Job ID = 11633439 sra ファイルのダウンロード中... Completed: 220602K bytes transferred in 5 seconds (360179K 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 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236216/ERR1162809.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236216/ERR1162809.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:08 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 269917 (6.75%) aligned concordantly 0 times 3403563 (85.09%) aligned concordantly exactly 1 time 326520 (8.16%) aligned concordantly >1 times ---- 269917 pairs aligned concordantly 0 times; of these: 60902 (22.56%) aligned discordantly 1 time ---- 209015 pairs aligned 0 times concordantly or discordantly; of these: 418030 mates make up the pairs; of these: 374489 (89.58%) aligned 0 times 27743 (6.64%) aligned exactly 1 time 15798 (3.78%) aligned >1 times 95.32% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 640147 / 3785921 = 0.1691 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 @ Fri, 15 Feb 2019 09:01:01: # Command line: callpeak -t ERX1236216.bam -f BAM -g 12100000 -n ERX1236216.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236216.20 # format = BAM # ChIP-seq file = ['ERX1236216.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 @ Fri, 15 Feb 2019 09:01:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:01: # Command line: callpeak -t ERX1236216.bam -f BAM -g 12100000 -n ERX1236216.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236216.10 # format = BAM # ChIP-seq file = ['ERX1236216.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 @ Fri, 15 Feb 2019 09:01:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:01: # Command line: callpeak -t ERX1236216.bam -f BAM -g 12100000 -n ERX1236216.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236216.05 # format = BAM # ChIP-seq file = ['ERX1236216.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 @ Fri, 15 Feb 2019 09:01:01: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:01:01: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:07: 1000000 INFO @ Fri, 15 Feb 2019 09:01:07: 1000000 INFO @ Fri, 15 Feb 2019 09:01:07: 1000000 INFO @ Fri, 15 Feb 2019 09:01:13: 2000000 INFO @ Fri, 15 Feb 2019 09:01:13: 2000000 INFO @ Fri, 15 Feb 2019 09:01:13: 2000000 INFO @ Fri, 15 Feb 2019 09:01:18: 3000000 INFO @ Fri, 15 Feb 2019 09:01:19: 3000000 INFO @ Fri, 15 Feb 2019 09:01:19: 3000000 INFO @ Fri, 15 Feb 2019 09:01:24: 4000000 INFO @ Fri, 15 Feb 2019 09:01:25: 4000000 INFO @ Fri, 15 Feb 2019 09:01:25: 4000000 INFO @ Fri, 15 Feb 2019 09:01:30: 5000000 INFO @ Fri, 15 Feb 2019 09:01:31: 5000000 INFO @ Fri, 15 Feb 2019 09:01:31: 5000000 INFO @ Fri, 15 Feb 2019 09:01:37: 6000000 INFO @ Fri, 15 Feb 2019 09:01:37: 6000000 INFO @ Fri, 15 Feb 2019 09:01:38: 6000000 INFO @ Fri, 15 Feb 2019 09:01:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:39: #1 total tags in treatment: 3103306 INFO @ Fri, 15 Feb 2019 09:01:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:01:39: #1 tags after filtering in treatment: 2709639 INFO @ Fri, 15 Feb 2019 09:01:39: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:39: #2 number of paired peaks: 120 WARNING @ Fri, 15 Feb 2019 09:01:39: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:39: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:39: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:39: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:39: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:39: #2 predicted fragment length is 133 bps INFO @ Fri, 15 Feb 2019 09:01:39: #2 alternative fragment length(s) may be 3,71,95,133,171 bps INFO @ Fri, 15 Feb 2019 09:01:39: #2.2 Generate R script for model : ERX1236216.20_model.r INFO @ Fri, 15 Feb 2019 09:01:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:39: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:39: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:39: #1 total tags in treatment: 3103306 INFO @ Fri, 15 Feb 2019 09:01:39: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:01:39: #1 tags after filtering in treatment: 2709639 INFO @ Fri, 15 Feb 2019 09:01:39: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:39: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:39: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:39: #2 number of paired peaks: 120 WARNING @ Fri, 15 Feb 2019 09:01:39: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:39: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:39: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:39: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:39: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:39: #2 predicted fragment length is 133 bps INFO @ Fri, 15 Feb 2019 09:01:39: #2 alternative fragment length(s) may be 3,71,95,133,171 bps INFO @ Fri, 15 Feb 2019 09:01:39: #2.2 Generate R script for model : ERX1236216.10_model.r INFO @ Fri, 15 Feb 2019 09:01:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:40: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:40: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:40: #1 total tags in treatment: 3103306 INFO @ Fri, 15 Feb 2019 09:01:40: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 09:01:40: #1 tags after filtering in treatment: 2709639 INFO @ Fri, 15 Feb 2019 09:01:40: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:40: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:40: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:40: #2 number of paired peaks: 120 WARNING @ Fri, 15 Feb 2019 09:01:40: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:40: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:40: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:40: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:40: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:40: #2 predicted fragment length is 133 bps INFO @ Fri, 15 Feb 2019 09:01:40: #2 alternative fragment length(s) may be 3,71,95,133,171 bps INFO @ Fri, 15 Feb 2019 09:01:40: #2.2 Generate R script for model : ERX1236216.05_model.r INFO @ Fri, 15 Feb 2019 09:01:40: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:46: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:47: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:48: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:49: #4 Write output xls file... ERX1236216.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:49: #4 Write peak in narrowPeak format file... ERX1236216.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:49: #4 Write summits bed file... ERX1236216.20_summits.bed INFO @ Fri, 15 Feb 2019 09:01:49: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (293 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write output xls file... ERX1236216.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write peak in narrowPeak format file... ERX1236216.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write summits bed file... ERX1236216.10_summits.bed INFO @ Fri, 15 Feb 2019 09:01:50: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (487 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write output xls file... ERX1236216.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write peak in narrowPeak format file... ERX1236216.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:50: #4 Write summits bed file... ERX1236216.05_summits.bed INFO @ Fri, 15 Feb 2019 09:01:50: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (865 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。