Job ID = 9029607 sra ファイルのダウンロード中... Completed: 780928K bytes transferred in 9 seconds (695274K 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 --:--:-- 0:00:06 --:--:-- 0 100 21556 0 21556 0 0 2742 0 --:--:-- 0:00:07 --:--:-- 14351 100 43276 0 43276 0 0 4979 0 --:--:-- 0:00:08 --:--:-- 18549 100 95958 0 95958 0 0 10077 0 --:--:-- 0:00:09 --:--:-- 30337 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 38257052 spots for /home/okishinya/chipatlas/results/dm3/SRX187589/SRR572653.sra Written 38257052 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: 00:08:10 38257052 reads; of these: 38257052 (100.00%) were unpaired; of these: 15311459 (40.02%) aligned 0 times 17601491 (46.01%) aligned exactly 1 time 5344102 (13.97%) aligned >1 times 59.98% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 13907385 / 22945593 = 0.6061 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 14:37:46: # Command line: callpeak -t SRX187589.bam -f BAM -g dm -n SRX187589.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX187589.10 # format = BAM # ChIP-seq file = ['SRX187589.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:37:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:46: # Command line: callpeak -t SRX187589.bam -f BAM -g dm -n SRX187589.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX187589.05 # format = BAM # ChIP-seq file = ['SRX187589.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:37:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:46: # Command line: callpeak -t SRX187589.bam -f BAM -g dm -n SRX187589.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX187589.20 # format = BAM # ChIP-seq file = ['SRX187589.bam'] # control file = None # effective genome size = 1.20e+08 # 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 14:37:46: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:37:46: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:37:52: 1000000 INFO @ Sat, 03 Jun 2017 14:37:52: 1000000 INFO @ Sat, 03 Jun 2017 14:37:52: 1000000 INFO @ Sat, 03 Jun 2017 14:37:58: 2000000 INFO @ Sat, 03 Jun 2017 14:37:58: 2000000 INFO @ Sat, 03 Jun 2017 14:37:58: 2000000 INFO @ Sat, 03 Jun 2017 14:38:04: 3000000 INFO @ Sat, 03 Jun 2017 14:38:04: 3000000 INFO @ Sat, 03 Jun 2017 14:38:04: 3000000 INFO @ Sat, 03 Jun 2017 14:38:10: 4000000 INFO @ Sat, 03 Jun 2017 14:38:10: 4000000 INFO @ Sat, 03 Jun 2017 14:38:10: 4000000 INFO @ Sat, 03 Jun 2017 14:38:16: 5000000 INFO @ Sat, 03 Jun 2017 14:38:16: 5000000 INFO @ Sat, 03 Jun 2017 14:38:17: 5000000 INFO @ Sat, 03 Jun 2017 14:38:22: 6000000 INFO @ Sat, 03 Jun 2017 14:38:22: 6000000 INFO @ Sat, 03 Jun 2017 14:38:23: 6000000 INFO @ Sat, 03 Jun 2017 14:38:28: 7000000 INFO @ Sat, 03 Jun 2017 14:38:28: 7000000 INFO @ Sat, 03 Jun 2017 14:38:29: 7000000 INFO @ Sat, 03 Jun 2017 14:38:34: 8000000 INFO @ Sat, 03 Jun 2017 14:38:34: 8000000 INFO @ Sat, 03 Jun 2017 14:38:35: 8000000 INFO @ Sat, 03 Jun 2017 14:38:40: 9000000 INFO @ Sat, 03 Jun 2017 14:38:40: 9000000 INFO @ Sat, 03 Jun 2017 14:38:40: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 14:38:40: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 14:38:40: #1 total tags in treatment: 9038208 INFO @ Sat, 03 Jun 2017 14:38:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:38:40: #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 14:38:41: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 14:38:41: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 14:38:41: #1 total tags in treatment: 9038208 INFO @ Sat, 03 Jun 2017 14:38:41: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:38:41: #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 14:38:41: 9000000 INFO @ Sat, 03 Jun 2017 14:38:42: #1 tag size is determined as 36 bps INFO @ Sat, 03 Jun 2017 14:38:42: #1 tag size = 36 INFO @ Sat, 03 Jun 2017 14:38:42: #1 total tags in treatment: 9038208 INFO @ Sat, 03 Jun 2017 14:38:42: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:38:42: #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 14:38:42: #1 tags after filtering in treatment: 9032616 INFO @ Sat, 03 Jun 2017 14:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:38:42: #1 finished! INFO @ Sat, 03 Jun 2017 14:38:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:38:42: #1 tags after filtering in treatment: 9032616 INFO @ Sat, 03 Jun 2017 14:38:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:38:42: #1 finished! INFO @ Sat, 03 Jun 2017 14:38:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:38:44: #1 tags after filtering in treatment: 9032616 INFO @ Sat, 03 Jun 2017 14:38:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:38:44: #1 finished! INFO @ Sat, 03 Jun 2017 14:38:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:38:44: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 14:38:44: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 14:38:44: start model_add_line... INFO @ Sat, 03 Jun 2017 14:38:44: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 14:38:44: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 14:38:44: start model_add_line... INFO @ Sat, 03 Jun 2017 14:38:45: #2 number of paired peaks: 311 WARNING @ Sat, 03 Jun 2017 14:38:45: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 03 Jun 2017 14:38:45: start model_add_line... INFO @ Sat, 03 Jun 2017 14:38:46: start X-correlation... INFO @ Sat, 03 Jun 2017 14:38:46: end of X-cor INFO @ Sat, 03 Jun 2017 14:38:46: #2 finished! INFO @ Sat, 03 Jun 2017 14:38:46: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 14:38:46: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 14:38:46: #2.2 Generate R script for model : SRX187589.05_model.r WARNING @ Sat, 03 Jun 2017 14:38:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:38:46: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 14:38:46: #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 14:38:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:38:46: start X-correlation... INFO @ Sat, 03 Jun 2017 14:38:46: end of X-cor INFO @ Sat, 03 Jun 2017 14:38:46: #2 finished! INFO @ Sat, 03 Jun 2017 14:38:46: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 14:38:46: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 14:38:46: #2.2 Generate R script for model : SRX187589.10_model.r WARNING @ Sat, 03 Jun 2017 14:38:46: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:38:46: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 14:38:46: #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 14:38:46: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:38:48: start X-correlation... INFO @ Sat, 03 Jun 2017 14:38:48: end of X-cor INFO @ Sat, 03 Jun 2017 14:38:48: #2 finished! INFO @ Sat, 03 Jun 2017 14:38:48: #2 predicted fragment length is 47 bps INFO @ Sat, 03 Jun 2017 14:38:48: #2 alternative fragment length(s) may be 47 bps INFO @ Sat, 03 Jun 2017 14:38:48: #2.2 Generate R script for model : SRX187589.20_model.r WARNING @ Sat, 03 Jun 2017 14:38:48: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 14:38:48: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Sat, 03 Jun 2017 14:38:48: #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 14:38:48: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:39:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:39:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:39:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:40:15: #4 Write output xls file... SRX187589.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:15: #4 Write peak in narrowPeak format file... SRX187589.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:15: #4 Write summits bed file... SRX187589.10_summits.bed INFO @ Sat, 03 Jun 2017 14:40:15: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1008 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:40:16: #4 Write output xls file... SRX187589.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:16: #4 Write peak in narrowPeak format file... SRX187589.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:16: #4 Write summits bed file... SRX187589.05_summits.bed INFO @ Sat, 03 Jun 2017 14:40:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2084 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:40:24: #4 Write output xls file... SRX187589.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:40:24: #4 Write peak in narrowPeak format file... SRX187589.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:40:24: #4 Write summits bed file... SRX187589.20_summits.bed INFO @ Sat, 03 Jun 2017 14:40:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (565 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。