Job ID = 10937498 sra ファイルのダウンロード中... Completed: 423066K bytes transferred in 24 seconds (141528K 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 4455549 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010305/SRR5833298.sra Written 4455549 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010305/SRR5833298.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: 00:05:37 4455549 reads; of these: 4455549 (100.00%) were paired; of these: 466723 (10.48%) aligned concordantly 0 times 3438173 (77.17%) aligned concordantly exactly 1 time 550653 (12.36%) aligned concordantly >1 times ---- 466723 pairs aligned concordantly 0 times; of these: 58386 (12.51%) aligned discordantly 1 time ---- 408337 pairs aligned 0 times concordantly or discordantly; of these: 816674 mates make up the pairs; of these: 705300 (86.36%) aligned 0 times 75146 (9.20%) aligned exactly 1 time 36228 (4.44%) aligned >1 times 92.09% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 81421 / 4020624 = 0.0203 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, 10 Aug 2018 02:31:34: # Command line: callpeak -t SRX3010305.bam -f BAM -g 12100000 -n SRX3010305.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010305.10 # format = BAM # ChIP-seq file = ['SRX3010305.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, 10 Aug 2018 02:31:34: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:34: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:34: # Command line: callpeak -t SRX3010305.bam -f BAM -g 12100000 -n SRX3010305.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010305.20 # format = BAM # ChIP-seq file = ['SRX3010305.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, 10 Aug 2018 02:31:34: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:34: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:34: # Command line: callpeak -t SRX3010305.bam -f BAM -g 12100000 -n SRX3010305.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010305.05 # format = BAM # ChIP-seq file = ['SRX3010305.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, 10 Aug 2018 02:31:34: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:31:34: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:31:41: 1000000 INFO @ Fri, 10 Aug 2018 02:31:41: 1000000 INFO @ Fri, 10 Aug 2018 02:31:42: 1000000 INFO @ Fri, 10 Aug 2018 02:31:47: 2000000 INFO @ Fri, 10 Aug 2018 02:31:48: 2000000 INFO @ Fri, 10 Aug 2018 02:31:50: 2000000 INFO @ Fri, 10 Aug 2018 02:31:54: 3000000 INFO @ Fri, 10 Aug 2018 02:31:54: 3000000 INFO @ Fri, 10 Aug 2018 02:31:57: 3000000 INFO @ Fri, 10 Aug 2018 02:32:01: 4000000 INFO @ Fri, 10 Aug 2018 02:32:01: 4000000 INFO @ Fri, 10 Aug 2018 02:32:04: 4000000 INFO @ Fri, 10 Aug 2018 02:32:08: 5000000 INFO @ Fri, 10 Aug 2018 02:32:09: 5000000 INFO @ Fri, 10 Aug 2018 02:32:12: 5000000 INFO @ Fri, 10 Aug 2018 02:32:15: 6000000 INFO @ Fri, 10 Aug 2018 02:32:16: 6000000 INFO @ Fri, 10 Aug 2018 02:32:19: 6000000 INFO @ Fri, 10 Aug 2018 02:32:22: 7000000 INFO @ Fri, 10 Aug 2018 02:32:23: 7000000 INFO @ Fri, 10 Aug 2018 02:32:27: 7000000 INFO @ Fri, 10 Aug 2018 02:32:29: 8000000 INFO @ Fri, 10 Aug 2018 02:32:30: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:30: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:30: #1 total tags in treatment: 3907642 INFO @ Fri, 10 Aug 2018 02:32:30: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:30: #1 tags after filtering in treatment: 3061643 INFO @ Fri, 10 Aug 2018 02:32:30: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Aug 2018 02:32:30: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:30: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:30: 8000000 INFO @ Fri, 10 Aug 2018 02:32:30: #2 number of paired peaks: 166 WARNING @ Fri, 10 Aug 2018 02:32:30: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 10 Aug 2018 02:32:30: start model_add_line... INFO @ Fri, 10 Aug 2018 02:32:30: start X-correlation... INFO @ Fri, 10 Aug 2018 02:32:30: end of X-cor INFO @ Fri, 10 Aug 2018 02:32:30: #2 finished! INFO @ Fri, 10 Aug 2018 02:32:30: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Aug 2018 02:32:30: #2 alternative fragment length(s) may be 1,16,49,92,137,160,199,244,268,310,511,548 bps INFO @ Fri, 10 Aug 2018 02:32:30: #2.2 Generate R script for model : SRX3010305.20_model.r WARNING @ Fri, 10 Aug 2018 02:32:30: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:32:30: #2 You may need to consider one of the other alternative d(s): 1,16,49,92,137,160,199,244,268,310,511,548 WARNING @ Fri, 10 Aug 2018 02:32:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:32:30: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:32:30: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:30: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:30: #1 total tags in treatment: 3907642 INFO @ Fri, 10 Aug 2018 02:32:30: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:30: #1 tags after filtering in treatment: 3061643 INFO @ Fri, 10 Aug 2018 02:32:30: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Aug 2018 02:32:30: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:30: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:30: #2 number of paired peaks: 166 WARNING @ Fri, 10 Aug 2018 02:32:30: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 10 Aug 2018 02:32:30: start model_add_line... INFO @ Fri, 10 Aug 2018 02:32:30: start X-correlation... INFO @ Fri, 10 Aug 2018 02:32:30: end of X-cor INFO @ Fri, 10 Aug 2018 02:32:30: #2 finished! INFO @ Fri, 10 Aug 2018 02:32:30: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Aug 2018 02:32:30: #2 alternative fragment length(s) may be 1,16,49,92,137,160,199,244,268,310,511,548 bps INFO @ Fri, 10 Aug 2018 02:32:30: #2.2 Generate R script for model : SRX3010305.10_model.r WARNING @ Fri, 10 Aug 2018 02:32:30: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:32:30: #2 You may need to consider one of the other alternative d(s): 1,16,49,92,137,160,199,244,268,310,511,548 WARNING @ Fri, 10 Aug 2018 02:32:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:32:30: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:32:34: 8000000 INFO @ Fri, 10 Aug 2018 02:32:35: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:32:35: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:32:35: #1 total tags in treatment: 3907642 INFO @ Fri, 10 Aug 2018 02:32:35: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:32:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:32:35: #1 tags after filtering in treatment: 3061643 INFO @ Fri, 10 Aug 2018 02:32:35: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 10 Aug 2018 02:32:35: #1 finished! INFO @ Fri, 10 Aug 2018 02:32:35: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:32:35: #2 number of paired peaks: 166 WARNING @ Fri, 10 Aug 2018 02:32:35: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 10 Aug 2018 02:32:35: start model_add_line... INFO @ Fri, 10 Aug 2018 02:32:35: start X-correlation... INFO @ Fri, 10 Aug 2018 02:32:35: end of X-cor INFO @ Fri, 10 Aug 2018 02:32:35: #2 finished! INFO @ Fri, 10 Aug 2018 02:32:35: #2 predicted fragment length is 199 bps INFO @ Fri, 10 Aug 2018 02:32:35: #2 alternative fragment length(s) may be 1,16,49,92,137,160,199,244,268,310,511,548 bps INFO @ Fri, 10 Aug 2018 02:32:35: #2.2 Generate R script for model : SRX3010305.05_model.r WARNING @ Fri, 10 Aug 2018 02:32:35: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Aug 2018 02:32:35: #2 You may need to consider one of the other alternative d(s): 1,16,49,92,137,160,199,244,268,310,511,548 WARNING @ Fri, 10 Aug 2018 02:32:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Aug 2018 02:32:35: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:32:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:32:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:32:39: #4 Write output xls file... SRX3010305.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:39: #4 Write peak in narrowPeak format file... SRX3010305.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:39: #4 Write summits bed file... SRX3010305.20_summits.bed INFO @ Fri, 10 Aug 2018 02:32:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:32:40: #4 Write output xls file... SRX3010305.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:40: #4 Write peak in narrowPeak format file... SRX3010305.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:40: #4 Write summits bed file... SRX3010305.10_summits.bed INFO @ Fri, 10 Aug 2018 02:32:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:32:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:32:44: #4 Write output xls file... SRX3010305.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:32:44: #4 Write peak in narrowPeak format file... SRX3010305.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:32:44: #4 Write summits bed file... SRX3010305.05_summits.bed INFO @ Fri, 10 Aug 2018 02:32:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (78 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。