Job ID = 9025506 sra ファイルのダウンロード中... Completed: 33794K bytes transferred in 3 seconds (78586K 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 --:--:-- 0 101 5455 0 5455 0 0 725 0 --:--:-- 0:00:07 --:--:-- 4776 100 36038 0 36038 0 0 4231 0 --:--:-- 0:00:08 --:--:-- 16855 100 42731 0 42731 0 0 5016 0 --:--:-- 0:00:08 --:--:-- 19977 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 1496149 spots for /home/okishinya/chipatlas/results/ce10/SRX1388755/SRR2832471.sra Written 1496149 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: 00:00:26 1496149 reads; of these: 1496149 (100.00%) were unpaired; of these: 113007 (7.55%) aligned 0 times 1137685 (76.04%) aligned exactly 1 time 245457 (16.41%) aligned >1 times 92.45% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 31461 / 1383142 = 0.0227 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 04:10:09: # Command line: callpeak -t SRX1388755.bam -f BAM -g ce -n SRX1388755.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1388755.10 # format = BAM # ChIP-seq file = ['SRX1388755.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 04:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:09: # Command line: callpeak -t SRX1388755.bam -f BAM -g ce -n SRX1388755.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1388755.20 # format = BAM # ChIP-seq file = ['SRX1388755.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 04:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:09: # Command line: callpeak -t SRX1388755.bam -f BAM -g ce -n SRX1388755.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1388755.05 # format = BAM # ChIP-seq file = ['SRX1388755.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 04:10:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:10:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:10:17: 1000000 INFO @ Sat, 03 Jun 2017 04:10:17: 1000000 INFO @ Sat, 03 Jun 2017 04:10:17: 1000000 INFO @ Sat, 03 Jun 2017 04:10:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:10:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:10:20: #1 total tags in treatment: 1351681 INFO @ Sat, 03 Jun 2017 04:10:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:10:20: #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 04:10:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:10:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:10:20: #1 total tags in treatment: 1351681 INFO @ Sat, 03 Jun 2017 04:10:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:10:20: #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 04:10:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:10:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:10:20: #1 total tags in treatment: 1351681 INFO @ Sat, 03 Jun 2017 04:10:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:10:20: #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 04:10:20: #1 tags after filtering in treatment: 1351561 INFO @ Sat, 03 Jun 2017 04:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:10:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:10:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:10:20: #1 tags after filtering in treatment: 1351561 INFO @ Sat, 03 Jun 2017 04:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:10:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:10:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:10:20: #1 tags after filtering in treatment: 1351561 INFO @ Sat, 03 Jun 2017 04:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:10:20: #1 finished! INFO @ Sat, 03 Jun 2017 04:10:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:10:20: #2 number of paired peaks: 302 WARNING @ Sat, 03 Jun 2017 04:10:20: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 03 Jun 2017 04:10:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:10:20: #2 number of paired peaks: 302 WARNING @ Sat, 03 Jun 2017 04:10:20: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 03 Jun 2017 04:10:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:10:20: #2 number of paired peaks: 302 WARNING @ Sat, 03 Jun 2017 04:10:20: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Sat, 03 Jun 2017 04:10:20: start model_add_line... INFO @ Sat, 03 Jun 2017 04:10:21: start X-correlation... INFO @ Sat, 03 Jun 2017 04:10:21: end of X-cor INFO @ Sat, 03 Jun 2017 04:10:21: #2 finished! INFO @ Sat, 03 Jun 2017 04:10:21: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2 alternative fragment length(s) may be 49,236,247,449,484 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2.2 Generate R script for model : SRX1388755.10_model.r INFO @ Sat, 03 Jun 2017 04:10:21: start X-correlation... INFO @ Sat, 03 Jun 2017 04:10:21: end of X-cor INFO @ Sat, 03 Jun 2017 04:10:21: #2 finished! INFO @ Sat, 03 Jun 2017 04:10:21: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2 alternative fragment length(s) may be 49,236,247,449,484 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2.2 Generate R script for model : SRX1388755.20_model.r INFO @ Sat, 03 Jun 2017 04:10:21: start X-correlation... WARNING @ Sat, 03 Jun 2017 04:10:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:10:21: #2 You may need to consider one of the other alternative d(s): 49,236,247,449,484 WARNING @ Sat, 03 Jun 2017 04:10:21: #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 04:10:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:10:21: end of X-cor INFO @ Sat, 03 Jun 2017 04:10:21: #2 finished! INFO @ Sat, 03 Jun 2017 04:10:21: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2 alternative fragment length(s) may be 49,236,247,449,484 bps INFO @ Sat, 03 Jun 2017 04:10:21: #2.2 Generate R script for model : SRX1388755.05_model.r WARNING @ Sat, 03 Jun 2017 04:10:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:10:21: #2 You may need to consider one of the other alternative d(s): 49,236,247,449,484 WARNING @ Sat, 03 Jun 2017 04:10:21: #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 04:10:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:10:21: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 04:10:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:10:21: #2 You may need to consider one of the other alternative d(s): 49,236,247,449,484 WARNING @ Sat, 03 Jun 2017 04:10:21: #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 04:10:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:10:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:10:35: #4 Write output xls file... SRX1388755.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:35: #4 Write peak in narrowPeak format file... SRX1388755.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:35: #4 Write summits bed file... SRX1388755.10_summits.bed INFO @ Sat, 03 Jun 2017 04:10:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write output xls file... SRX1388755.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write peak in narrowPeak format file... SRX1388755.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write summits bed file... SRX1388755.20_summits.bed INFO @ Sat, 03 Jun 2017 04:10:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write output xls file... SRX1388755.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write peak in narrowPeak format file... SRX1388755.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:10:36: #4 Write summits bed file... SRX1388755.05_summits.bed INFO @ Sat, 03 Jun 2017 04:10:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (207 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。