Job ID = 9025627 sra ファイルのダウンロード中... Completed: 438592K bytes transferred in 7 seconds (483319K 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 7663 0 7663 0 0 993 0 --:--:-- 0:00:07 --:--:-- 6617 100 30317 0 30317 0 0 3479 0 --:--:-- 0:00:08 --:--:-- 14074 100 63312 0 63312 0 0 6634 0 --:--:-- 0:00:09 --:--:-- 21210 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 13454005 spots for /home/okishinya/chipatlas/results/ce10/SRX208769/SRR628903.sra Written 13454005 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: 00:04:55 13454005 reads; of these: 13454005 (100.00%) were unpaired; of these: 1263773 (9.39%) aligned 0 times 10493837 (78.00%) aligned exactly 1 time 1696395 (12.61%) aligned >1 times 90.61% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 3329071 / 12190232 = 0.2731 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 04:51:48: # Command line: callpeak -t SRX208769.bam -f BAM -g ce -n SRX208769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208769.10 # format = BAM # ChIP-seq file = ['SRX208769.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 04:51:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:48: # Command line: callpeak -t SRX208769.bam -f BAM -g ce -n SRX208769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208769.05 # format = BAM # ChIP-seq file = ['SRX208769.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 04:51:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:48: # Command line: callpeak -t SRX208769.bam -f BAM -g ce -n SRX208769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208769.20 # format = BAM # ChIP-seq file = ['SRX208769.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 04:51:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:51:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:51:55: 1000000 INFO @ Sat, 03 Jun 2017 04:51:55: 1000000 INFO @ Sat, 03 Jun 2017 04:51:56: 1000000 INFO @ Sat, 03 Jun 2017 04:52:01: 2000000 INFO @ Sat, 03 Jun 2017 04:52:02: 2000000 INFO @ Sat, 03 Jun 2017 04:52:03: 2000000 INFO @ Sat, 03 Jun 2017 04:52:07: 3000000 INFO @ Sat, 03 Jun 2017 04:52:09: 3000000 INFO @ Sat, 03 Jun 2017 04:52:11: 3000000 INFO @ Sat, 03 Jun 2017 04:52:13: 4000000 INFO @ Sat, 03 Jun 2017 04:52:17: 4000000 INFO @ Sat, 03 Jun 2017 04:52:18: 4000000 INFO @ Sat, 03 Jun 2017 04:52:19: 5000000 INFO @ Sat, 03 Jun 2017 04:52:24: 5000000 INFO @ Sat, 03 Jun 2017 04:52:26: 6000000 INFO @ Sat, 03 Jun 2017 04:52:26: 5000000 INFO @ Sat, 03 Jun 2017 04:52:31: 6000000 INFO @ Sat, 03 Jun 2017 04:52:32: 7000000 INFO @ Sat, 03 Jun 2017 04:52:33: 6000000 INFO @ Sat, 03 Jun 2017 04:52:38: 7000000 INFO @ Sat, 03 Jun 2017 04:52:38: 8000000 INFO @ Sat, 03 Jun 2017 04:52:41: 7000000 INFO @ Sat, 03 Jun 2017 04:52:44: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:44: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:44: #1 total tags in treatment: 8861161 INFO @ Sat, 03 Jun 2017 04:52:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:44: #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 04:52:45: #1 tags after filtering in treatment: 8546004 INFO @ Sat, 03 Jun 2017 04:52:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 03 Jun 2017 04:52:45: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:45: 8000000 INFO @ Sat, 03 Jun 2017 04:52:46: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 04:52:46: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:46: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:48: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:48: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:48: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:48: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:52:48: #2 alternative fragment length(s) may be 2,43,62,96,128,521,581 bps INFO @ Sat, 03 Jun 2017 04:52:48: #2.2 Generate R script for model : SRX208769.20_model.r WARNING @ Sat, 03 Jun 2017 04:52:48: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:48: #2 You may need to consider one of the other alternative d(s): 2,43,62,96,128,521,581 WARNING @ Sat, 03 Jun 2017 04:52:48: #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 04:52:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:49: 8000000 INFO @ Sat, 03 Jun 2017 04:52:51: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:51: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:51: #1 total tags in treatment: 8861161 INFO @ Sat, 03 Jun 2017 04:52:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:51: #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 04:52:53: #1 tags after filtering in treatment: 8546004 INFO @ Sat, 03 Jun 2017 04:52:53: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 03 Jun 2017 04:52:53: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:53: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:55: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 04:52:55: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:55: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:55: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:52:55: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:52:55: #1 total tags in treatment: 8861161 INFO @ Sat, 03 Jun 2017 04:52:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:52:55: #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 04:52:56: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:56: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:56: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:56: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:52:56: #2 alternative fragment length(s) may be 2,43,62,96,128,521,581 bps INFO @ Sat, 03 Jun 2017 04:52:56: #2.2 Generate R script for model : SRX208769.10_model.r WARNING @ Sat, 03 Jun 2017 04:52:56: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:56: #2 You may need to consider one of the other alternative d(s): 2,43,62,96,128,521,581 WARNING @ Sat, 03 Jun 2017 04:52:56: #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 04:52:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:52:56: #1 tags after filtering in treatment: 8546004 INFO @ Sat, 03 Jun 2017 04:52:56: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 03 Jun 2017 04:52:56: #1 finished! INFO @ Sat, 03 Jun 2017 04:52:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:52:58: #2 number of paired peaks: 110 WARNING @ Sat, 03 Jun 2017 04:52:58: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 03 Jun 2017 04:52:58: start model_add_line... INFO @ Sat, 03 Jun 2017 04:52:59: start X-correlation... INFO @ Sat, 03 Jun 2017 04:52:59: end of X-cor INFO @ Sat, 03 Jun 2017 04:52:59: #2 finished! INFO @ Sat, 03 Jun 2017 04:52:59: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Jun 2017 04:52:59: #2 alternative fragment length(s) may be 2,43,62,96,128,521,581 bps INFO @ Sat, 03 Jun 2017 04:52:59: #2.2 Generate R script for model : SRX208769.05_model.r WARNING @ Sat, 03 Jun 2017 04:52:59: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 04:52:59: #2 You may need to consider one of the other alternative d(s): 2,43,62,96,128,521,581 WARNING @ Sat, 03 Jun 2017 04:52:59: #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 04:52:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:53:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:53:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:53:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:54:06: #4 Write output xls file... SRX208769.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:06: #4 Write peak in narrowPeak format file... SRX208769.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:06: #4 Write summits bed file... SRX208769.20_summits.bed INFO @ Sat, 03 Jun 2017 04:54:06: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:54:18: #4 Write output xls file... SRX208769.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:18: #4 Write peak in narrowPeak format file... SRX208769.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:18: #4 Write summits bed file... SRX208769.10_summits.bed INFO @ Sat, 03 Jun 2017 04:54:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:54:26: #4 Write output xls file... SRX208769.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:54:26: #4 Write peak in narrowPeak format file... SRX208769.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:54:26: #4 Write summits bed file... SRX208769.05_summits.bed INFO @ Sat, 03 Jun 2017 04:54:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (334 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。