Job ID = 9025449 sra ファイルのダウンロード中... Completed: 278825K bytes transferred in 5 seconds (391768K 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 14324 0 14324 0 0 1747 0 --:--:-- 0:00:08 --:--:-- 8157 100 40382 0 40382 0 0 4391 0 --:--:-- 0:00:09 --:--:-- 14673 100 45847 0 45847 0 0 4897 0 --:--:-- 0:00:09 --:--:-- 15706 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 9133015 spots for /home/okishinya/chipatlas/results/ce10/SRX1007134/SRR1993094.sra Written 9133015 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: 00:01:23 9133015 reads; of these: 9133015 (100.00%) were unpaired; of these: 4063126 (44.49%) aligned 0 times 4074988 (44.62%) aligned exactly 1 time 994901 (10.89%) aligned >1 times 55.51% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 328009 / 5069889 = 0.0647 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 03:52:40: # Command line: callpeak -t SRX1007134.bam -f BAM -g ce -n SRX1007134.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1007134.20 # format = BAM # ChIP-seq file = ['SRX1007134.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 03:52:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:52:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:52:40: # Command line: callpeak -t SRX1007134.bam -f BAM -g ce -n SRX1007134.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1007134.10 # format = BAM # ChIP-seq file = ['SRX1007134.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 03:52:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:52:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:52:40: # Command line: callpeak -t SRX1007134.bam -f BAM -g ce -n SRX1007134.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1007134.05 # format = BAM # ChIP-seq file = ['SRX1007134.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 03:52:40: #1 read tag files... INFO @ Sat, 03 Jun 2017 03:52:40: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 03:52:47: 1000000 INFO @ Sat, 03 Jun 2017 03:52:48: 1000000 INFO @ Sat, 03 Jun 2017 03:52:48: 1000000 INFO @ Sat, 03 Jun 2017 03:52:54: 2000000 INFO @ Sat, 03 Jun 2017 03:52:55: 2000000 INFO @ Sat, 03 Jun 2017 03:52:55: 2000000 INFO @ Sat, 03 Jun 2017 03:53:02: 3000000 INFO @ Sat, 03 Jun 2017 03:53:03: 3000000 INFO @ Sat, 03 Jun 2017 03:53:03: 3000000 INFO @ Sat, 03 Jun 2017 03:53:09: 4000000 INFO @ Sat, 03 Jun 2017 03:53:11: 4000000 INFO @ Sat, 03 Jun 2017 03:53:11: 4000000 INFO @ Sat, 03 Jun 2017 03:53:14: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:53:14: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:53:14: #1 total tags in treatment: 4741880 INFO @ Sat, 03 Jun 2017 03:53:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:53:14: #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 03:53:15: #1 tags after filtering in treatment: 4740402 INFO @ Sat, 03 Jun 2017 03:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:53:15: #1 finished! INFO @ Sat, 03 Jun 2017 03:53:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:53:16: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 03:53:16: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 03:53:16: start model_add_line... INFO @ Sat, 03 Jun 2017 03:53:16: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:53:16: #1 tag size is determined as 40 bps INFO @ Sat, 03 Jun 2017 03:53:16: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:53:16: #1 tag size = 40 INFO @ Sat, 03 Jun 2017 03:53:16: #1 total tags in treatment: 4741880 INFO @ Sat, 03 Jun 2017 03:53:16: #1 total tags in treatment: 4741880 INFO @ Sat, 03 Jun 2017 03:53:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:53:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 03:53:16: #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 03:53:16: #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 03:53:17: #1 tags after filtering in treatment: 4740402 INFO @ Sat, 03 Jun 2017 03:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:53:17: #1 finished! INFO @ Sat, 03 Jun 2017 03:53:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:53:17: #1 tags after filtering in treatment: 4740402 INFO @ Sat, 03 Jun 2017 03:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 03:53:17: #1 finished! INFO @ Sat, 03 Jun 2017 03:53:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 03:53:18: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 03:53:18: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 03:53:18: start model_add_line... INFO @ Sat, 03 Jun 2017 03:53:18: #2 number of paired peaks: 375 WARNING @ Sat, 03 Jun 2017 03:53:18: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Sat, 03 Jun 2017 03:53:18: start model_add_line... INFO @ Sat, 03 Jun 2017 03:53:19: start X-correlation... INFO @ Sat, 03 Jun 2017 03:53:19: end of X-cor INFO @ Sat, 03 Jun 2017 03:53:19: #2 finished! INFO @ Sat, 03 Jun 2017 03:53:19: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 03:53:19: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sat, 03 Jun 2017 03:53:19: #2.2 Generate R script for model : SRX1007134.20_model.r WARNING @ Sat, 03 Jun 2017 03:53:19: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:53:19: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sat, 03 Jun 2017 03:53:19: #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 03:53:19: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:53:21: start X-correlation... INFO @ Sat, 03 Jun 2017 03:53:21: end of X-cor INFO @ Sat, 03 Jun 2017 03:53:21: #2 finished! INFO @ Sat, 03 Jun 2017 03:53:21: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 03:53:21: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sat, 03 Jun 2017 03:53:21: #2.2 Generate R script for model : SRX1007134.05_model.r WARNING @ Sat, 03 Jun 2017 03:53:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:53:21: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sat, 03 Jun 2017 03:53:21: #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 03:53:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:53:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:53:22: start X-correlation... INFO @ Sat, 03 Jun 2017 03:53:22: end of X-cor INFO @ Sat, 03 Jun 2017 03:53:22: #2 finished! INFO @ Sat, 03 Jun 2017 03:53:22: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 03:53:22: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sat, 03 Jun 2017 03:53:22: #2.2 Generate R script for model : SRX1007134.10_model.r WARNING @ Sat, 03 Jun 2017 03:53:22: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 03:53:22: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sat, 03 Jun 2017 03:53:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 03:53:22: #3 Call peaks... INFO @ Sat, 03 Jun 2017 03:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 03:53:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:53:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:53:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 03:54:06: #4 Write output xls file... SRX1007134.20_peaks.xls INFO @ Sat, 03 Jun 2017 03:54:06: #4 Write peak in narrowPeak format file... SRX1007134.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:54:06: #4 Write summits bed file... SRX1007134.20_summits.bed INFO @ Sat, 03 Jun 2017 03:54:06: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (126 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 03:54:07: #4 Write output xls file... SRX1007134.05_peaks.xls INFO @ Sat, 03 Jun 2017 03:54:07: #4 Write peak in narrowPeak format file... SRX1007134.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:54:07: #4 Write summits bed file... SRX1007134.05_summits.bed INFO @ Sat, 03 Jun 2017 03:54:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (749 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 03:54:12: #4 Write output xls file... SRX1007134.10_peaks.xls INFO @ Sat, 03 Jun 2017 03:54:12: #4 Write peak in narrowPeak format file... SRX1007134.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 03:54:12: #4 Write summits bed file... SRX1007134.10_summits.bed INFO @ Sat, 03 Jun 2017 03:54:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (294 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。