Job ID = 11633471 sra ファイルのダウンロード中... Completed: 220455K bytes transferred in 5 seconds (322419K 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/ERX1236248/ERR1162841.sra Written 4000000 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236248/ERR1162841.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: 00:03:20 4000000 reads; of these: 4000000 (100.00%) were paired; of these: 176866 (4.42%) aligned concordantly 0 times 3423377 (85.58%) aligned concordantly exactly 1 time 399757 (9.99%) aligned concordantly >1 times ---- 176866 pairs aligned concordantly 0 times; of these: 7558 (4.27%) aligned discordantly 1 time ---- 169308 pairs aligned 0 times concordantly or discordantly; of these: 338616 mates make up the pairs; of these: 310790 (91.78%) aligned 0 times 22082 (6.52%) aligned exactly 1 time 5744 (1.70%) aligned >1 times 96.12% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 926873 / 3826903 = 0.2422 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 09:00:57: # Command line: callpeak -t ERX1236248.bam -f BAM -g 12100000 -n ERX1236248.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236248.10 # format = BAM # ChIP-seq file = ['ERX1236248.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 09:00:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:57: # Command line: callpeak -t ERX1236248.bam -f BAM -g 12100000 -n ERX1236248.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236248.20 # format = BAM # ChIP-seq file = ['ERX1236248.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 09:00:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:00:57: # Command line: callpeak -t ERX1236248.bam -f BAM -g 12100000 -n ERX1236248.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236248.05 # format = BAM # ChIP-seq file = ['ERX1236248.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 09:00:57: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:00:57: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:01:03: 1000000 INFO @ Fri, 15 Feb 2019 09:01:03: 1000000 INFO @ Fri, 15 Feb 2019 09:01:03: 1000000 INFO @ Fri, 15 Feb 2019 09:01:09: 2000000 INFO @ Fri, 15 Feb 2019 09:01:09: 2000000 INFO @ Fri, 15 Feb 2019 09:01:09: 2000000 INFO @ Fri, 15 Feb 2019 09:01:15: 3000000 INFO @ Fri, 15 Feb 2019 09:01:16: 3000000 INFO @ Fri, 15 Feb 2019 09:01:16: 3000000 INFO @ Fri, 15 Feb 2019 09:01:21: 4000000 INFO @ Fri, 15 Feb 2019 09:01:22: 4000000 INFO @ Fri, 15 Feb 2019 09:01:22: 4000000 INFO @ Fri, 15 Feb 2019 09:01:27: 5000000 INFO @ Fri, 15 Feb 2019 09:01:28: 5000000 INFO @ Fri, 15 Feb 2019 09:01:28: 5000000 INFO @ Fri, 15 Feb 2019 09:01:32: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:32: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:32: #1 total tags in treatment: 2897567 INFO @ Fri, 15 Feb 2019 09:01:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:32: #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 09:01:32: #1 tags after filtering in treatment: 2518719 INFO @ Fri, 15 Feb 2019 09:01:32: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:32: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:32: #2 number of paired peaks: 129 WARNING @ Fri, 15 Feb 2019 09:01:32: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:32: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:32: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:32: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:32: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:32: #2 predicted fragment length is 120 bps INFO @ Fri, 15 Feb 2019 09:01:32: #2 alternative fragment length(s) may be 3,120,157,211 bps INFO @ Fri, 15 Feb 2019 09:01:32: #2.2 Generate R script for model : ERX1236248.10_model.r INFO @ Fri, 15 Feb 2019 09:01:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:33: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:01:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:33: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:01:33: #1 total tags in treatment: 2897567 INFO @ Fri, 15 Feb 2019 09:01:33: #1 total tags in treatment: 2897567 INFO @ Fri, 15 Feb 2019 09:01:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:33: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:01:33: #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 09:01:33: #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 09:01:33: #1 tags after filtering in treatment: 2518719 INFO @ Fri, 15 Feb 2019 09:01:33: #1 tags after filtering in treatment: 2518719 INFO @ Fri, 15 Feb 2019 09:01:33: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:33: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 09:01:33: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:33: #1 finished! INFO @ Fri, 15 Feb 2019 09:01:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:01:33: #2 number of paired peaks: 129 WARNING @ Fri, 15 Feb 2019 09:01:33: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:33: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:33: #2 number of paired peaks: 129 WARNING @ Fri, 15 Feb 2019 09:01:33: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Fri, 15 Feb 2019 09:01:33: start model_add_line... INFO @ Fri, 15 Feb 2019 09:01:33: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:33: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:33: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:33: #2 predicted fragment length is 120 bps INFO @ Fri, 15 Feb 2019 09:01:33: #2 alternative fragment length(s) may be 3,120,157,211 bps INFO @ Fri, 15 Feb 2019 09:01:33: #2.2 Generate R script for model : ERX1236248.20_model.r INFO @ Fri, 15 Feb 2019 09:01:33: start X-correlation... INFO @ Fri, 15 Feb 2019 09:01:33: end of X-cor INFO @ Fri, 15 Feb 2019 09:01:33: #2 finished! INFO @ Fri, 15 Feb 2019 09:01:33: #2 predicted fragment length is 120 bps INFO @ Fri, 15 Feb 2019 09:01:33: #2 alternative fragment length(s) may be 3,120,157,211 bps INFO @ Fri, 15 Feb 2019 09:01:33: #2.2 Generate R script for model : ERX1236248.05_model.r INFO @ Fri, 15 Feb 2019 09:01:33: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:33: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:01:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:01:39: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:40: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:01:41: #4 Write output xls file... ERX1236248.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:41: #4 Write peak in narrowPeak format file... ERX1236248.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:41: #4 Write summits bed file... ERX1236248.10_summits.bed INFO @ Fri, 15 Feb 2019 09:01:41: Done! pass1 - making usageList (16 chroms): 7 millis pass2 - checking and writing primary data (432 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:01:42: #4 Write output xls file... ERX1236248.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:43: #4 Write peak in narrowPeak format file... ERX1236248.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:43: #4 Write summits bed file... ERX1236248.20_summits.bed INFO @ Fri, 15 Feb 2019 09:01:43: Done! pass1 - making usageList (16 chroms): 6 millis pass2 - checking and writing primary data (240 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:01:43: #4 Write output xls file... ERX1236248.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:01:43: #4 Write peak in narrowPeak format file... ERX1236248.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:01:43: #4 Write summits bed file... ERX1236248.05_summits.bed INFO @ Fri, 15 Feb 2019 09:01:43: Done! pass1 - making usageList (16 chroms): 5 millis pass2 - checking and writing primary data (727 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。