Job ID = 9027416 sra ファイルのダウンロード中... Completed: 906083K bytes transferred in 10 seconds (680624K 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 0 942 0 --:--:-- 0:00:08 --:--:-- 5034 100 30318 0 30318 0 0 3321 0 --:--:-- 0:00:09 --:--:-- 12040 100 47176 0 47176 0 0 4817 0 --:--:-- 0:00:09 --:--:-- 14830 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 18755646 spots for /home/okishinya/chipatlas/results/ce10/SRX466585/SRR1163651.sra Written 18755646 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: 00:05:10 18755646 reads; of these: 18755646 (100.00%) were unpaired; of these: 184580 (0.98%) aligned 0 times 15171604 (80.89%) aligned exactly 1 time 3399462 (18.13%) aligned >1 times 99.02% overall alignment rate Time searching: 00:05:10 Overall time: 00:05:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4539693 / 18571066 = 0.2444 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 08:40:29: # Command line: callpeak -t SRX466585.bam -f BAM -g ce -n SRX466585.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX466585.10 # format = BAM # ChIP-seq file = ['SRX466585.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 08:40:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:40:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:40:29: # Command line: callpeak -t SRX466585.bam -f BAM -g ce -n SRX466585.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX466585.20 # format = BAM # ChIP-seq file = ['SRX466585.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 08:40:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:40:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:40:29: # Command line: callpeak -t SRX466585.bam -f BAM -g ce -n SRX466585.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX466585.05 # format = BAM # ChIP-seq file = ['SRX466585.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 08:40:29: #1 read tag files... INFO @ Sat, 03 Jun 2017 08:40:29: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 08:40:36: 1000000 INFO @ Sat, 03 Jun 2017 08:40:36: 1000000 INFO @ Sat, 03 Jun 2017 08:40:36: 1000000 INFO @ Sat, 03 Jun 2017 08:40:42: 2000000 INFO @ Sat, 03 Jun 2017 08:40:43: 2000000 INFO @ Sat, 03 Jun 2017 08:40:43: 2000000 INFO @ Sat, 03 Jun 2017 08:40:49: 3000000 INFO @ Sat, 03 Jun 2017 08:40:50: 3000000 INFO @ Sat, 03 Jun 2017 08:40:50: 3000000 INFO @ Sat, 03 Jun 2017 08:40:55: 4000000 INFO @ Sat, 03 Jun 2017 08:40:57: 4000000 INFO @ Sat, 03 Jun 2017 08:40:57: 4000000 INFO @ Sat, 03 Jun 2017 08:41:02: 5000000 INFO @ Sat, 03 Jun 2017 08:41:04: 5000000 INFO @ Sat, 03 Jun 2017 08:41:05: 5000000 INFO @ Sat, 03 Jun 2017 08:41:08: 6000000 INFO @ Sat, 03 Jun 2017 08:41:11: 6000000 INFO @ Sat, 03 Jun 2017 08:41:13: 6000000 INFO @ Sat, 03 Jun 2017 08:41:15: 7000000 INFO @ Sat, 03 Jun 2017 08:41:18: 7000000 INFO @ Sat, 03 Jun 2017 08:41:21: 7000000 INFO @ Sat, 03 Jun 2017 08:41:21: 8000000 INFO @ Sat, 03 Jun 2017 08:41:25: 8000000 INFO @ Sat, 03 Jun 2017 08:41:28: 9000000 INFO @ Sat, 03 Jun 2017 08:41:28: 8000000 INFO @ Sat, 03 Jun 2017 08:41:32: 9000000 INFO @ Sat, 03 Jun 2017 08:41:34: 10000000 INFO @ Sat, 03 Jun 2017 08:41:36: 9000000 INFO @ Sat, 03 Jun 2017 08:41:40: 10000000 INFO @ Sat, 03 Jun 2017 08:41:40: 11000000 INFO @ Sat, 03 Jun 2017 08:41:44: 10000000 INFO @ Sat, 03 Jun 2017 08:41:47: 11000000 INFO @ Sat, 03 Jun 2017 08:41:47: 12000000 INFO @ Sat, 03 Jun 2017 08:41:52: 11000000 INFO @ Sat, 03 Jun 2017 08:41:53: 13000000 INFO @ Sat, 03 Jun 2017 08:41:54: 12000000 INFO @ Sat, 03 Jun 2017 08:41:59: 14000000 INFO @ Sat, 03 Jun 2017 08:41:59: 12000000 INFO @ Sat, 03 Jun 2017 08:42:00: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 08:42:00: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 08:42:00: #1 total tags in treatment: 14031373 INFO @ Sat, 03 Jun 2017 08:42:00: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:42:00: #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 08:42:01: 13000000 INFO @ Sat, 03 Jun 2017 08:42:02: #1 tags after filtering in treatment: 14030327 INFO @ Sat, 03 Jun 2017 08:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:42:02: #1 finished! INFO @ Sat, 03 Jun 2017 08:42:02: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:42:05: #2 number of paired peaks: 438 WARNING @ Sat, 03 Jun 2017 08:42:05: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Jun 2017 08:42:05: start model_add_line... INFO @ Sat, 03 Jun 2017 08:42:07: 13000000 INFO @ Sat, 03 Jun 2017 08:42:08: 14000000 INFO @ Sat, 03 Jun 2017 08:42:08: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 08:42:08: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 08:42:08: #1 total tags in treatment: 14031373 INFO @ Sat, 03 Jun 2017 08:42:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:42:08: #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 08:42:11: #1 tags after filtering in treatment: 14030327 INFO @ Sat, 03 Jun 2017 08:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:42:11: #1 finished! INFO @ Sat, 03 Jun 2017 08:42:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:42:12: start X-correlation... INFO @ Sat, 03 Jun 2017 08:42:12: end of X-cor INFO @ Sat, 03 Jun 2017 08:42:12: #2 finished! INFO @ Sat, 03 Jun 2017 08:42:12: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 08:42:12: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Jun 2017 08:42:12: #2.2 Generate R script for model : SRX466585.05_model.r WARNING @ Sat, 03 Jun 2017 08:42:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:42:12: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Jun 2017 08:42:12: #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 08:42:12: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:42:13: #2 number of paired peaks: 438 WARNING @ Sat, 03 Jun 2017 08:42:13: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Jun 2017 08:42:13: start model_add_line... INFO @ Sat, 03 Jun 2017 08:42:14: 14000000 INFO @ Sat, 03 Jun 2017 08:42:15: #1 tag size is determined as 42 bps INFO @ Sat, 03 Jun 2017 08:42:15: #1 tag size = 42 INFO @ Sat, 03 Jun 2017 08:42:15: #1 total tags in treatment: 14031373 INFO @ Sat, 03 Jun 2017 08:42:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 08:42:15: #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 08:42:17: #1 tags after filtering in treatment: 14030327 INFO @ Sat, 03 Jun 2017 08:42:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 08:42:17: #1 finished! INFO @ Sat, 03 Jun 2017 08:42:17: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 08:42:20: #2 number of paired peaks: 438 WARNING @ Sat, 03 Jun 2017 08:42:20: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Sat, 03 Jun 2017 08:42:20: start model_add_line... INFO @ Sat, 03 Jun 2017 08:42:21: start X-correlation... INFO @ Sat, 03 Jun 2017 08:42:21: end of X-cor INFO @ Sat, 03 Jun 2017 08:42:21: #2 finished! INFO @ Sat, 03 Jun 2017 08:42:21: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 08:42:21: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Jun 2017 08:42:21: #2.2 Generate R script for model : SRX466585.20_model.r WARNING @ Sat, 03 Jun 2017 08:42:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:42:21: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Jun 2017 08:42:21: #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 08:42:21: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:42:27: start X-correlation... INFO @ Sat, 03 Jun 2017 08:42:27: end of X-cor INFO @ Sat, 03 Jun 2017 08:42:27: #2 finished! INFO @ Sat, 03 Jun 2017 08:42:27: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Jun 2017 08:42:27: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Jun 2017 08:42:27: #2.2 Generate R script for model : SRX466585.10_model.r WARNING @ Sat, 03 Jun 2017 08:42:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 08:42:27: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Jun 2017 08:42:27: #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 08:42:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 08:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 08:43:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:43:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:43:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 08:44:14: #4 Write output xls file... SRX466585.05_peaks.xls INFO @ Sat, 03 Jun 2017 08:44:14: #4 Write peak in narrowPeak format file... SRX466585.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:44:14: #4 Write summits bed file... SRX466585.05_summits.bed INFO @ Sat, 03 Jun 2017 08:44:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1273 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 08:44:28: #4 Write output xls file... SRX466585.20_peaks.xls INFO @ Sat, 03 Jun 2017 08:44:28: #4 Write peak in narrowPeak format file... SRX466585.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:44:28: #4 Write summits bed file... SRX466585.20_summits.bed INFO @ Sat, 03 Jun 2017 08:44:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 08:44:29: #4 Write output xls file... SRX466585.10_peaks.xls INFO @ Sat, 03 Jun 2017 08:44:29: #4 Write peak in narrowPeak format file... SRX466585.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 08:44:29: #4 Write summits bed file... SRX466585.10_summits.bed INFO @ Sat, 03 Jun 2017 08:44:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (525 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。