Job ID = 9028843 sra ファイルのダウンロード中... Completed: 523038K bytes transferred in 7 seconds (552754K 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 --:--:-- 0 100 7663 0 7663 0 0 818 0 --:--:-- 0:00:09 --:--:-- 2598 100 36038 0 36038 0 0 3477 0 --:--:-- 0:00:10 --:--:-- 9135 100 47714 0 47714 0 0 4531 0 --:--:-- 0:00:10 --:--:-- 11606 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 14661660 spots for /home/okishinya/chipatlas/results/ce10/SRX982073/SRR1956552.sra Written 14661660 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: 00:04:02 14661660 reads; of these: 14661660 (100.00%) were unpaired; of these: 323165 (2.20%) aligned 0 times 11234301 (76.62%) aligned exactly 1 time 3104194 (21.17%) aligned >1 times 97.80% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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] 2044271 / 14338495 = 0.1426 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 12:08:10: # Command line: callpeak -t SRX982073.bam -f BAM -g ce -n SRX982073.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX982073.10 # format = BAM # ChIP-seq file = ['SRX982073.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 12:08:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:10: # Command line: callpeak -t SRX982073.bam -f BAM -g ce -n SRX982073.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX982073.05 # format = BAM # ChIP-seq file = ['SRX982073.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 12:08:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:10: # Command line: callpeak -t SRX982073.bam -f BAM -g ce -n SRX982073.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX982073.20 # format = BAM # ChIP-seq file = ['SRX982073.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 12:08:10: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:08:10: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:08:16: 1000000 INFO @ Sat, 03 Jun 2017 12:08:16: 1000000 INFO @ Sat, 03 Jun 2017 12:08:17: 1000000 INFO @ Sat, 03 Jun 2017 12:08:22: 2000000 INFO @ Sat, 03 Jun 2017 12:08:22: 2000000 INFO @ Sat, 03 Jun 2017 12:08:23: 2000000 INFO @ Sat, 03 Jun 2017 12:08:28: 3000000 INFO @ Sat, 03 Jun 2017 12:08:28: 3000000 INFO @ Sat, 03 Jun 2017 12:08:30: 3000000 INFO @ Sat, 03 Jun 2017 12:08:35: 4000000 INFO @ Sat, 03 Jun 2017 12:08:35: 4000000 INFO @ Sat, 03 Jun 2017 12:08:36: 4000000 INFO @ Sat, 03 Jun 2017 12:08:41: 5000000 INFO @ Sat, 03 Jun 2017 12:08:41: 5000000 INFO @ Sat, 03 Jun 2017 12:08:43: 5000000 INFO @ Sat, 03 Jun 2017 12:08:47: 6000000 INFO @ Sat, 03 Jun 2017 12:08:47: 6000000 INFO @ Sat, 03 Jun 2017 12:08:50: 6000000 INFO @ Sat, 03 Jun 2017 12:08:53: 7000000 INFO @ Sat, 03 Jun 2017 12:08:53: 7000000 INFO @ Sat, 03 Jun 2017 12:08:56: 7000000 INFO @ Sat, 03 Jun 2017 12:08:59: 8000000 INFO @ Sat, 03 Jun 2017 12:08:59: 8000000 INFO @ Sat, 03 Jun 2017 12:09:03: 8000000 INFO @ Sat, 03 Jun 2017 12:09:05: 9000000 INFO @ Sat, 03 Jun 2017 12:09:05: 9000000 INFO @ Sat, 03 Jun 2017 12:09:09: 9000000 INFO @ Sat, 03 Jun 2017 12:09:11: 10000000 INFO @ Sat, 03 Jun 2017 12:09:12: 10000000 INFO @ Sat, 03 Jun 2017 12:09:16: 10000000 INFO @ Sat, 03 Jun 2017 12:09:18: 11000000 INFO @ Sat, 03 Jun 2017 12:09:18: 11000000 INFO @ Sat, 03 Jun 2017 12:09:23: 11000000 INFO @ Sat, 03 Jun 2017 12:09:24: 12000000 INFO @ Sat, 03 Jun 2017 12:09:24: 12000000 INFO @ Sat, 03 Jun 2017 12:09:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:26: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:26: #1 total tags in treatment: 12294224 INFO @ Sat, 03 Jun 2017 12:09:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:26: #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 12:09:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:26: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:26: #1 total tags in treatment: 12294224 INFO @ Sat, 03 Jun 2017 12:09:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:26: #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 12:09:28: #1 tags after filtering in treatment: 12292821 INFO @ Sat, 03 Jun 2017 12:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:28: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:28: #1 tags after filtering in treatment: 12292821 INFO @ Sat, 03 Jun 2017 12:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:28: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:29: 12000000 INFO @ Sat, 03 Jun 2017 12:09:30: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 12:09:30: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:30: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 12:09:30: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:30: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:30: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:09:30: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:09:30: #1 total tags in treatment: 12294224 INFO @ Sat, 03 Jun 2017 12:09:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:09:30: #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 12:09:33: #1 tags after filtering in treatment: 12292821 INFO @ Sat, 03 Jun 2017 12:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:09:33: #1 finished! INFO @ Sat, 03 Jun 2017 12:09:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:09:35: #2 number of paired peaks: 478 WARNING @ Sat, 03 Jun 2017 12:09:35: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Sat, 03 Jun 2017 12:09:35: start model_add_line... INFO @ Sat, 03 Jun 2017 12:09:38: start X-correlation... INFO @ Sat, 03 Jun 2017 12:09:38: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:38: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:38: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:09:38: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 12:09:38: #2.2 Generate R script for model : SRX982073.10_model.r WARNING @ Sat, 03 Jun 2017 12:09:38: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Sat, 03 Jun 2017 12:09:38: start X-correlation... WARNING @ Sat, 03 Jun 2017 12:09:38: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 12:09:38: #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 12:09:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:38: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:38: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:38: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:09:38: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 12:09:38: #2.2 Generate R script for model : SRX982073.20_model.r WARNING @ Sat, 03 Jun 2017 12:09:38: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:09:38: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 12:09:38: #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 12:09:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:09:42: start X-correlation... INFO @ Sat, 03 Jun 2017 12:09:42: end of X-cor INFO @ Sat, 03 Jun 2017 12:09:42: #2 finished! INFO @ Sat, 03 Jun 2017 12:09:42: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 12:09:42: #2 alternative fragment length(s) may be 3,56 bps INFO @ Sat, 03 Jun 2017 12:09:42: #2.2 Generate R script for model : SRX982073.05_model.r WARNING @ Sat, 03 Jun 2017 12:09:42: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 12:09:42: #2 You may need to consider one of the other alternative d(s): 3,56 WARNING @ Sat, 03 Jun 2017 12:09:42: #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 12:09:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:09:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:10:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:10:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:10:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:11:27: #4 Write output xls file... SRX982073.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:27: #4 Write peak in narrowPeak format file... SRX982073.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:27: #4 Write summits bed file... SRX982073.20_summits.bed INFO @ Sat, 03 Jun 2017 12:11:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (219 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:11:28: #4 Write output xls file... SRX982073.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:28: #4 Write peak in narrowPeak format file... SRX982073.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:28: #4 Write summits bed file... SRX982073.10_summits.bed INFO @ Sat, 03 Jun 2017 12:11:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (649 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:11:42: #4 Write output xls file... SRX982073.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:11:42: #4 Write peak in narrowPeak format file... SRX982073.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:11:42: #4 Write summits bed file... SRX982073.05_summits.bed INFO @ Sat, 03 Jun 2017 12:11:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1827 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。