Job ID = 9026723 sra ファイルのダウンロード中... Completed: 413899K bytes transferred in 6 seconds (513315K 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 14324 0 14324 0 0 1512 0 --:--:-- 0:00:09 --:--:-- 4652 100 60229 0 60229 0 0 5753 0 --:--:-- 0:00:10 --:--:-- 14780 100 62100 0 62100 0 0 5931 0 --:--:-- 0:00:10 --:--:-- 15235 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 13823502 spots for /home/okishinya/chipatlas/results/ce10/SRX466482/SRR1163548.sra Written 13823502 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: 00:03:47 13823502 reads; of these: 13823502 (100.00%) were unpaired; of these: 855806 (6.19%) aligned 0 times 9883443 (71.50%) aligned exactly 1 time 3084253 (22.31%) aligned >1 times 93.81% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 3855920 / 12967696 = 0.2973 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 07:26:50: # Command line: callpeak -t SRX466482.bam -f BAM -g ce -n SRX466482.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX466482.20 # format = BAM # ChIP-seq file = ['SRX466482.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 07:26:50: # Command line: callpeak -t SRX466482.bam -f BAM -g ce -n SRX466482.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX466482.10 # format = BAM # ChIP-seq file = ['SRX466482.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 07:26:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:26:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:26:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:26:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:26:50: # Command line: callpeak -t SRX466482.bam -f BAM -g ce -n SRX466482.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX466482.05 # format = BAM # ChIP-seq file = ['SRX466482.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 07:26:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 07:26:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 07:26:57: 1000000 INFO @ Sat, 03 Jun 2017 07:26:57: 1000000 INFO @ Sat, 03 Jun 2017 07:26:58: 1000000 INFO @ Sat, 03 Jun 2017 07:27:03: 2000000 INFO @ Sat, 03 Jun 2017 07:27:05: 2000000 INFO @ Sat, 03 Jun 2017 07:27:07: 2000000 INFO @ Sat, 03 Jun 2017 07:27:10: 3000000 INFO @ Sat, 03 Jun 2017 07:27:12: 3000000 INFO @ Sat, 03 Jun 2017 07:27:15: 3000000 INFO @ Sat, 03 Jun 2017 07:27:16: 4000000 INFO @ Sat, 03 Jun 2017 07:27:19: 4000000 INFO @ Sat, 03 Jun 2017 07:27:23: 5000000 INFO @ Sat, 03 Jun 2017 07:27:24: 4000000 INFO @ Sat, 03 Jun 2017 07:27:27: 5000000 INFO @ Sat, 03 Jun 2017 07:27:30: 6000000 INFO @ Sat, 03 Jun 2017 07:27:32: 5000000 INFO @ Sat, 03 Jun 2017 07:27:34: 6000000 INFO @ Sat, 03 Jun 2017 07:27:36: 7000000 INFO @ Sat, 03 Jun 2017 07:27:40: 6000000 INFO @ Sat, 03 Jun 2017 07:27:41: 7000000 INFO @ Sat, 03 Jun 2017 07:27:43: 8000000 INFO @ Sat, 03 Jun 2017 07:27:49: 7000000 INFO @ Sat, 03 Jun 2017 07:27:49: 8000000 INFO @ Sat, 03 Jun 2017 07:27:50: 9000000 INFO @ Sat, 03 Jun 2017 07:27:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 07:27:50: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 07:27:50: #1 total tags in treatment: 9111776 INFO @ Sat, 03 Jun 2017 07:27:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:27:50: #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 07:27:52: #1 tags after filtering in treatment: 9109744 INFO @ Sat, 03 Jun 2017 07:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:27:52: #1 finished! INFO @ Sat, 03 Jun 2017 07:27:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:27:54: #2 number of paired peaks: 552 WARNING @ Sat, 03 Jun 2017 07:27:54: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 03 Jun 2017 07:27:54: start model_add_line... INFO @ Sat, 03 Jun 2017 07:27:56: 9000000 INFO @ Sat, 03 Jun 2017 07:27:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 07:27:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 07:27:57: #1 total tags in treatment: 9111776 INFO @ Sat, 03 Jun 2017 07:27:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:27:57: #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 07:27:57: 8000000 INFO @ Sat, 03 Jun 2017 07:27:58: #1 tags after filtering in treatment: 9109744 INFO @ Sat, 03 Jun 2017 07:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:27:58: #1 finished! INFO @ Sat, 03 Jun 2017 07:27:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:28:00: #2 number of paired peaks: 552 WARNING @ Sat, 03 Jun 2017 07:28:00: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 03 Jun 2017 07:28:00: start model_add_line... INFO @ Sat, 03 Jun 2017 07:28:01: start X-correlation... INFO @ Sat, 03 Jun 2017 07:28:01: end of X-cor INFO @ Sat, 03 Jun 2017 07:28:01: #2 finished! INFO @ Sat, 03 Jun 2017 07:28:01: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:28:01: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 03 Jun 2017 07:28:01: #2.2 Generate R script for model : SRX466482.10_model.r WARNING @ Sat, 03 Jun 2017 07:28:01: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:28:01: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 03 Jun 2017 07:28:01: #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 07:28:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:28:04: 9000000 INFO @ Sat, 03 Jun 2017 07:28:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 07:28:04: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 07:28:04: #1 total tags in treatment: 9111776 INFO @ Sat, 03 Jun 2017 07:28:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 07:28:04: #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 07:28:07: #1 tags after filtering in treatment: 9109744 INFO @ Sat, 03 Jun 2017 07:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 07:28:07: #1 finished! INFO @ Sat, 03 Jun 2017 07:28:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 07:28:07: start X-correlation... INFO @ Sat, 03 Jun 2017 07:28:07: end of X-cor INFO @ Sat, 03 Jun 2017 07:28:07: #2 finished! INFO @ Sat, 03 Jun 2017 07:28:07: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:28:07: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 03 Jun 2017 07:28:07: #2.2 Generate R script for model : SRX466482.05_model.r WARNING @ Sat, 03 Jun 2017 07:28:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:28:07: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 03 Jun 2017 07:28:07: #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 07:28:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:28:08: #2 number of paired peaks: 552 WARNING @ Sat, 03 Jun 2017 07:28:08: Fewer paired peaks (552) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 552 pairs to build model! INFO @ Sat, 03 Jun 2017 07:28:08: start model_add_line... INFO @ Sat, 03 Jun 2017 07:28:15: start X-correlation... INFO @ Sat, 03 Jun 2017 07:28:15: end of X-cor INFO @ Sat, 03 Jun 2017 07:28:15: #2 finished! INFO @ Sat, 03 Jun 2017 07:28:15: #2 predicted fragment length is 46 bps INFO @ Sat, 03 Jun 2017 07:28:15: #2 alternative fragment length(s) may be 2,46 bps INFO @ Sat, 03 Jun 2017 07:28:15: #2.2 Generate R script for model : SRX466482.20_model.r WARNING @ Sat, 03 Jun 2017 07:28:15: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 07:28:15: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Sat, 03 Jun 2017 07:28:15: #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 07:28:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 07:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 07:28:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:28:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:29:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 07:29:26: #4 Write output xls file... SRX466482.10_peaks.xls INFO @ Sat, 03 Jun 2017 07:29:26: #4 Write peak in narrowPeak format file... SRX466482.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:29:26: #4 Write summits bed file... SRX466482.10_summits.bed INFO @ Sat, 03 Jun 2017 07:29:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 07:29:34: #4 Write output xls file... SRX466482.05_peaks.xls INFO @ Sat, 03 Jun 2017 07:29:34: #4 Write peak in narrowPeak format file... SRX466482.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:29:34: #4 Write summits bed file... SRX466482.05_summits.bed INFO @ Sat, 03 Jun 2017 07:29:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 07:29:43: #4 Write output xls file... SRX466482.20_peaks.xls INFO @ Sat, 03 Jun 2017 07:29:43: #4 Write peak in narrowPeak format file... SRX466482.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 07:29:43: #4 Write summits bed file... SRX466482.20_summits.bed INFO @ Sat, 03 Jun 2017 07:29:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 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。