Job ID = 10714464 sra ファイルのダウンロード中... Completed: 790939K bytes transferred in 81 seconds (79376K 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 12502185 spots for /home/okishinya/chipatlas/results/ce10/SRX4085380/SRR7167409.sra Written 12502185 spots for /home/okishinya/chipatlas/results/ce10/SRX4085380/SRR7167409.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: 00:08:30 12502185 reads; of these: 12502185 (100.00%) were paired; of these: 9150648 (73.19%) aligned concordantly 0 times 2942678 (23.54%) aligned concordantly exactly 1 time 408859 (3.27%) aligned concordantly >1 times ---- 9150648 pairs aligned concordantly 0 times; of these: 280489 (3.07%) aligned discordantly 1 time ---- 8870159 pairs aligned 0 times concordantly or discordantly; of these: 17740318 mates make up the pairs; of these: 12344381 (69.58%) aligned 0 times 4789585 (27.00%) aligned exactly 1 time 606352 (3.42%) aligned >1 times 50.63% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 210978 / 3490796 = 0.0604 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 @ Sun, 03 Jun 2018 12:54:30: # Command line: callpeak -t SRX4085380.bam -f BAM -g ce -n SRX4085380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085380.05 # format = BAM # ChIP-seq file = ['SRX4085380.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 03 Jun 2018 12:54:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:30: # Command line: callpeak -t SRX4085380.bam -f BAM -g ce -n SRX4085380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085380.20 # format = BAM # ChIP-seq file = ['SRX4085380.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 03 Jun 2018 12:54:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:30: # Command line: callpeak -t SRX4085380.bam -f BAM -g ce -n SRX4085380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085380.10 # format = BAM # ChIP-seq file = ['SRX4085380.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 03 Jun 2018 12:54:30: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:54:30: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:54:37: 1000000 INFO @ Sun, 03 Jun 2018 12:54:37: 1000000 INFO @ Sun, 03 Jun 2018 12:54:37: 1000000 INFO @ Sun, 03 Jun 2018 12:54:44: 2000000 INFO @ Sun, 03 Jun 2018 12:54:44: 2000000 INFO @ Sun, 03 Jun 2018 12:54:44: 2000000 INFO @ Sun, 03 Jun 2018 12:54:51: 3000000 INFO @ Sun, 03 Jun 2018 12:54:51: 3000000 INFO @ Sun, 03 Jun 2018 12:54:51: 3000000 INFO @ Sun, 03 Jun 2018 12:54:58: 4000000 INFO @ Sun, 03 Jun 2018 12:54:58: 4000000 INFO @ Sun, 03 Jun 2018 12:54:58: 4000000 INFO @ Sun, 03 Jun 2018 12:55:04: 5000000 INFO @ Sun, 03 Jun 2018 12:55:05: 5000000 INFO @ Sun, 03 Jun 2018 12:55:05: 5000000 INFO @ Sun, 03 Jun 2018 12:55:11: 6000000 INFO @ Sun, 03 Jun 2018 12:55:12: 6000000 INFO @ Sun, 03 Jun 2018 12:55:12: 6000000 INFO @ Sun, 03 Jun 2018 12:55:18: 7000000 INFO @ Sun, 03 Jun 2018 12:55:18: 7000000 INFO @ Sun, 03 Jun 2018 12:55:19: 7000000 INFO @ Sun, 03 Jun 2018 12:55:25: 8000000 INFO @ Sun, 03 Jun 2018 12:55:25: 8000000 INFO @ Sun, 03 Jun 2018 12:55:25: 8000000 INFO @ Sun, 03 Jun 2018 12:55:31: 9000000 INFO @ Sun, 03 Jun 2018 12:55:32: 9000000 INFO @ Sun, 03 Jun 2018 12:55:32: 9000000 INFO @ Sun, 03 Jun 2018 12:55:38: 10000000 INFO @ Sun, 03 Jun 2018 12:55:39: 10000000 INFO @ Sun, 03 Jun 2018 12:55:39: 10000000 INFO @ Sun, 03 Jun 2018 12:55:45: 11000000 INFO @ Sun, 03 Jun 2018 12:55:46: 11000000 INFO @ Sun, 03 Jun 2018 12:55:46: 11000000 INFO @ Sun, 03 Jun 2018 12:55:51: 12000000 INFO @ Sun, 03 Jun 2018 12:55:52: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:52: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:52: #1 total tags in treatment: 3147942 INFO @ Sun, 03 Jun 2018 12:55:52: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:53: #1 tags after filtering in treatment: 2998272 INFO @ Sun, 03 Jun 2018 12:55:53: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:55:53: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:53: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:53: #2 number of paired peaks: 253 WARNING @ Sun, 03 Jun 2018 12:55:53: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:53: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:53: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:53: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:53: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:53: #2 predicted fragment length is 166 bps INFO @ Sun, 03 Jun 2018 12:55:53: #2 alternative fragment length(s) may be 125,166,589 bps INFO @ Sun, 03 Jun 2018 12:55:53: #2.2 Generate R script for model : SRX4085380.20_model.r INFO @ Sun, 03 Jun 2018 12:55:53: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:53: 12000000 INFO @ Sun, 03 Jun 2018 12:55:53: 12000000 INFO @ Sun, 03 Jun 2018 12:55:54: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:54: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:54: #1 total tags in treatment: 3147942 INFO @ Sun, 03 Jun 2018 12:55:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:54: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:55:54: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:55:54: #1 total tags in treatment: 3147942 INFO @ Sun, 03 Jun 2018 12:55:54: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:55:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:55:54: #1 tags after filtering in treatment: 2998272 INFO @ Sun, 03 Jun 2018 12:55:54: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:55:54: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:54: #1 tags after filtering in treatment: 2998272 INFO @ Sun, 03 Jun 2018 12:55:54: #1 Redundant rate of treatment: 0.05 INFO @ Sun, 03 Jun 2018 12:55:54: #1 finished! INFO @ Sun, 03 Jun 2018 12:55:54: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:55:55: #2 number of paired peaks: 253 WARNING @ Sun, 03 Jun 2018 12:55:55: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:55: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:55: #2 number of paired peaks: 253 WARNING @ Sun, 03 Jun 2018 12:55:55: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 03 Jun 2018 12:55:55: start model_add_line... INFO @ Sun, 03 Jun 2018 12:55:55: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:55: start X-correlation... INFO @ Sun, 03 Jun 2018 12:55:55: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:55: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:55: #2 predicted fragment length is 166 bps INFO @ Sun, 03 Jun 2018 12:55:55: #2 alternative fragment length(s) may be 125,166,589 bps INFO @ Sun, 03 Jun 2018 12:55:55: #2.2 Generate R script for model : SRX4085380.10_model.r INFO @ Sun, 03 Jun 2018 12:55:55: end of X-cor INFO @ Sun, 03 Jun 2018 12:55:55: #2 finished! INFO @ Sun, 03 Jun 2018 12:55:55: #2 predicted fragment length is 166 bps INFO @ Sun, 03 Jun 2018 12:55:55: #2 alternative fragment length(s) may be 125,166,589 bps INFO @ Sun, 03 Jun 2018 12:55:55: #2.2 Generate R script for model : SRX4085380.05_model.r INFO @ Sun, 03 Jun 2018 12:55:55: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:55:55: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:56:00: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:56:04: #4 Write output xls file... SRX4085380.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:04: #4 Write peak in narrowPeak format file... SRX4085380.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:04: #4 Write summits bed file... SRX4085380.20_summits.bed INFO @ Sun, 03 Jun 2018 12:56:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write output xls file... SRX4085380.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write peak in narrowPeak format file... SRX4085380.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write summits bed file... SRX4085380.10_summits.bed INFO @ Sun, 03 Jun 2018 12:56:06: Done! INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write output xls file... SRX4085380.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write peak in narrowPeak format file... SRX4085380.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:56:06: #4 Write summits bed file... SRX4085380.05_summits.bed INFO @ Sun, 03 Jun 2018 12:56:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。