4000000 INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write output xls file... SRX4337724.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write peak in narrowPeak format file... SRX4337724.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write summits bed file... SRX4337724.10_summits.bed INFO @ Sat, 15 Sep 2018 11:05:33: Done! INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write output xls file... SRX4337724.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write peak in narrowPeak format file... SRX4337724.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:33: #4 Write summits bed file... SRX4337724.20_summits.bed INFO @ Sat, 15 Sep 2018 11:05:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (239 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:05:35: #1 tag size is determined as 43 bps INFO @ Sat, 15 Sep 2018 11:05:35: #1 tag size = 43 INFO @ Sat, 15 Sep 2018 11:05:35: #1 total tags in treatment: 649932 INFO @ Sat, 15 Sep 2018 11:05:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:05:35: #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 11:05:35: #1 tags after filtering in treatment: 446210 INFO @ Sat, 15 Sep 2018 11:05:35: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 15 Sep 2018 11:05:35: #1 finished! INFO @ Sat, 15 Sep 2018 11:05:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:05:36: #2 number of paired peaks: 153 WARNING @ Sat, 15 Sep 2018 11:05:36: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Sat, 15 Sep 2018 11:05:36: start model_add_line... INFO @ Sat, 15 Sep 2018 11:05:36: start X-correlation... INFO @ Sat, 15 Sep 2018 11:05:36: end of X-cor INFO @ Sat, 15 Sep 2018 11:05:36: #2 finished! INFO @ Sat, 15 Sep 2018 11:05:36: #2 predicted fragment length is 200 bps INFO @ Sat, 15 Sep 2018 11:05:36: #2 alternative fragment length(s) may be 200 bps INFO @ Sat, 15 Sep 2018 11:05:36: #2.2 Generate R script for model : SRX4337724.05_model.r INFO @ Sat, 15 Sep 2018 11:05:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:05:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:05:38: #4 Write output xls file... SRX4337724.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:05:38: #4 Write peak in narrowPeak format file... SRX4337724.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:05:38: #4 Write summits bed file... SRX4337724.05_summits.bed INFO @ Sat, 15 Sep 2018 11:05:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (358 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。