Job ID = 9161783 sra ファイルのダウンロード中... Completed: 1029076K bytes transferred in 15 seconds (550323K 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 18739414 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1044172/SRR2045653.sra Written 18739414 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: 00:06:42 18739414 reads; of these: 18739414 (100.00%) were paired; of these: 11737984 (62.64%) aligned concordantly 0 times 6380972 (34.05%) aligned concordantly exactly 1 time 620458 (3.31%) aligned concordantly >1 times ---- 11737984 pairs aligned concordantly 0 times; of these: 259755 (2.21%) aligned discordantly 1 time ---- 11478229 pairs aligned 0 times concordantly or discordantly; of these: 22956458 mates make up the pairs; of these: 22786464 (99.26%) aligned 0 times 102483 (0.45%) aligned exactly 1 time 67511 (0.29%) aligned >1 times 39.20% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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 8 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] 5113472 / 7222839 = 0.7080 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 04:44:56: # Command line: callpeak -t SRX1044172.bam -f BAM -g 12100000 -n SRX1044172.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1044172.05 # format = BAM # ChIP-seq file = ['SRX1044172.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 04:44:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:56: # Command line: callpeak -t SRX1044172.bam -f BAM -g 12100000 -n SRX1044172.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1044172.20 # format = BAM # ChIP-seq file = ['SRX1044172.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 04:44:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:44:56: # Command line: callpeak -t SRX1044172.bam -f BAM -g 12100000 -n SRX1044172.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1044172.10 # format = BAM # ChIP-seq file = ['SRX1044172.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 04:44:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:44:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:45:02: 1000000 INFO @ Wed, 28 Jun 2017 04:45:03: 1000000 INFO @ Wed, 28 Jun 2017 04:45:03: 1000000 INFO @ Wed, 28 Jun 2017 04:45:08: 2000000 INFO @ Wed, 28 Jun 2017 04:45:09: 2000000 INFO @ Wed, 28 Jun 2017 04:45:09: 2000000 INFO @ Wed, 28 Jun 2017 04:45:14: 3000000 INFO @ Wed, 28 Jun 2017 04:45:16: 3000000 INFO @ Wed, 28 Jun 2017 04:45:16: 3000000 INFO @ Wed, 28 Jun 2017 04:45:20: 4000000 INFO @ Wed, 28 Jun 2017 04:45:23: 4000000 INFO @ Wed, 28 Jun 2017 04:45:23: 4000000 INFO @ Wed, 28 Jun 2017 04:45:23: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:23: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:23: #1 total tags in treatment: 2024716 INFO @ Wed, 28 Jun 2017 04:45:23: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:23: #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 04:45:23: #1 tags after filtering in treatment: 1668749 INFO @ Wed, 28 Jun 2017 04:45:23: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 04:45:23: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:23: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:23: #2 number of paired peaks: 214 WARNING @ Wed, 28 Jun 2017 04:45:23: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:23: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:23: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:23: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:23: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:23: #2 predicted fragment length is 76 bps INFO @ Wed, 28 Jun 2017 04:45:23: #2 alternative fragment length(s) may be 3,55,76,92 bps INFO @ Wed, 28 Jun 2017 04:45:23: #2.2 Generate R script for model : SRX1044172.20_model.r WARNING @ Wed, 28 Jun 2017 04:45:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:23: #2 You may need to consider one of the other alternative d(s): 3,55,76,92 WARNING @ Wed, 28 Jun 2017 04:45:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 04:45:23: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:45:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:26: #1 total tags in treatment: 2024716 INFO @ Wed, 28 Jun 2017 04:45:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:26: #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 04:45:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 04:45:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 04:45:26: #1 total tags in treatment: 2024716 INFO @ Wed, 28 Jun 2017 04:45:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:45:26: #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 04:45:26: #1 tags after filtering in treatment: 1668749 INFO @ Wed, 28 Jun 2017 04:45:26: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 04:45:26: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:26: #1 tags after filtering in treatment: 1668749 INFO @ Wed, 28 Jun 2017 04:45:26: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 28 Jun 2017 04:45:26: #1 finished! INFO @ Wed, 28 Jun 2017 04:45:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:45:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:45:26: #2 number of paired peaks: 214 WARNING @ Wed, 28 Jun 2017 04:45:26: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:26: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:26: #2 number of paired peaks: 214 WARNING @ Wed, 28 Jun 2017 04:45:26: Fewer paired peaks (214) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 214 pairs to build model! INFO @ Wed, 28 Jun 2017 04:45:26: start model_add_line... INFO @ Wed, 28 Jun 2017 04:45:26: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:26: start X-correlation... INFO @ Wed, 28 Jun 2017 04:45:26: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:26: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:26: #2 predicted fragment length is 76 bps INFO @ Wed, 28 Jun 2017 04:45:26: #2 alternative fragment length(s) may be 3,55,76,92 bps INFO @ Wed, 28 Jun 2017 04:45:26: #2.2 Generate R script for model : SRX1044172.10_model.r INFO @ Wed, 28 Jun 2017 04:45:26: end of X-cor INFO @ Wed, 28 Jun 2017 04:45:26: #2 finished! INFO @ Wed, 28 Jun 2017 04:45:26: #2 predicted fragment length is 76 bps INFO @ Wed, 28 Jun 2017 04:45:26: #2 alternative fragment length(s) may be 3,55,76,92 bps INFO @ Wed, 28 Jun 2017 04:45:26: #2.2 Generate R script for model : SRX1044172.05_model.r WARNING @ Wed, 28 Jun 2017 04:45:26: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:26: #2 You may need to consider one of the other alternative d(s): 3,55,76,92 WARNING @ Wed, 28 Jun 2017 04:45:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 04:45:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:26: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 28 Jun 2017 04:45:26: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 04:45:26: #2 You may need to consider one of the other alternative d(s): 3,55,76,92 WARNING @ Wed, 28 Jun 2017 04:45:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 04:45:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:45:27: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:45:29: #4 Write output xls file... SRX1044172.20_peaks.xls INFO @ Wed, 28 Jun 2017 04:45:29: #4 Write peak in narrowPeak format file... SRX1044172.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:45:29: #4 Write summits bed file... SRX1044172.20_summits.bed INFO @ Wed, 28 Jun 2017 04:45:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (153 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:45:30: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:45:30: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write output xls file... SRX1044172.10_peaks.xls INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write peak in narrowPeak format file... SRX1044172.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write summits bed file... SRX1044172.10_summits.bed INFO @ Wed, 28 Jun 2017 04:45:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write output xls file... SRX1044172.05_peaks.xls INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write peak in narrowPeak format file... SRX1044172.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 04:45:32: #4 Write summits bed file... SRX1044172.05_summits.bed INFO @ Wed, 28 Jun 2017 04:45:32: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (651 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。