Job ID = 9029213 sra ファイルのダウンロード中... Completed: 554241K bytes transferred in 10 seconds (446902K 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 20110 0 20110 0 0 2632 0 --:--:-- 0:00:07 --:--:-- 15143 100 51966 0 51966 0 0 6016 0 --:--:-- 0:00:08 --:--:-- 22350 100 61462 0 61462 0 0 6982 0 --:--:-- 0:00:08 --:--:-- 24673 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 23001437 spots for /home/okishinya/chipatlas/results/dm3/SRX1433353/SRR2919818.sra Written 23001437 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: 00:09:02 23001437 reads; of these: 23001437 (100.00%) were unpaired; of these: 688222 (2.99%) aligned 0 times 17485731 (76.02%) aligned exactly 1 time 4827484 (20.99%) aligned >1 times 97.01% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3599257 / 22313215 = 0.1613 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 13:07:38: # Command line: callpeak -t SRX1433353.bam -f BAM -g dm -n SRX1433353.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433353.05 # format = BAM # ChIP-seq file = ['SRX1433353.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 13:07:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:38: # Command line: callpeak -t SRX1433353.bam -f BAM -g dm -n SRX1433353.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433353.10 # format = BAM # ChIP-seq file = ['SRX1433353.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 13:07:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:38: # Command line: callpeak -t SRX1433353.bam -f BAM -g dm -n SRX1433353.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433353.20 # format = BAM # ChIP-seq file = ['SRX1433353.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 13:07:38: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:07:38: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:07:44: 1000000 INFO @ Sat, 03 Jun 2017 13:07:44: 1000000 INFO @ Sat, 03 Jun 2017 13:07:44: 1000000 INFO @ Sat, 03 Jun 2017 13:07:51: 2000000 INFO @ Sat, 03 Jun 2017 13:07:51: 2000000 INFO @ Sat, 03 Jun 2017 13:07:51: 2000000 INFO @ Sat, 03 Jun 2017 13:07:57: 3000000 INFO @ Sat, 03 Jun 2017 13:07:57: 3000000 INFO @ Sat, 03 Jun 2017 13:07:57: 3000000 INFO @ Sat, 03 Jun 2017 13:08:03: 4000000 INFO @ Sat, 03 Jun 2017 13:08:03: 4000000 INFO @ Sat, 03 Jun 2017 13:08:03: 4000000 INFO @ Sat, 03 Jun 2017 13:08:09: 5000000 INFO @ Sat, 03 Jun 2017 13:08:10: 5000000 INFO @ Sat, 03 Jun 2017 13:08:10: 5000000 INFO @ Sat, 03 Jun 2017 13:08:16: 6000000 INFO @ Sat, 03 Jun 2017 13:08:16: 6000000 INFO @ Sat, 03 Jun 2017 13:08:16: 6000000 INFO @ Sat, 03 Jun 2017 13:08:22: 7000000 INFO @ Sat, 03 Jun 2017 13:08:22: 7000000 INFO @ Sat, 03 Jun 2017 13:08:23: 7000000 INFO @ Sat, 03 Jun 2017 13:08:29: 8000000 INFO @ Sat, 03 Jun 2017 13:08:29: 8000000 INFO @ Sat, 03 Jun 2017 13:08:29: 8000000 INFO @ Sat, 03 Jun 2017 13:08:35: 9000000 INFO @ Sat, 03 Jun 2017 13:08:36: 9000000 INFO @ Sat, 03 Jun 2017 13:08:36: 9000000 INFO @ Sat, 03 Jun 2017 13:08:42: 10000000 INFO @ Sat, 03 Jun 2017 13:08:42: 10000000 INFO @ Sat, 03 Jun 2017 13:08:42: 10000000 INFO @ Sat, 03 Jun 2017 13:08:49: 11000000 INFO @ Sat, 03 Jun 2017 13:08:49: 11000000 INFO @ Sat, 03 Jun 2017 13:08:49: 11000000 INFO @ Sat, 03 Jun 2017 13:08:56: 12000000 INFO @ Sat, 03 Jun 2017 13:08:56: 12000000 INFO @ Sat, 03 Jun 2017 13:08:56: 12000000 INFO @ Sat, 03 Jun 2017 13:09:03: 13000000 INFO @ Sat, 03 Jun 2017 13:09:03: 13000000 INFO @ Sat, 03 Jun 2017 13:09:04: 13000000 INFO @ Sat, 03 Jun 2017 13:09:10: 14000000 INFO @ Sat, 03 Jun 2017 13:09:11: 14000000 INFO @ Sat, 03 Jun 2017 13:09:12: 14000000 INFO @ Sat, 03 Jun 2017 13:09:18: 15000000 INFO @ Sat, 03 Jun 2017 13:09:19: 15000000 INFO @ Sat, 03 Jun 2017 13:09:20: 15000000 INFO @ Sat, 03 Jun 2017 13:09:26: 16000000 INFO @ Sat, 03 Jun 2017 13:09:26: 16000000 INFO @ Sat, 03 Jun 2017 13:09:29: 16000000 INFO @ Sat, 03 Jun 2017 13:09:33: 17000000 INFO @ Sat, 03 Jun 2017 13:09:34: 17000000 INFO @ Sat, 03 Jun 2017 13:09:37: 17000000 INFO @ Sat, 03 Jun 2017 13:09:41: 18000000 INFO @ Sat, 03 Jun 2017 13:09:41: 18000000 INFO @ Sat, 03 Jun 2017 13:09:44: 18000000 INFO @ Sat, 03 Jun 2017 13:09:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:46: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:46: #1 total tags in treatment: 18713958 INFO @ Sat, 03 Jun 2017 13:09:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:46: #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 13:09:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:46: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:46: #1 total tags in treatment: 18713958 INFO @ Sat, 03 Jun 2017 13:09:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:46: #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 13:09:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:09:49: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:09:49: #1 total tags in treatment: 18713958 INFO @ Sat, 03 Jun 2017 13:09:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:09:49: #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 13:09:49: #1 tags after filtering in treatment: 18709827 INFO @ Sat, 03 Jun 2017 13:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:49: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:50: #1 tags after filtering in treatment: 18709827 INFO @ Sat, 03 Jun 2017 13:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:52: #2 number of paired peaks: 165 WARNING @ Sat, 03 Jun 2017 13:09:52: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:52: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:52: #1 tags after filtering in treatment: 18709827 INFO @ Sat, 03 Jun 2017 13:09:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:09:52: #1 finished! INFO @ Sat, 03 Jun 2017 13:09:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:09:53: #2 number of paired peaks: 165 WARNING @ Sat, 03 Jun 2017 13:09:53: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:53: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:55: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2 alternative fragment length(s) may be 4,53,528,532,546 bps INFO @ Sat, 03 Jun 2017 13:09:55: #2.2 Generate R script for model : SRX1433353.05_model.r WARNING @ Sat, 03 Jun 2017 13:09:55: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:55: #2 You may need to consider one of the other alternative d(s): 4,53,528,532,546 WARNING @ Sat, 03 Jun 2017 13:09:55: #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 13:09:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:09:55: #2 number of paired peaks: 165 WARNING @ Sat, 03 Jun 2017 13:09:55: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 03 Jun 2017 13:09:55: start model_add_line... INFO @ Sat, 03 Jun 2017 13:09:56: start X-correlation... INFO @ Sat, 03 Jun 2017 13:09:56: end of X-cor INFO @ Sat, 03 Jun 2017 13:09:56: #2 finished! INFO @ Sat, 03 Jun 2017 13:09:56: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 13:09:56: #2 alternative fragment length(s) may be 4,53,528,532,546 bps INFO @ Sat, 03 Jun 2017 13:09:56: #2.2 Generate R script for model : SRX1433353.10_model.r WARNING @ Sat, 03 Jun 2017 13:09:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:09:56: #2 You may need to consider one of the other alternative d(s): 4,53,528,532,546 WARNING @ Sat, 03 Jun 2017 13:09:56: #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 13:09:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:09:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:10:00: start X-correlation... INFO @ Sat, 03 Jun 2017 13:10:00: end of X-cor INFO @ Sat, 03 Jun 2017 13:10:00: #2 finished! INFO @ Sat, 03 Jun 2017 13:10:00: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 13:10:00: #2 alternative fragment length(s) may be 4,53,528,532,546 bps INFO @ Sat, 03 Jun 2017 13:10:00: #2.2 Generate R script for model : SRX1433353.20_model.r WARNING @ Sat, 03 Jun 2017 13:10:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:10:00: #2 You may need to consider one of the other alternative d(s): 4,53,528,532,546 WARNING @ Sat, 03 Jun 2017 13:10:00: #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 13:10:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:11:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write output xls file... SRX1433353.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write peak in narrowPeak format file... SRX1433353.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:43: #4 Write summits bed file... SRX1433353.05_summits.bed INFO @ Sat, 03 Jun 2017 13:12:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1949 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:44: #4 Write output xls file... SRX1433353.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:44: #4 Write peak in narrowPeak format file... SRX1433353.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:44: #4 Write summits bed file... SRX1433353.10_summits.bed INFO @ Sat, 03 Jun 2017 13:12:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1272 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:12:59: #4 Write output xls file... SRX1433353.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:12:59: #4 Write peak in narrowPeak format file... SRX1433353.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:12:59: #4 Write summits bed file... SRX1433353.20_summits.bed INFO @ Sat, 03 Jun 2017 13:12:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (743 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。