Job ID = 9162005 sra ファイルのダウンロード中... Completed: 906553K bytes transferred in 10 seconds (696020K bits/sec), in 1 file, 2 directories. 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... Written 21059642 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1423737/SRR2931026.sra Written 21059642 spots total 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: 00:11:58 21059642 reads; of these: 21059642 (100.00%) were paired; of these: 6685144 (31.74%) aligned concordantly 0 times 12801458 (60.79%) aligned concordantly exactly 1 time 1573040 (7.47%) aligned concordantly >1 times ---- 6685144 pairs aligned concordantly 0 times; of these: 16533 (0.25%) aligned discordantly 1 time ---- 6668611 pairs aligned 0 times concordantly or discordantly; of these: 13337222 mates make up the pairs; of these: 13149351 (98.59%) aligned 0 times 158169 (1.19%) aligned exactly 1 time 29702 (0.22%) aligned >1 times 68.78% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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_sort_core] merging from 12 files... [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] 13484879 / 14378869 = 0.9378 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 @ Wed, 28 Jun 2017 05:30:44: # Command line: callpeak -t SRX1423737.bam -f BAM -g 12100000 -n SRX1423737.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1423737.10 # format = BAM # ChIP-seq file = ['SRX1423737.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 @ Wed, 28 Jun 2017 05:30:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:44: # Command line: callpeak -t SRX1423737.bam -f BAM -g 12100000 -n SRX1423737.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1423737.20 # format = BAM # ChIP-seq file = ['SRX1423737.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 @ Wed, 28 Jun 2017 05:30:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:44: # Command line: callpeak -t SRX1423737.bam -f BAM -g 12100000 -n SRX1423737.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1423737.05 # format = BAM # ChIP-seq file = ['SRX1423737.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 @ Wed, 28 Jun 2017 05:30:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 05:30:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 05:30:51: 1000000 INFO @ Wed, 28 Jun 2017 05:30:51: 1000000 INFO @ Wed, 28 Jun 2017 05:30:51: 1000000 INFO @ Wed, 28 Jun 2017 05:30:57: 2000000 INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:30:57: #1 total tags in treatment: 894048 INFO @ Wed, 28 Jun 2017 05:30:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:30:57: #1 tags after filtering in treatment: 826369 INFO @ Wed, 28 Jun 2017 05:30:57: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 05:30:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:30:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:30:57: 2000000 INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:30:57: #1 total tags in treatment: 894048 INFO @ Wed, 28 Jun 2017 05:30:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:30:57: #1 tags after filtering in treatment: 826369 INFO @ Wed, 28 Jun 2017 05:30:57: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 05:30:57: #1 finished! INFO @ Wed, 28 Jun 2017 05:30:57: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:30:57: #2 number of paired peaks: 239 WARNING @ Wed, 28 Jun 2017 05:30:57: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 28 Jun 2017 05:30:57: start model_add_line... INFO @ Wed, 28 Jun 2017 05:30:57: start X-correlation... INFO @ Wed, 28 Jun 2017 05:30:57: #2 number of paired peaks: 239 WARNING @ Wed, 28 Jun 2017 05:30:57: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 28 Jun 2017 05:30:57: start model_add_line... INFO @ Wed, 28 Jun 2017 05:30:57: start X-correlation... INFO @ Wed, 28 Jun 2017 05:30:57: end of X-cor INFO @ Wed, 28 Jun 2017 05:30:57: #2 finished! INFO @ Wed, 28 Jun 2017 05:30:57: #2 predicted fragment length is 177 bps INFO @ Wed, 28 Jun 2017 05:30:57: #2 alternative fragment length(s) may be 3,23,124,154,177,198,248,586 bps INFO @ Wed, 28 Jun 2017 05:30:57: #2.2 Generate R script for model : SRX1423737.10_model.r INFO @ Wed, 28 Jun 2017 05:30:57: end of X-cor INFO @ Wed, 28 Jun 2017 05:30:57: #2 finished! INFO @ Wed, 28 Jun 2017 05:30:57: #2 predicted fragment length is 177 bps INFO @ Wed, 28 Jun 2017 05:30:57: #2 alternative fragment length(s) may be 3,23,124,154,177,198,248,586 bps INFO @ Wed, 28 Jun 2017 05:30:57: #2.2 Generate R script for model : SRX1423737.20_model.r INFO @ Wed, 28 Jun 2017 05:30:57: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:30:57: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:30:57: 2000000 INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 05:30:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 05:30:57: #1 total tags in treatment: 894048 INFO @ Wed, 28 Jun 2017 05:30:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 05:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 05:30:58: #1 tags after filtering in treatment: 826369 INFO @ Wed, 28 Jun 2017 05:30:58: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 05:30:58: #1 finished! INFO @ Wed, 28 Jun 2017 05:30:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 05:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 05:30:58: #2 number of paired peaks: 239 WARNING @ Wed, 28 Jun 2017 05:30:58: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 28 Jun 2017 05:30:58: start model_add_line... INFO @ Wed, 28 Jun 2017 05:30:58: start X-correlation... INFO @ Wed, 28 Jun 2017 05:30:58: end of X-cor INFO @ Wed, 28 Jun 2017 05:30:58: #2 finished! INFO @ Wed, 28 Jun 2017 05:30:58: #2 predicted fragment length is 177 bps INFO @ Wed, 28 Jun 2017 05:30:58: #2 alternative fragment length(s) may be 3,23,124,154,177,198,248,586 bps INFO @ Wed, 28 Jun 2017 05:30:58: #2.2 Generate R script for model : SRX1423737.05_model.r INFO @ Wed, 28 Jun 2017 05:30:58: #3 Call peaks... INFO @ Wed, 28 Jun 2017 05:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 05:31:00: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:00: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:00: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write output xls file... SRX1423737.20_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write peak in narrowPeak format file... SRX1423737.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write summits bed file... SRX1423737.20_summits.bed INFO @ Wed, 28 Jun 2017 05:31:01: Done! INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write output xls file... SRX1423737.10_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write peak in narrowPeak format file... SRX1423737.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:01: #4 Write summits bed file... SRX1423737.10_summits.bed INFO @ Wed, 28 Jun 2017 05:31:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 05:31:02: #4 Write output xls file... SRX1423737.05_peaks.xls INFO @ Wed, 28 Jun 2017 05:31:02: #4 Write peak in narrowPeak format file... SRX1423737.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 05:31:02: #4 Write summits bed file... SRX1423737.05_summits.bed INFO @ Wed, 28 Jun 2017 05:31:02: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (454 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。