Job ID = 10608877 sra ファイルのダウンロード中... Completed: 530762K bytes transferred in 49 seconds (88227K 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 16668341 spots for /home/okishinya/chipatlas/results/rn6/SRX3144995/SRR5989284.sra Written 16668341 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:02 16668341 reads; of these: 16668341 (100.00%) were unpaired; of these: 520917 (3.13%) aligned 0 times 11733567 (70.39%) aligned exactly 1 time 4413857 (26.48%) aligned >1 times 96.87% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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_sort_core] merging from 8 files... [bam_rmdupse_core] 720613 / 16147424 = 0.0446 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 @ Thu, 03 May 2018 22:35:20: # Command line: callpeak -t SRX3144995.bam -f BAM -g 2.15e9 -n SRX3144995.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3144995.20 # format = BAM # ChIP-seq file = ['SRX3144995.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 @ Thu, 03 May 2018 22:35:20: # Command line: callpeak -t SRX3144995.bam -f BAM -g 2.15e9 -n SRX3144995.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3144995.10 # format = BAM # ChIP-seq file = ['SRX3144995.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 @ Thu, 03 May 2018 22:35:20: # Command line: callpeak -t SRX3144995.bam -f BAM -g 2.15e9 -n SRX3144995.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3144995.05 # format = BAM # ChIP-seq file = ['SRX3144995.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 @ Thu, 03 May 2018 22:35:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:35:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:35:20: #1 read tag files... INFO @ Thu, 03 May 2018 22:35:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:35:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:35:20: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:35:28: 1000000 INFO @ Thu, 03 May 2018 22:35:28: 1000000 INFO @ Thu, 03 May 2018 22:35:28: 1000000 INFO @ Thu, 03 May 2018 22:35:36: 2000000 INFO @ Thu, 03 May 2018 22:35:36: 2000000 INFO @ Thu, 03 May 2018 22:35:36: 2000000 INFO @ Thu, 03 May 2018 22:35:43: 3000000 INFO @ Thu, 03 May 2018 22:35:44: 3000000 INFO @ Thu, 03 May 2018 22:35:44: 3000000 INFO @ Thu, 03 May 2018 22:35:51: 4000000 INFO @ Thu, 03 May 2018 22:35:51: 4000000 INFO @ Thu, 03 May 2018 22:35:51: 4000000 INFO @ Thu, 03 May 2018 22:35:58: 5000000 INFO @ Thu, 03 May 2018 22:35:59: 5000000 INFO @ Thu, 03 May 2018 22:35:59: 5000000 INFO @ Thu, 03 May 2018 22:36:05: 6000000 INFO @ Thu, 03 May 2018 22:36:07: 6000000 INFO @ Thu, 03 May 2018 22:36:07: 6000000 INFO @ Thu, 03 May 2018 22:36:13: 7000000 INFO @ Thu, 03 May 2018 22:36:14: 7000000 INFO @ Thu, 03 May 2018 22:36:14: 7000000 INFO @ Thu, 03 May 2018 22:36:20: 8000000 INFO @ Thu, 03 May 2018 22:36:22: 8000000 INFO @ Thu, 03 May 2018 22:36:22: 8000000 INFO @ Thu, 03 May 2018 22:36:27: 9000000 INFO @ Thu, 03 May 2018 22:36:30: 9000000 INFO @ Thu, 03 May 2018 22:36:30: 9000000 INFO @ Thu, 03 May 2018 22:36:35: 10000000 INFO @ Thu, 03 May 2018 22:36:38: 10000000 INFO @ Thu, 03 May 2018 22:36:38: 10000000 INFO @ Thu, 03 May 2018 22:36:43: 11000000 INFO @ Thu, 03 May 2018 22:36:45: 11000000 INFO @ Thu, 03 May 2018 22:36:45: 11000000 INFO @ Thu, 03 May 2018 22:36:50: 12000000 INFO @ Thu, 03 May 2018 22:36:53: 12000000 INFO @ Thu, 03 May 2018 22:36:53: 12000000 INFO @ Thu, 03 May 2018 22:36:58: 13000000 INFO @ Thu, 03 May 2018 22:37:01: 13000000 INFO @ Thu, 03 May 2018 22:37:01: 13000000 INFO @ Thu, 03 May 2018 22:37:05: 14000000 INFO @ Thu, 03 May 2018 22:37:08: 14000000 INFO @ Thu, 03 May 2018 22:37:08: 14000000 INFO @ Thu, 03 May 2018 22:37:12: 15000000 INFO @ Thu, 03 May 2018 22:37:16: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:37:16: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:37:16: #1 total tags in treatment: 15426811 INFO @ Thu, 03 May 2018 22:37:16: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:37:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:37:16: 15000000 INFO @ Thu, 03 May 2018 22:37:16: 15000000 INFO @ Thu, 03 May 2018 22:37:16: #1 tags after filtering in treatment: 15426620 INFO @ Thu, 03 May 2018 22:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:37:16: #1 finished! INFO @ Thu, 03 May 2018 22:37:16: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:37:18: #2 number of paired peaks: 5661 INFO @ Thu, 03 May 2018 22:37:18: start model_add_line... INFO @ Thu, 03 May 2018 22:37:18: start X-correlation... INFO @ Thu, 03 May 2018 22:37:18: end of X-cor INFO @ Thu, 03 May 2018 22:37:18: #2 finished! INFO @ Thu, 03 May 2018 22:37:18: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:37:18: #2 alternative fragment length(s) may be 51,230 bps INFO @ Thu, 03 May 2018 22:37:18: #2.2 Generate R script for model : SRX3144995.20_model.r WARNING @ Thu, 03 May 2018 22:37:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:37:18: #2 You may need to consider one of the other alternative d(s): 51,230 WARNING @ Thu, 03 May 2018 22:37:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:37:18: #3 Call peaks... INFO @ Thu, 03 May 2018 22:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:37:19: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:37:19: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:37:19: #1 total tags in treatment: 15426811 INFO @ Thu, 03 May 2018 22:37:19: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:37:19: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:37:19: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:37:19: #1 total tags in treatment: 15426811 INFO @ Thu, 03 May 2018 22:37:19: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:37:20: #1 tags after filtering in treatment: 15426620 INFO @ Thu, 03 May 2018 22:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:37:20: #1 finished! INFO @ Thu, 03 May 2018 22:37:20: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:37:20: #1 tags after filtering in treatment: 15426620 INFO @ Thu, 03 May 2018 22:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:37:20: #1 finished! INFO @ Thu, 03 May 2018 22:37:20: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:37:22: #2 number of paired peaks: 5661 INFO @ Thu, 03 May 2018 22:37:22: start model_add_line... INFO @ Thu, 03 May 2018 22:37:22: #2 number of paired peaks: 5661 INFO @ Thu, 03 May 2018 22:37:22: start model_add_line... INFO @ Thu, 03 May 2018 22:37:22: start X-correlation... INFO @ Thu, 03 May 2018 22:37:22: end of X-cor INFO @ Thu, 03 May 2018 22:37:22: #2 finished! INFO @ Thu, 03 May 2018 22:37:22: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:37:22: #2 alternative fragment length(s) may be 51,230 bps INFO @ Thu, 03 May 2018 22:37:22: #2.2 Generate R script for model : SRX3144995.10_model.r WARNING @ Thu, 03 May 2018 22:37:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:37:22: #2 You may need to consider one of the other alternative d(s): 51,230 WARNING @ Thu, 03 May 2018 22:37:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:37:22: #3 Call peaks... INFO @ Thu, 03 May 2018 22:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:37:22: start X-correlation... INFO @ Thu, 03 May 2018 22:37:22: end of X-cor INFO @ Thu, 03 May 2018 22:37:22: #2 finished! INFO @ Thu, 03 May 2018 22:37:22: #2 predicted fragment length is 51 bps INFO @ Thu, 03 May 2018 22:37:22: #2 alternative fragment length(s) may be 51,230 bps INFO @ Thu, 03 May 2018 22:37:22: #2.2 Generate R script for model : SRX3144995.05_model.r WARNING @ Thu, 03 May 2018 22:37:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 03 May 2018 22:37:22: #2 You may need to consider one of the other alternative d(s): 51,230 WARNING @ Thu, 03 May 2018 22:37:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 03 May 2018 22:37:22: #3 Call peaks... INFO @ Thu, 03 May 2018 22:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:37:57: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:38:00: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:38:01: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:38:17: #4 Write output xls file... SRX3144995.20_peaks.xls INFO @ Thu, 03 May 2018 22:38:17: #4 Write peak in narrowPeak format file... SRX3144995.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:38:17: #4 Write summits bed file... SRX3144995.20_summits.bed INFO @ Thu, 03 May 2018 22:38:17: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:38:23: #4 Write output xls file... SRX3144995.10_peaks.xls INFO @ Thu, 03 May 2018 22:38:23: #4 Write peak in narrowPeak format file... SRX3144995.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:38:23: #4 Write summits bed file... SRX3144995.10_summits.bed INFO @ Thu, 03 May 2018 22:38:23: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:38:23: #4 Write output xls file... SRX3144995.05_peaks.xls INFO @ Thu, 03 May 2018 22:38:23: #4 Write peak in narrowPeak format file... SRX3144995.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:38:23: #4 Write summits bed file... SRX3144995.05_summits.bed INFO @ Thu, 03 May 2018 22:38:23: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1292 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。