Job ID = 9025623 sra ファイルのダウンロード中... Completed: 488554K bytes transferred in 6 seconds (579863K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 100 7663 0 7663 0 0 765 0 --:--:-- 0:00:10 --:--:-- 2110 100 39347 0 39347 0 0 3575 0 --:--:-- 0:00:11 --:--:-- 8503 100 41218 0 41218 0 0 3744 0 --:--:-- 0:00:11 --:--:-- 11370 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 13338445 spots for /home/okishinya/chipatlas/results/ce10/SRX208765/SRR628899.sra Written 13338445 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: 00:05:10 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 1949218 (14.61%) aligned 0 times 9828676 (73.69%) aligned exactly 1 time 1560551 (11.70%) aligned >1 times 85.39% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2392988 / 11389227 = 0.2101 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 04:47:35: # Command line: callpeak -t SRX208765.bam -f BAM -g ce -n SRX208765.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208765.10 # format = BAM # ChIP-seq file = ['SRX208765.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 04:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:47:35: # Command line: callpeak -t SRX208765.bam -f BAM -g ce -n SRX208765.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208765.05 # format = BAM # ChIP-seq file = ['SRX208765.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 04:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:47:35: # Command line: callpeak -t SRX208765.bam -f BAM -g ce -n SRX208765.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208765.20 # format = BAM # ChIP-seq file = ['SRX208765.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 04:47:35: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:47:35: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:47:41: 1000000 INFO @ Sat, 03 Jun 2017 04:47:41: 1000000 INFO @ Sat, 03 Jun 2017 04:47:41: 1000000 INFO @ Sat, 03 Jun 2017 04:47:47: 2000000 INFO @ Sat, 03 Jun 2017 04:47:47: 2000000 INFO @ Sat, 03 Jun 2017 04:47:47: 2000000 INFO @ Sat, 03 Jun 2017 04:47:53: 3000000 INFO @ Sat, 03 Jun 2017 04:47:53: 3000000 INFO @ Sat, 03 Jun 2017 04:47:53: 3000000 INFO @ Sat, 03 Jun 2017 04:47:59: 4000000 INFO @ Sat, 03 Jun 2017 04:47:59: 4000000 INFO @ Sat, 03 Jun 2017 04:47:59: 4000000 INFO @ Sat, 03 Jun 2017 04:48:05: 5000000 INFO @ Sat, 03 Jun 2017 04:48:05: 5000000 INFO @ Sat, 03 Jun 2017 04:48:06: 5000000 INFO @ Sat, 03 Jun 2017 04:48:11: 6000000 INFO @ Sat, 03 Jun 2017 04:48:11: 6000000 INFO @ Sat, 03 Jun 2017 04:48:12: 6000000 INFO @ Sat, 03 Jun 2017 04:48:17: 7000000 INFO @ Sat, 03 Jun 2017 04:48:18: 7000000 INFO @ Sat, 03 Jun 2017 04:48:19: 7000000 INFO @ Sat, 03 Jun 2017 04:48:23: 8000000 INFO @ Sat, 03 Jun 2017 04:48:25: 8000000 INFO @ Sat, 03 Jun 2017 04:48:26: 8000000 INFO @ Sat, 03 Jun 2017 04:48:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:29: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:29: #1 total tags in treatment: 8996239 INFO @ Sat, 03 Jun 2017 04:48:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:29: #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 04:48:31: #1 tags after filtering in treatment: 8846113 INFO @ Sat, 03 Jun 2017 04:48:31: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:48:31: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:31: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:31: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:31: #1 total tags in treatment: 8996239 INFO @ Sat, 03 Jun 2017 04:48:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:31: #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 04:48:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:48:33: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:48:33: #1 total tags in treatment: 8996239 INFO @ Sat, 03 Jun 2017 04:48:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:48:33: #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 04:48:33: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 04:48:33: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:33: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:33: #1 tags after filtering in treatment: 8846113 INFO @ Sat, 03 Jun 2017 04:48:33: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:48:33: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:48:34: #1 tags after filtering in treatment: 8846113 INFO @ Sat, 03 Jun 2017 04:48:34: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Jun 2017 04:48:34: #1 finished! INFO @ Sat, 03 Jun 2017 04:48:34: #2 Build Peak Model... 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 55 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2 alternative fragment length(s) may be 1,55,104,111,176,266,287,416,507,543,552,559,593 bps INFO @ Sat, 03 Jun 2017 04:48:34: #2.2 Generate R script for model : SRX208765.10_model.r WARNING @ Sat, 03 Jun 2017 04:48:34: #2 Since the d (55) 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): 1,55,104,111,176,266,287,416,507,543,552,559,593 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 04:48:35: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 04:48:35: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:35: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:36: #2 number of paired peaks: 121 WARNING @ Sat, 03 Jun 2017 04:48:36: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Sat, 03 Jun 2017 04:48:36: start model_add_line... INFO @ Sat, 03 Jun 2017 04:48:36: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:36: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:36: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:36: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 04:48:36: #2 alternative fragment length(s) may be 1,55,104,111,176,266,287,416,507,543,552,559,593 bps INFO @ Sat, 03 Jun 2017 04:48:36: #2.2 Generate R script for model : SRX208765.05_model.r WARNING @ Sat, 03 Jun 2017 04:48:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:48:36: #2 You may need to consider one of the other alternative d(s): 1,55,104,111,176,266,287,416,507,543,552,559,593 WARNING @ Sat, 03 Jun 2017 04:48:36: #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 04:48:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:48:38: start X-correlation... INFO @ Sat, 03 Jun 2017 04:48:38: end of X-cor INFO @ Sat, 03 Jun 2017 04:48:38: #2 finished! INFO @ Sat, 03 Jun 2017 04:48:38: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Jun 2017 04:48:38: #2 alternative fragment length(s) may be 1,55,104,111,176,266,287,416,507,543,552,559,593 bps INFO @ Sat, 03 Jun 2017 04:48:38: #2.2 Generate R script for model : SRX208765.20_model.r WARNING @ Sat, 03 Jun 2017 04:48:38: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:48:38: #2 You may need to consider one of the other alternative d(s): 1,55,104,111,176,266,287,416,507,543,552,559,593 WARNING @ Sat, 03 Jun 2017 04:48:38: #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 04:48:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:49:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write output xls file... SRX208765.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write peak in narrowPeak format file... SRX208765.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:56: #4 Write summits bed file... SRX208765.10_summits.bed INFO @ Sat, 03 Jun 2017 04:49:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:49:58: #4 Write output xls file... SRX208765.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:49:58: #4 Write peak in narrowPeak format file... SRX208765.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:49:58: #4 Write summits bed file... SRX208765.05_summits.bed INFO @ Sat, 03 Jun 2017 04:49:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:50:00: #4 Write output xls file... SRX208765.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:50:00: #4 Write peak in narrowPeak format file... SRX208765.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:50:00: #4 Write summits bed file... SRX208765.20_summits.bed INFO @ Sat, 03 Jun 2017 04:50:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (21 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。