Job ID = 9025639 sra ファイルのダウンロード中... Completed: 114835K bytes transferred in 4 seconds (193122K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 12695 0 12695 0 0 1591 0 --:--:-- 0:00:07 --:--:-- 8335 100 45489 0 45489 0 0 5068 0 --:--:-- 0:00:08 --:--:-- 18065 100 45489 0 45489 0 0 5068 0 --:--:-- 0:00:08 --:--:-- 18058 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 4913051 spots for /home/okishinya/chipatlas/results/ce10/SRX2144165/SRR4188769.sra Written 4913051 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: 00:01:35 4913051 reads; of these: 4913051 (100.00%) were unpaired; of these: 334829 (6.82%) aligned 0 times 3446181 (70.14%) aligned exactly 1 time 1132041 (23.04%) aligned >1 times 93.18% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 315135 / 4578222 = 0.0688 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, 03 Jun 2017 04:48:03: # Command line: callpeak -t SRX2144165.bam -f BAM -g ce -n SRX2144165.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2144165.05 # format = BAM # ChIP-seq file = ['SRX2144165.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 INFO @ Sat, 03 Jun 2017 04:48:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:03: # Command line: callpeak -t SRX2144165.bam -f BAM -g ce -n SRX2144165.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2144165.20 # format = BAM # ChIP-seq file = ['SRX2144165.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 INFO @ Sat, 03 Jun 2017 04:48:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:03: # Command line: callpeak -t SRX2144165.bam -f BAM -g ce -n SRX2144165.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2144165.10 # format = BAM # ChIP-seq file = ['SRX2144165.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 INFO @ Sat, 03 Jun 2017 04:48:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:48:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:48:09: 1000000 INFO @ Sat, 03 Jun 2017 04:48:09: 1000000 INFO @ Sat, 03 Jun 2017 04:48:09: 1000000 INFO @ Sat, 03 Jun 2017 04:48:14: 2000000 INFO @ Sat, 03 Jun 2017 04:48:14: 2000000 INFO @ Sat, 03 Jun 2017 04:48:15: 2000000 INFO @ Sat, 03 Jun 2017 04:48:20: 3000000 INFO @ Sat, 03 Jun 2017 04:48:20: 3000000 INFO @ Sat, 03 Jun 2017 04:48:20: 3000000 INFO @ Sat, 03 Jun 2017 04:48:26: 4000000 INFO @ Sat, 03 Jun 2017 04:48:26: 4000000 INFO @ Sat, 03 Jun 2017 04:48:26: 4000000 INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:28: #1 total tags in treatment: 4263087 INFO @ Sat, 03 Jun 2017 04:48:28: #1 total tags in treatment: 4263087 INFO @ Sat, 03 Jun 2017 04:48:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:48:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:28: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:28: #1 total tags in treatment: 4263087 INFO @ Sat, 03 Jun 2017 04:48:28: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:48:28: #1 tags after filtering in treatment: 4262359 INFO @ Sat, 03 Jun 2017 04:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:28: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:28: #1 tags after filtering in treatment: 4262359 INFO @ Sat, 03 Jun 2017 04:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:28: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:29: #1 tags after filtering in treatment: 4262359 INFO @ Sat, 03 Jun 2017 04:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:48:29: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:29: #2 number of paired peaks: 699 WARNING @ Sat, 03 Jun 2017 04:48:29: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:29: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:29: #2 number of paired peaks: 699 WARNING @ Sat, 03 Jun 2017 04:48:29: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:29: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:29: #2 number of paired peaks: 699 WARNING @ Sat, 03 Jun 2017 04:48:29: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:29: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:34: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2 alternative fragment length(s) may be 4,51,566,580 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2.2 Generate R script for model : SRX2144165.05_model.r WARNING @ Sat, 03 Jun 2017 04:48:34: #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, 03 Jun 2017 04:48:34: #2 You may need to consider one of the other alternative d(s): 4,51,566,580 WARNING @ Sat, 03 Jun 2017 04:48:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:48:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:34: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2 alternative fragment length(s) may be 4,51,566,580 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2.2 Generate R script for model : SRX2144165.10_model.r WARNING @ Sat, 03 Jun 2017 04:48:34: #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, 03 Jun 2017 04:48:34: #2 You may need to consider one of the other alternative d(s): 4,51,566,580 WARNING @ Sat, 03 Jun 2017 04:48:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:48:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:34: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:34: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:34: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:34: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2 alternative fragment length(s) may be 4,51,566,580 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2.2 Generate R script for model : SRX2144165.20_model.r WARNING @ Sat, 03 Jun 2017 04:48:34: #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, 03 Jun 2017 04:48:34: #2 You may need to consider one of the other alternative d(s): 4,51,566,580 WARNING @ Sat, 03 Jun 2017 04:48:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 04:48:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:48:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:16: #4 Write output xls file... SRX2144165.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:16: #4 Write peak in narrowPeak format file... SRX2144165.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:16: #4 Write summits bed file... SRX2144165.10_summits.bed INFO @ Sat, 03 Jun 2017 04:49:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write output xls file... SRX2144165.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write peak in narrowPeak format file... SRX2144165.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write summits bed file... SRX2144165.20_summits.bed INFO @ Sat, 03 Jun 2017 04:49:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write output xls file... SRX2144165.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write peak in narrowPeak format file... SRX2144165.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:17: #4 Write summits bed file... SRX2144165.05_summits.bed INFO @ Sat, 03 Jun 2017 04:49:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (554 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。