Job ID = 9029784 sra ファイルのダウンロード中... Completed: 939154K bytes transferred in 12 seconds (619427K 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 29047 0 29047 0 0 3649 0 --:--:-- 0:00:07 --:--:-- 19172 100 30918 0 30918 0 0 3883 0 --:--:-- 0:00:07 --:--:-- 20394 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 19192206 spots for /home/okishinya/chipatlas/results/dm3/SRX2055965/SRR4069197.sra Written 19192206 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: 00:08:16 19192206 reads; of these: 19192206 (100.00%) were unpaired; of these: 1937498 (10.10%) aligned 0 times 11717915 (61.06%) aligned exactly 1 time 5536793 (28.85%) aligned >1 times 89.90% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 1327448 / 17254708 = 0.0769 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 15:25:25: # Command line: callpeak -t SRX2055965.bam -f BAM -g dm -n SRX2055965.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055965.10 # format = BAM # ChIP-seq file = ['SRX2055965.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 15:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:25: # Command line: callpeak -t SRX2055965.bam -f BAM -g dm -n SRX2055965.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055965.20 # format = BAM # ChIP-seq file = ['SRX2055965.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 15:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:25: # Command line: callpeak -t SRX2055965.bam -f BAM -g dm -n SRX2055965.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055965.05 # format = BAM # ChIP-seq file = ['SRX2055965.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 15:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:25:31: 1000000 INFO @ Sat, 03 Jun 2017 15:25:31: 1000000 INFO @ Sat, 03 Jun 2017 15:25:31: 1000000 INFO @ Sat, 03 Jun 2017 15:25:36: 2000000 INFO @ Sat, 03 Jun 2017 15:25:37: 2000000 INFO @ Sat, 03 Jun 2017 15:25:38: 2000000 INFO @ Sat, 03 Jun 2017 15:25:42: 3000000 INFO @ Sat, 03 Jun 2017 15:25:42: 3000000 INFO @ Sat, 03 Jun 2017 15:25:44: 3000000 INFO @ Sat, 03 Jun 2017 15:25:48: 4000000 INFO @ Sat, 03 Jun 2017 15:25:48: 4000000 INFO @ Sat, 03 Jun 2017 15:25:51: 4000000 INFO @ Sat, 03 Jun 2017 15:25:54: 5000000 INFO @ Sat, 03 Jun 2017 15:25:54: 5000000 INFO @ Sat, 03 Jun 2017 15:25:57: 5000000 INFO @ Sat, 03 Jun 2017 15:26:00: 6000000 INFO @ Sat, 03 Jun 2017 15:26:00: 6000000 INFO @ Sat, 03 Jun 2017 15:26:04: 6000000 INFO @ Sat, 03 Jun 2017 15:26:06: 7000000 INFO @ Sat, 03 Jun 2017 15:26:07: 7000000 INFO @ Sat, 03 Jun 2017 15:26:11: 7000000 INFO @ Sat, 03 Jun 2017 15:26:12: 8000000 INFO @ Sat, 03 Jun 2017 15:26:13: 8000000 INFO @ Sat, 03 Jun 2017 15:26:18: 9000000 INFO @ Sat, 03 Jun 2017 15:26:18: 8000000 INFO @ Sat, 03 Jun 2017 15:26:19: 9000000 INFO @ Sat, 03 Jun 2017 15:26:24: 10000000 INFO @ Sat, 03 Jun 2017 15:26:25: 9000000 INFO @ Sat, 03 Jun 2017 15:26:25: 10000000 INFO @ Sat, 03 Jun 2017 15:26:30: 11000000 INFO @ Sat, 03 Jun 2017 15:26:31: 11000000 INFO @ Sat, 03 Jun 2017 15:26:31: 10000000 INFO @ Sat, 03 Jun 2017 15:26:36: 12000000 INFO @ Sat, 03 Jun 2017 15:26:37: 12000000 INFO @ Sat, 03 Jun 2017 15:26:38: 11000000 INFO @ Sat, 03 Jun 2017 15:26:42: 13000000 INFO @ Sat, 03 Jun 2017 15:26:43: 13000000 INFO @ Sat, 03 Jun 2017 15:26:44: 12000000 INFO @ Sat, 03 Jun 2017 15:26:48: 14000000 INFO @ Sat, 03 Jun 2017 15:26:49: 14000000 INFO @ Sat, 03 Jun 2017 15:26:51: 13000000 INFO @ Sat, 03 Jun 2017 15:26:53: 15000000 INFO @ Sat, 03 Jun 2017 15:26:55: 15000000 INFO @ Sat, 03 Jun 2017 15:26:58: 14000000 INFO @ Sat, 03 Jun 2017 15:26:59: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:26:59: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:26:59: #1 total tags in treatment: 15927260 INFO @ Sat, 03 Jun 2017 15:26:59: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:26:59: #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 15:27:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:01: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:01: #1 total tags in treatment: 15927260 INFO @ Sat, 03 Jun 2017 15:27:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:01: #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 15:27:02: #1 tags after filtering in treatment: 15924947 INFO @ Sat, 03 Jun 2017 15:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:02: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:04: 15000000 INFO @ Sat, 03 Jun 2017 15:27:04: #1 tags after filtering in treatment: 15924947 INFO @ Sat, 03 Jun 2017 15:27:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:04: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:05: #2 number of paired peaks: 732 WARNING @ Sat, 03 Jun 2017 15:27:05: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:05: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:07: #2 number of paired peaks: 732 WARNING @ Sat, 03 Jun 2017 15:27:07: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:07: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:10: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:27:10: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:27:10: #1 total tags in treatment: 15927260 INFO @ Sat, 03 Jun 2017 15:27:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:27:10: #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 15:27:12: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:12: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:12: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:12: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 15:27:12: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 03 Jun 2017 15:27:12: #2.2 Generate R script for model : SRX2055965.20_model.r WARNING @ Sat, 03 Jun 2017 15:27:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:12: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 03 Jun 2017 15:27:12: #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 15:27:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:13: #1 tags after filtering in treatment: 15924947 INFO @ Sat, 03 Jun 2017 15:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:27:13: #1 finished! INFO @ Sat, 03 Jun 2017 15:27:13: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:27:15: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:15: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:15: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:15: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 15:27:15: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 03 Jun 2017 15:27:15: #2.2 Generate R script for model : SRX2055965.05_model.r WARNING @ Sat, 03 Jun 2017 15:27:15: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:15: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 03 Jun 2017 15:27:15: #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 15:27:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:27:15: #2 number of paired peaks: 732 WARNING @ Sat, 03 Jun 2017 15:27:15: Fewer paired peaks (732) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 732 pairs to build model! INFO @ Sat, 03 Jun 2017 15:27:15: start model_add_line... INFO @ Sat, 03 Jun 2017 15:27:23: start X-correlation... INFO @ Sat, 03 Jun 2017 15:27:23: end of X-cor INFO @ Sat, 03 Jun 2017 15:27:23: #2 finished! INFO @ Sat, 03 Jun 2017 15:27:23: #2 predicted fragment length is 54 bps INFO @ Sat, 03 Jun 2017 15:27:23: #2 alternative fragment length(s) may be 4,54 bps INFO @ Sat, 03 Jun 2017 15:27:23: #2.2 Generate R script for model : SRX2055965.10_model.r WARNING @ Sat, 03 Jun 2017 15:27:23: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:27:23: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Sat, 03 Jun 2017 15:27:23: #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 15:27:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:28:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:28:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:29:40: #4 Write output xls file... SRX2055965.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:40: #4 Write peak in narrowPeak format file... SRX2055965.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:40: #4 Write summits bed file... SRX2055965.20_summits.bed INFO @ Sat, 03 Jun 2017 15:29:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1144 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:44: #4 Write output xls file... SRX2055965.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:44: #4 Write peak in narrowPeak format file... SRX2055965.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:44: #4 Write summits bed file... SRX2055965.05_summits.bed INFO @ Sat, 03 Jun 2017 15:29:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3257 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:29:51: #4 Write output xls file... SRX2055965.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:29:51: #4 Write peak in narrowPeak format file... SRX2055965.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:29:51: #4 Write summits bed file... SRX2055965.10_summits.bed INFO @ Sat, 03 Jun 2017 15:29:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2208 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。