Job ID = 10194834 sra ファイルのダウンロード中... Completed: 660809K bytes transferred in 17 seconds (315426K 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: SINGLE fastq に変換中... Written 36125220 spots for /home/okishinya/chipatlas/results/rn6/SRX1977124/SRR3952256.sra Written 36125220 spots total 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:28:32 36125220 reads; of these: 36125220 (100.00%) were unpaired; of these: 28691085 (79.42%) aligned 0 times 4361311 (12.07%) aligned exactly 1 time 3072824 (8.51%) aligned >1 times 20.58% overall alignment rate Time searching: 00:28:35 Overall time: 00:28:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 1144079 / 7434135 = 0.1539 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, 11 Nov 2017 02:19:34: # Command line: callpeak -t SRX1977124.bam -f BAM -g 2.15e9 -n SRX1977124.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977124.05 # format = BAM # ChIP-seq file = ['SRX1977124.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 11 Nov 2017 02:19:34: # Command line: callpeak -t SRX1977124.bam -f BAM -g 2.15e9 -n SRX1977124.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977124.10 # format = BAM # ChIP-seq file = ['SRX1977124.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 11 Nov 2017 02:19:34: # Command line: callpeak -t SRX1977124.bam -f BAM -g 2.15e9 -n SRX1977124.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977124.20 # format = BAM # ChIP-seq file = ['SRX1977124.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 11 Nov 2017 02:19:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:19:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:19:34: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:19:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:19:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:19:34: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:19:41: 1000000 INFO @ Sat, 11 Nov 2017 02:19:41: 1000000 INFO @ Sat, 11 Nov 2017 02:19:41: 1000000 INFO @ Sat, 11 Nov 2017 02:19:48: 2000000 INFO @ Sat, 11 Nov 2017 02:19:49: 2000000 INFO @ Sat, 11 Nov 2017 02:19:49: 2000000 INFO @ Sat, 11 Nov 2017 02:19:55: 3000000 INFO @ Sat, 11 Nov 2017 02:19:56: 3000000 INFO @ Sat, 11 Nov 2017 02:19:56: 3000000 INFO @ Sat, 11 Nov 2017 02:20:02: 4000000 INFO @ Sat, 11 Nov 2017 02:20:03: 4000000 INFO @ Sat, 11 Nov 2017 02:20:03: 4000000 INFO @ Sat, 11 Nov 2017 02:20:09: 5000000 INFO @ Sat, 11 Nov 2017 02:20:10: 5000000 INFO @ Sat, 11 Nov 2017 02:20:11: 5000000 INFO @ Sat, 11 Nov 2017 02:20:16: 6000000 INFO @ Sat, 11 Nov 2017 02:20:18: 6000000 INFO @ Sat, 11 Nov 2017 02:20:18: 6000000 INFO @ Sat, 11 Nov 2017 02:20:18: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:20:18: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:20:18: #1 total tags in treatment: 6290056 INFO @ Sat, 11 Nov 2017 02:20:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:20:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:20:18: #1 tags after filtering in treatment: 6289828 INFO @ Sat, 11 Nov 2017 02:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:20:18: #1 finished! INFO @ Sat, 11 Nov 2017 02:20:18: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:20:20: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:20:20: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:20:20: #1 total tags in treatment: 6290056 INFO @ Sat, 11 Nov 2017 02:20:20: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:20:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:20:20: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:20:20: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:20:20: #1 total tags in treatment: 6290056 INFO @ Sat, 11 Nov 2017 02:20:20: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:20:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:20:20: #1 tags after filtering in treatment: 6289828 INFO @ Sat, 11 Nov 2017 02:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:20:20: #1 finished! INFO @ Sat, 11 Nov 2017 02:20:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:20:20: #1 tags after filtering in treatment: 6289828 INFO @ Sat, 11 Nov 2017 02:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:20:20: #1 finished! INFO @ Sat, 11 Nov 2017 02:20:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:20:22: #2 number of paired peaks: 54377 INFO @ Sat, 11 Nov 2017 02:20:22: start model_add_line... INFO @ Sat, 11 Nov 2017 02:20:22: start X-correlation... INFO @ Sat, 11 Nov 2017 02:20:22: end of X-cor INFO @ Sat, 11 Nov 2017 02:20:22: #2 finished! INFO @ Sat, 11 Nov 2017 02:20:22: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:20:22: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:20:22: #2.2 Generate R script for model : SRX1977124.05_model.r WARNING @ Sat, 11 Nov 2017 02:20:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:20:22: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:20:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:20:22: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:20:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:20:23: #2 number of paired peaks: 54377 INFO @ Sat, 11 Nov 2017 02:20:23: start model_add_line... INFO @ Sat, 11 Nov 2017 02:20:23: start X-correlation... INFO @ Sat, 11 Nov 2017 02:20:23: end of X-cor INFO @ Sat, 11 Nov 2017 02:20:23: #2 finished! INFO @ Sat, 11 Nov 2017 02:20:23: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:20:23: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:20:23: #2.2 Generate R script for model : SRX1977124.10_model.r WARNING @ Sat, 11 Nov 2017 02:20:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:20:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:20:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:20:24: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:20:24: #2 number of paired peaks: 54377 INFO @ Sat, 11 Nov 2017 02:20:24: start model_add_line... INFO @ Sat, 11 Nov 2017 02:20:24: start X-correlation... INFO @ Sat, 11 Nov 2017 02:20:24: end of X-cor INFO @ Sat, 11 Nov 2017 02:20:24: #2 finished! INFO @ Sat, 11 Nov 2017 02:20:24: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 02:20:24: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Nov 2017 02:20:24: #2.2 Generate R script for model : SRX1977124.20_model.r WARNING @ Sat, 11 Nov 2017 02:20:24: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:20:24: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Nov 2017 02:20:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:20:24: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:20:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:20:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:20:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:20:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:20:46: #4 Write output xls file... SRX1977124.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:20:46: #4 Write peak in narrowPeak format file... SRX1977124.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:20:46: #4 Write summits bed file... SRX1977124.05_summits.bed INFO @ Sat, 11 Nov 2017 02:20:46: Done! pass1 - making usageList (106 chroms): 2 millis pass2 - checking and writing primary data (7630 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:20:47: #4 Write output xls file... SRX1977124.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:20:47: #4 Write peak in narrowPeak format file... SRX1977124.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:20:47: #4 Write summits bed file... SRX1977124.20_summits.bed INFO @ Sat, 11 Nov 2017 02:20:47: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (627 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:20:48: #4 Write output xls file... SRX1977124.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:20:48: #4 Write peak in narrowPeak format file... SRX1977124.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:20:48: #4 Write summits bed file... SRX1977124.10_summits.bed INFO @ Sat, 11 Nov 2017 02:20:48: Done! pass1 - making usageList (72 chroms): 1 millis pass2 - checking and writing primary data (2483 records, 4 fields): 30 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。