Job ID = 11633537 sra ファイルのダウンロード中... Completed: 136091K bytes transferred in 4 seconds (240341K 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 2281457 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236314/ERR1162907.sra Written 2281457 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1236314/ERR1162907.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: 00:01:32 2281457 reads; of these: 2281457 (100.00%) were paired; of these: 480444 (21.06%) aligned concordantly 0 times 1606240 (70.40%) aligned concordantly exactly 1 time 194773 (8.54%) aligned concordantly >1 times ---- 480444 pairs aligned concordantly 0 times; of these: 15495 (3.23%) aligned discordantly 1 time ---- 464949 pairs aligned 0 times concordantly or discordantly; of these: 929898 mates make up the pairs; of these: 920203 (98.96%) aligned 0 times 5233 (0.56%) aligned exactly 1 time 4462 (0.48%) aligned >1 times 79.83% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 433231 / 1816213 = 0.2385 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 09:02:50: # Command line: callpeak -t ERX1236314.bam -f BAM -g 12100000 -n ERX1236314.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1236314.10 # format = BAM # ChIP-seq file = ['ERX1236314.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 09:02:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:02:50: # Command line: callpeak -t ERX1236314.bam -f BAM -g 12100000 -n ERX1236314.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1236314.20 # format = BAM # ChIP-seq file = ['ERX1236314.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 09:02:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:02:50: # Command line: callpeak -t ERX1236314.bam -f BAM -g 12100000 -n ERX1236314.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1236314.05 # format = BAM # ChIP-seq file = ['ERX1236314.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 09:02:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 09:02:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 09:02:56: 1000000 INFO @ Fri, 15 Feb 2019 09:02:56: 1000000 INFO @ Fri, 15 Feb 2019 09:02:56: 1000000 INFO @ Fri, 15 Feb 2019 09:03:01: 2000000 INFO @ Fri, 15 Feb 2019 09:03:01: 2000000 INFO @ Fri, 15 Feb 2019 09:03:02: 2000000 INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:06: #1 total tags in treatment: 1371779 INFO @ Fri, 15 Feb 2019 09:03:06: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:06: #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 09:03:06: #1 tags after filtering in treatment: 1275288 INFO @ Fri, 15 Feb 2019 09:03:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:03:06: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #2 number of paired peaks: 138 WARNING @ Fri, 15 Feb 2019 09:03:06: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:06: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:06: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:06: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:06: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 predicted fragment length is 132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2 alternative fragment length(s) may be 4,93,99,117,132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2.2 Generate R script for model : ERX1236314.10_model.r INFO @ Fri, 15 Feb 2019 09:03:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:06: #1 total tags in treatment: 1371779 INFO @ Fri, 15 Feb 2019 09:03:06: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:06: #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 09:03:06: #1 tags after filtering in treatment: 1275288 INFO @ Fri, 15 Feb 2019 09:03:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:03:06: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 09:03:06: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 09:03:06: #1 total tags in treatment: 1371779 INFO @ Fri, 15 Feb 2019 09:03:06: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 09:03:06: #2 number of paired peaks: 138 INFO @ Fri, 15 Feb 2019 09:03:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Fri, 15 Feb 2019 09:03:06: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:06: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:06: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:06: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:06: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 predicted fragment length is 132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2 alternative fragment length(s) may be 4,93,99,117,132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2.2 Generate R script for model : ERX1236314.05_model.r INFO @ Fri, 15 Feb 2019 09:03:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:06: #1 tags after filtering in treatment: 1275288 INFO @ Fri, 15 Feb 2019 09:03:06: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 15 Feb 2019 09:03:06: #1 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 09:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #2 number of paired peaks: 138 WARNING @ Fri, 15 Feb 2019 09:03:06: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Fri, 15 Feb 2019 09:03:06: start model_add_line... INFO @ Fri, 15 Feb 2019 09:03:06: start X-correlation... INFO @ Fri, 15 Feb 2019 09:03:06: end of X-cor INFO @ Fri, 15 Feb 2019 09:03:06: #2 finished! INFO @ Fri, 15 Feb 2019 09:03:06: #2 predicted fragment length is 132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2 alternative fragment length(s) may be 4,93,99,117,132 bps INFO @ Fri, 15 Feb 2019 09:03:06: #2.2 Generate R script for model : ERX1236314.20_model.r INFO @ Fri, 15 Feb 2019 09:03:06: #3 Call peaks... INFO @ Fri, 15 Feb 2019 09:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 09:03:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:09: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:10: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 09:03:10: #4 Write output xls file... ERX1236314.10_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:10: #4 Write peak in narrowPeak format file... ERX1236314.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:03:10: #4 Write summits bed file... ERX1236314.10_summits.bed INFO @ Fri, 15 Feb 2019 09:03:10: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (250 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write output xls file... ERX1236314.20_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write peak in narrowPeak format file... ERX1236314.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write summits bed file... ERX1236314.20_summits.bed INFO @ Fri, 15 Feb 2019 09:03:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (109 records, 4 fields): 3 millis INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write output xls file... ERX1236314.05_peaks.xls INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write peak in narrowPeak format file... ERX1236314.05_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 09:03:11: #4 Write summits bed file... ERX1236314.05_summits.bed INFO @ Fri, 15 Feb 2019 09:03:11: Done! pass1 - making usageList (16 chroms): 3 millis pass2 - checking and writing primary data (431 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。