Job ID = 11193217 sra ファイルのダウンロード中... Completed: 298748K bytes transferred in 5 seconds (414857K 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 6987071 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977503/SRR1951349.sra Written 6987071 spots for /home/okishinya/chipatlas/results/sacCer3/SRX977503/SRR1951349.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: 00:03:59 6987071 reads; of these: 6987071 (100.00%) were paired; of these: 1888984 (27.04%) aligned concordantly 0 times 4549015 (65.11%) aligned concordantly exactly 1 time 549072 (7.86%) aligned concordantly >1 times ---- 1888984 pairs aligned concordantly 0 times; of these: 241714 (12.80%) aligned discordantly 1 time ---- 1647270 pairs aligned 0 times concordantly or discordantly; of these: 3294540 mates make up the pairs; of these: 3063628 (92.99%) aligned 0 times 157967 (4.79%) aligned exactly 1 time 72945 (2.21%) aligned >1 times 78.08% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 2850313 / 5279616 = 0.5399 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 11:17:51: # Command line: callpeak -t SRX977503.bam -f BAM -g 12100000 -n SRX977503.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX977503.05 # format = BAM # ChIP-seq file = ['SRX977503.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 11:17:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:51: # Command line: callpeak -t SRX977503.bam -f BAM -g 12100000 -n SRX977503.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX977503.10 # format = BAM # ChIP-seq file = ['SRX977503.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 11:17:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:51: # Command line: callpeak -t SRX977503.bam -f BAM -g 12100000 -n SRX977503.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX977503.20 # format = BAM # ChIP-seq file = ['SRX977503.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 11:17:51: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:17:51: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:17:58: 1000000 INFO @ Sat, 15 Sep 2018 11:17:59: 1000000 INFO @ Sat, 15 Sep 2018 11:17:59: 1000000 INFO @ Sat, 15 Sep 2018 11:18:05: 2000000 INFO @ Sat, 15 Sep 2018 11:18:07: 2000000 INFO @ Sat, 15 Sep 2018 11:18:07: 2000000 INFO @ Sat, 15 Sep 2018 11:18:12: 3000000 INFO @ Sat, 15 Sep 2018 11:18:15: 3000000 INFO @ Sat, 15 Sep 2018 11:18:16: 3000000 INFO @ Sat, 15 Sep 2018 11:18:19: 4000000 INFO @ Sat, 15 Sep 2018 11:18:23: 4000000 INFO @ Sat, 15 Sep 2018 11:18:25: 4000000 INFO @ Sat, 15 Sep 2018 11:18:25: 5000000 INFO @ Sat, 15 Sep 2018 11:18:27: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:27: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:27: #1 total tags in treatment: 2368449 INFO @ Sat, 15 Sep 2018 11:18:27: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:27: #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 11:18:27: #1 tags after filtering in treatment: 1838987 INFO @ Sat, 15 Sep 2018 11:18:27: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 11:18:27: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:18:27: #2 number of paired peaks: 223 WARNING @ Sat, 15 Sep 2018 11:18:27: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:27: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:27: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:27: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:27: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:27: #2 predicted fragment length is 15 bps INFO @ Sat, 15 Sep 2018 11:18:27: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Sep 2018 11:18:27: #2.2 Generate R script for model : SRX977503.10_model.r WARNING @ Sat, 15 Sep 2018 11:18:27: #2 Since the d (15) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:27: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Sep 2018 11:18:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:18:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:31: 5000000 INFO @ Sat, 15 Sep 2018 11:18:33: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:33: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:33: #1 total tags in treatment: 2368449 INFO @ Sat, 15 Sep 2018 11:18:33: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:33: #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 11:18:33: #4 Write output xls file... SRX977503.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:33: #4 Write peak in narrowPeak format file... SRX977503.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:33: #4 Write summits bed file... SRX977503.10_summits.bed INFO @ Sat, 15 Sep 2018 11:18:33: Done! INFO @ Sat, 15 Sep 2018 11:18:33: #1 tags after filtering in treatment: 1838987 INFO @ Sat, 15 Sep 2018 11:18:33: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 11:18:33: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:33: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:33: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:18:33: #2 number of paired peaks: 223 WARNING @ Sat, 15 Sep 2018 11:18:33: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:33: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:33: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:33: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:33: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:33: #2 predicted fragment length is 15 bps INFO @ Sat, 15 Sep 2018 11:18:33: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Sep 2018 11:18:33: #2.2 Generate R script for model : SRX977503.20_model.r WARNING @ Sat, 15 Sep 2018 11:18:33: #2 Since the d (15) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:33: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Sep 2018 11:18:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:18:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:33: 5000000 INFO @ Sat, 15 Sep 2018 11:18:34: #1 tag size is determined as 40 bps INFO @ Sat, 15 Sep 2018 11:18:34: #1 tag size = 40 INFO @ Sat, 15 Sep 2018 11:18:34: #1 total tags in treatment: 2368449 INFO @ Sat, 15 Sep 2018 11:18:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:18:34: #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 11:18:35: #1 tags after filtering in treatment: 1838987 INFO @ Sat, 15 Sep 2018 11:18:35: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Sep 2018 11:18:35: #1 finished! INFO @ Sat, 15 Sep 2018 11:18:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:18:35: #2 number of paired peaks: 223 WARNING @ Sat, 15 Sep 2018 11:18:35: Fewer paired peaks (223) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 223 pairs to build model! INFO @ Sat, 15 Sep 2018 11:18:35: start model_add_line... INFO @ Sat, 15 Sep 2018 11:18:35: start X-correlation... INFO @ Sat, 15 Sep 2018 11:18:35: end of X-cor INFO @ Sat, 15 Sep 2018 11:18:35: #2 finished! INFO @ Sat, 15 Sep 2018 11:18:35: #2 predicted fragment length is 15 bps INFO @ Sat, 15 Sep 2018 11:18:35: #2 alternative fragment length(s) may be 3,15 bps INFO @ Sat, 15 Sep 2018 11:18:35: #2.2 Generate R script for model : SRX977503.05_model.r WARNING @ Sat, 15 Sep 2018 11:18:35: #2 Since the d (15) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 11:18:35: #2 You may need to consider one of the other alternative d(s): 3,15 WARNING @ Sat, 15 Sep 2018 11:18:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 11:18:35: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:18:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:18:38: #4 Write output xls file... SRX977503.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:38: #4 Write peak in narrowPeak format file... SRX977503.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:38: #4 Write summits bed file... SRX977503.20_summits.bed INFO @ Sat, 15 Sep 2018 11:18:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:18:40: #4 Write output xls file... SRX977503.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:18:40: #4 Write peak in narrowPeak format file... SRX977503.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:18:40: #4 Write summits bed file... SRX977503.05_summits.bed INFO @ Sat, 15 Sep 2018 11:18:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1367 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。