Job ID = 9029226 sra ファイルのダウンロード中... Completed: 220545K bytes transferred in 6 seconds (273767K 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 14324 0 14324 0 0 1938 0 --:--:-- 0:00:07 --:--:-- 14112 100 38318 0 38318 0 0 4571 0 --:--:-- 0:00:08 --:--:-- 19063 100 53356 0 53356 0 0 6122 0 --:--:-- 0:00:08 --:--:-- 22782 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 10383708 spots for /home/okishinya/chipatlas/results/dm3/SRX1433366/SRR2919831.sra Written 10383708 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: 00:03:59 10383708 reads; of these: 10383708 (100.00%) were unpaired; of these: 289406 (2.79%) aligned 0 times 7763009 (74.76%) aligned exactly 1 time 2331293 (22.45%) aligned >1 times 97.21% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 831663 / 10094302 = 0.0824 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 12:59:16: # Command line: callpeak -t SRX1433366.bam -f BAM -g dm -n SRX1433366.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433366.10 # format = BAM # ChIP-seq file = ['SRX1433366.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 12:59:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:59:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:59:16: # Command line: callpeak -t SRX1433366.bam -f BAM -g dm -n SRX1433366.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433366.05 # format = BAM # ChIP-seq file = ['SRX1433366.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 12:59:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:59:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:59:16: # Command line: callpeak -t SRX1433366.bam -f BAM -g dm -n SRX1433366.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433366.20 # format = BAM # ChIP-seq file = ['SRX1433366.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 12:59:16: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:59:16: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:59:23: 1000000 INFO @ Sat, 03 Jun 2017 12:59:23: 1000000 INFO @ Sat, 03 Jun 2017 12:59:24: 1000000 INFO @ Sat, 03 Jun 2017 12:59:30: 2000000 INFO @ Sat, 03 Jun 2017 12:59:31: 2000000 INFO @ Sat, 03 Jun 2017 12:59:31: 2000000 INFO @ Sat, 03 Jun 2017 12:59:38: 3000000 INFO @ Sat, 03 Jun 2017 12:59:38: 3000000 INFO @ Sat, 03 Jun 2017 12:59:38: 3000000 INFO @ Sat, 03 Jun 2017 12:59:45: 4000000 INFO @ Sat, 03 Jun 2017 12:59:45: 4000000 INFO @ Sat, 03 Jun 2017 12:59:45: 4000000 INFO @ Sat, 03 Jun 2017 12:59:52: 5000000 INFO @ Sat, 03 Jun 2017 12:59:52: 5000000 INFO @ Sat, 03 Jun 2017 12:59:52: 5000000 INFO @ Sat, 03 Jun 2017 12:59:59: 6000000 INFO @ Sat, 03 Jun 2017 13:00:00: 6000000 INFO @ Sat, 03 Jun 2017 13:00:00: 6000000 INFO @ Sat, 03 Jun 2017 13:00:06: 7000000 INFO @ Sat, 03 Jun 2017 13:00:07: 7000000 INFO @ Sat, 03 Jun 2017 13:00:07: 7000000 INFO @ Sat, 03 Jun 2017 13:00:13: 8000000 INFO @ Sat, 03 Jun 2017 13:00:14: 8000000 INFO @ Sat, 03 Jun 2017 13:00:16: 8000000 INFO @ Sat, 03 Jun 2017 13:00:20: 9000000 INFO @ Sat, 03 Jun 2017 13:00:21: 9000000 INFO @ Sat, 03 Jun 2017 13:00:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:00:22: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:00:22: #1 total tags in treatment: 9262639 INFO @ Sat, 03 Jun 2017 13:00:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:22: #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 13:00:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:00:22: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:00:22: #1 total tags in treatment: 9262639 INFO @ Sat, 03 Jun 2017 13:00:22: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:22: #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 13:00:24: #1 tags after filtering in treatment: 9261280 INFO @ Sat, 03 Jun 2017 13:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:24: #1 tags after filtering in treatment: 9261280 INFO @ Sat, 03 Jun 2017 13:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:24: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:24: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:24: 9000000 INFO @ Sat, 03 Jun 2017 13:00:26: #2 number of paired peaks: 324 WARNING @ Sat, 03 Jun 2017 13:00:26: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 03 Jun 2017 13:00:26: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:26: #2 number of paired peaks: 324 WARNING @ Sat, 03 Jun 2017 13:00:26: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 03 Jun 2017 13:00:26: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:00:26: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:00:26: #1 total tags in treatment: 9262639 INFO @ Sat, 03 Jun 2017 13:00:26: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:26: #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 13:00:28: #1 tags after filtering in treatment: 9261280 INFO @ Sat, 03 Jun 2017 13:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:28: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:28: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:28: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:28: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:00:28: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:00:28: #2.2 Generate R script for model : SRX1433366.20_model.r WARNING @ Sat, 03 Jun 2017 13:00:28: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:00:28: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:00:28: #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 13:00:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:00:28: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:28: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:28: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:28: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:00:28: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:00:28: #2.2 Generate R script for model : SRX1433366.05_model.r WARNING @ Sat, 03 Jun 2017 13:00:28: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:00:28: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:00:28: #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 13:00:28: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:00:30: #2 number of paired peaks: 324 WARNING @ Sat, 03 Jun 2017 13:00:30: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sat, 03 Jun 2017 13:00:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:33: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:33: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:33: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:33: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Jun 2017 13:00:33: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 03 Jun 2017 13:00:33: #2.2 Generate R script for model : SRX1433366.10_model.r WARNING @ Sat, 03 Jun 2017 13:00:33: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:00:33: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 03 Jun 2017 13:00:33: #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 13:00:33: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:01:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:01:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:01:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:01:55: #4 Write output xls file... SRX1433366.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:01:55: #4 Write peak in narrowPeak format file... SRX1433366.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:01:55: #4 Write summits bed file... SRX1433366.05_summits.bed INFO @ Sat, 03 Jun 2017 13:01:55: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1453 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:01:56: #4 Write output xls file... SRX1433366.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:01:56: #4 Write peak in narrowPeak format file... SRX1433366.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:01:56: #4 Write summits bed file... SRX1433366.20_summits.bed INFO @ Sat, 03 Jun 2017 13:01:56: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (729 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:02:10: #4 Write output xls file... SRX1433366.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:02:10: #4 Write peak in narrowPeak format file... SRX1433366.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:02:10: #4 Write summits bed file... SRX1433366.10_summits.bed INFO @ Sat, 03 Jun 2017 13:02:10: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1026 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。