Job ID = 9041698 sra ファイルのダウンロード中... Completed: 1993809K bytes transferred in 18 seconds (900572K 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 --:--:-- 0 100 7663 0 7663 0 0 1054 0 --:--:-- 0:00:07 --:--:-- 11089 100 28797 0 28797 0 0 3485 0 --:--:-- 0:00:08 --:--:-- 17080 100 64997 0 64997 0 0 7021 0 --:--:-- 0:00:09 --:--:-- 24234 100 91502 0 91502 0 0 9542 0 --:--:-- 0:00:09 --:--:-- 30369 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 59592662 spots for /home/okishinya/chipatlas/results/dm3/SRX1361346/SRR2749784.sra Written 59592662 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: 00:16:13 59592662 reads; of these: 59592662 (100.00%) were unpaired; of these: 1660264 (2.79%) aligned 0 times 26794307 (44.96%) aligned exactly 1 time 31138091 (52.25%) aligned >1 times 97.21% overall alignment rate Time searching: 00:16:13 Overall time: 00:16:13 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 24 files... [bam_rmdupse_core] 27173192 / 57932398 = 0.4691 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 @ Mon, 05 Jun 2017 01:54:50: # Command line: callpeak -t SRX1361346.bam -f BAM -g dm -n SRX1361346.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361346.10 # format = BAM # ChIP-seq file = ['SRX1361346.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 @ Mon, 05 Jun 2017 01:54:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:54:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:54:50: # Command line: callpeak -t SRX1361346.bam -f BAM -g dm -n SRX1361346.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361346.20 # format = BAM # ChIP-seq file = ['SRX1361346.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 @ Mon, 05 Jun 2017 01:54:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:54:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:54:50: # Command line: callpeak -t SRX1361346.bam -f BAM -g dm -n SRX1361346.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361346.05 # format = BAM # ChIP-seq file = ['SRX1361346.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 @ Mon, 05 Jun 2017 01:54:50: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:54:50: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:54:56: 1000000 INFO @ Mon, 05 Jun 2017 01:54:56: 1000000 INFO @ Mon, 05 Jun 2017 01:54:56: 1000000 INFO @ Mon, 05 Jun 2017 01:55:02: 2000000 INFO @ Mon, 05 Jun 2017 01:55:02: 2000000 INFO @ Mon, 05 Jun 2017 01:55:02: 2000000 INFO @ Mon, 05 Jun 2017 01:55:08: 3000000 INFO @ Mon, 05 Jun 2017 01:55:08: 3000000 INFO @ Mon, 05 Jun 2017 01:55:08: 3000000 INFO @ Mon, 05 Jun 2017 01:55:14: 4000000 INFO @ Mon, 05 Jun 2017 01:55:14: 4000000 INFO @ Mon, 05 Jun 2017 01:55:14: 4000000 INFO @ Mon, 05 Jun 2017 01:55:20: 5000000 INFO @ Mon, 05 Jun 2017 01:55:20: 5000000 INFO @ Mon, 05 Jun 2017 01:55:20: 5000000 INFO @ Mon, 05 Jun 2017 01:55:26: 6000000 INFO @ Mon, 05 Jun 2017 01:55:26: 6000000 INFO @ Mon, 05 Jun 2017 01:55:26: 6000000 INFO @ Mon, 05 Jun 2017 01:55:32: 7000000 INFO @ Mon, 05 Jun 2017 01:55:32: 7000000 INFO @ Mon, 05 Jun 2017 01:55:32: 7000000 INFO @ Mon, 05 Jun 2017 01:55:38: 8000000 INFO @ Mon, 05 Jun 2017 01:55:38: 8000000 INFO @ Mon, 05 Jun 2017 01:55:38: 8000000 INFO @ Mon, 05 Jun 2017 01:55:43: 9000000 INFO @ Mon, 05 Jun 2017 01:55:44: 9000000 INFO @ Mon, 05 Jun 2017 01:55:44: 9000000 INFO @ Mon, 05 Jun 2017 01:55:49: 10000000 INFO @ Mon, 05 Jun 2017 01:55:50: 10000000 INFO @ Mon, 05 Jun 2017 01:55:50: 10000000 INFO @ Mon, 05 Jun 2017 01:55:55: 11000000 INFO @ Mon, 05 Jun 2017 01:55:55: 11000000 INFO @ Mon, 05 Jun 2017 01:55:56: 11000000 INFO @ Mon, 05 Jun 2017 01:56:01: 12000000 INFO @ Mon, 05 Jun 2017 01:56:01: 12000000 INFO @ Mon, 05 Jun 2017 01:56:01: 12000000 INFO @ Mon, 05 Jun 2017 01:56:07: 13000000 INFO @ Mon, 05 Jun 2017 01:56:07: 13000000 INFO @ Mon, 05 Jun 2017 01:56:07: 13000000 INFO @ Mon, 05 Jun 2017 01:56:13: 14000000 INFO @ Mon, 05 Jun 2017 01:56:13: 14000000 INFO @ Mon, 05 Jun 2017 01:56:13: 14000000 INFO @ Mon, 05 Jun 2017 01:56:19: 15000000 INFO @ Mon, 05 Jun 2017 01:56:19: 15000000 INFO @ Mon, 05 Jun 2017 01:56:19: 15000000 INFO @ Mon, 05 Jun 2017 01:56:25: 16000000 INFO @ Mon, 05 Jun 2017 01:56:25: 16000000 INFO @ Mon, 05 Jun 2017 01:56:25: 16000000 INFO @ Mon, 05 Jun 2017 01:56:31: 17000000 INFO @ Mon, 05 Jun 2017 01:56:31: 17000000 INFO @ Mon, 05 Jun 2017 01:56:31: 17000000 INFO @ Mon, 05 Jun 2017 01:56:37: 18000000 INFO @ Mon, 05 Jun 2017 01:56:37: 18000000 INFO @ Mon, 05 Jun 2017 01:56:37: 18000000 INFO @ Mon, 05 Jun 2017 01:56:42: 19000000 INFO @ Mon, 05 Jun 2017 01:56:43: 19000000 INFO @ Mon, 05 Jun 2017 01:56:43: 19000000 INFO @ Mon, 05 Jun 2017 01:56:48: 20000000 INFO @ Mon, 05 Jun 2017 01:56:49: 20000000 INFO @ Mon, 05 Jun 2017 01:56:49: 20000000 INFO @ Mon, 05 Jun 2017 01:56:54: 21000000 INFO @ Mon, 05 Jun 2017 01:56:55: 21000000 INFO @ Mon, 05 Jun 2017 01:56:55: 21000000 INFO @ Mon, 05 Jun 2017 01:57:00: 22000000 INFO @ Mon, 05 Jun 2017 01:57:01: 22000000 INFO @ Mon, 05 Jun 2017 01:57:01: 22000000 INFO @ Mon, 05 Jun 2017 01:57:06: 23000000 INFO @ Mon, 05 Jun 2017 01:57:07: 23000000 INFO @ Mon, 05 Jun 2017 01:57:07: 23000000 INFO @ Mon, 05 Jun 2017 01:57:12: 24000000 INFO @ Mon, 05 Jun 2017 01:57:13: 24000000 INFO @ Mon, 05 Jun 2017 01:57:13: 24000000 INFO @ Mon, 05 Jun 2017 01:57:18: 25000000 INFO @ Mon, 05 Jun 2017 01:57:19: 25000000 INFO @ Mon, 05 Jun 2017 01:57:19: 25000000 INFO @ Mon, 05 Jun 2017 01:57:24: 26000000 INFO @ Mon, 05 Jun 2017 01:57:25: 26000000 INFO @ Mon, 05 Jun 2017 01:57:25: 26000000 INFO @ Mon, 05 Jun 2017 01:57:30: 27000000 INFO @ Mon, 05 Jun 2017 01:57:31: 27000000 INFO @ Mon, 05 Jun 2017 01:57:31: 27000000 INFO @ Mon, 05 Jun 2017 01:57:37: 28000000 INFO @ Mon, 05 Jun 2017 01:57:37: 28000000 INFO @ Mon, 05 Jun 2017 01:57:37: 28000000 INFO @ Mon, 05 Jun 2017 01:57:43: 29000000 INFO @ Mon, 05 Jun 2017 01:57:44: 29000000 INFO @ Mon, 05 Jun 2017 01:57:45: 29000000 INFO @ Mon, 05 Jun 2017 01:57:50: 30000000 INFO @ Mon, 05 Jun 2017 01:57:51: 30000000 INFO @ Mon, 05 Jun 2017 01:57:52: 30000000 INFO @ Mon, 05 Jun 2017 01:57:56: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:57:56: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:57:56: #1 total tags in treatment: 30759206 INFO @ Mon, 05 Jun 2017 01:57:56: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:57:57: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:57:57: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:57:57: #1 total tags in treatment: 30759206 INFO @ Mon, 05 Jun 2017 01:57:57: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:57:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:57:58: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 01:57:58: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 01:57:58: #1 total tags in treatment: 30759206 INFO @ Mon, 05 Jun 2017 01:57:58: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 01:57:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 01:58:02: #1 tags after filtering in treatment: 30742196 INFO @ Mon, 05 Jun 2017 01:58:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:58:02: #1 finished! INFO @ Mon, 05 Jun 2017 01:58:02: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:58:03: #1 tags after filtering in treatment: 30742196 INFO @ Mon, 05 Jun 2017 01:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:58:03: #1 finished! INFO @ Mon, 05 Jun 2017 01:58:03: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:58:03: #1 tags after filtering in treatment: 30742196 INFO @ Mon, 05 Jun 2017 01:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 01:58:03: #1 finished! INFO @ Mon, 05 Jun 2017 01:58:03: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 01:58:08: #2 number of paired peaks: 535 WARNING @ Mon, 05 Jun 2017 01:58:08: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Mon, 05 Jun 2017 01:58:08: start model_add_line... INFO @ Mon, 05 Jun 2017 01:58:08: #2 number of paired peaks: 535 WARNING @ Mon, 05 Jun 2017 01:58:08: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Mon, 05 Jun 2017 01:58:08: start model_add_line... INFO @ Mon, 05 Jun 2017 01:58:08: #2 number of paired peaks: 535 WARNING @ Mon, 05 Jun 2017 01:58:08: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Mon, 05 Jun 2017 01:58:08: start model_add_line... INFO @ Mon, 05 Jun 2017 01:58:19: start X-correlation... INFO @ Mon, 05 Jun 2017 01:58:19: end of X-cor INFO @ Mon, 05 Jun 2017 01:58:19: #2 finished! INFO @ Mon, 05 Jun 2017 01:58:19: #2 predicted fragment length is 44 bps INFO @ Mon, 05 Jun 2017 01:58:19: #2 alternative fragment length(s) may be 3,44 bps INFO @ Mon, 05 Jun 2017 01:58:19: #2.2 Generate R script for model : SRX1361346.05_model.r WARNING @ Mon, 05 Jun 2017 01:58:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:58:19: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Mon, 05 Jun 2017 01:58:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:58:19: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:58:19: start X-correlation... INFO @ Mon, 05 Jun 2017 01:58:19: end of X-cor INFO @ Mon, 05 Jun 2017 01:58:19: #2 finished! INFO @ Mon, 05 Jun 2017 01:58:19: #2 predicted fragment length is 44 bps INFO @ Mon, 05 Jun 2017 01:58:19: #2 alternative fragment length(s) may be 3,44 bps INFO @ Mon, 05 Jun 2017 01:58:19: #2.2 Generate R script for model : SRX1361346.10_model.r WARNING @ Mon, 05 Jun 2017 01:58:19: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:58:19: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Mon, 05 Jun 2017 01:58:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:58:19: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 01:58:20: start X-correlation... INFO @ Mon, 05 Jun 2017 01:58:20: end of X-cor INFO @ Mon, 05 Jun 2017 01:58:20: #2 finished! INFO @ Mon, 05 Jun 2017 01:58:20: #2 predicted fragment length is 44 bps INFO @ Mon, 05 Jun 2017 01:58:20: #2 alternative fragment length(s) may be 3,44 bps INFO @ Mon, 05 Jun 2017 01:58:20: #2.2 Generate R script for model : SRX1361346.20_model.r WARNING @ Mon, 05 Jun 2017 01:58:20: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 01:58:20: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Mon, 05 Jun 2017 01:58:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 05 Jun 2017 01:58:20: #3 Call peaks... INFO @ Mon, 05 Jun 2017 01:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:00:27: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:00:32: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:00:37: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:02:02: #4 Write output xls file... SRX1361346.20_peaks.xls INFO @ Mon, 05 Jun 2017 02:02:02: #4 Write peak in narrowPeak format file... SRX1361346.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:02:02: #4 Write summits bed file... SRX1361346.20_summits.bed INFO @ Mon, 05 Jun 2017 02:02:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2016 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:02:12: #4 Write output xls file... SRX1361346.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:02:12: #4 Write peak in narrowPeak format file... SRX1361346.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:02:12: #4 Write summits bed file... SRX1361346.10_summits.bed INFO @ Mon, 05 Jun 2017 02:02:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10459 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:02:30: #4 Write output xls file... SRX1361346.05_peaks.xls INFO @ Mon, 05 Jun 2017 02:02:30: #4 Write peak in narrowPeak format file... SRX1361346.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:02:30: #4 Write summits bed file... SRX1361346.05_summits.bed INFO @ Mon, 05 Jun 2017 02:02:30: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (21158 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。