Job ID = 9040662 sra ファイルのダウンロード中... Completed: 108037K bytes transferred in 4 seconds (197678K 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 1845 0 --:--:-- 0:00:07 --:--:-- 12564 100 43935 0 43935 0 0 5114 0 --:--:-- 0:00:08 --:--:-- 22290 100 45806 0 45806 0 0 5330 0 --:--:-- 0:00:08 --:--:-- 23216 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 6037201 spots for /home/okishinya/chipatlas/results/dm3/SRX1149358/SRR2162761.sra Written 6037201 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:08 6037201 reads; of these: 6037201 (100.00%) were unpaired; of these: 578083 (9.58%) aligned 0 times 3495143 (57.89%) aligned exactly 1 time 1963975 (32.53%) aligned >1 times 90.42% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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_rmdupse_core] 1764471 / 5459118 = 0.3232 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 00:09:05: # Command line: callpeak -t SRX1149358.bam -f BAM -g dm -n SRX1149358.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1149358.20 # format = BAM # ChIP-seq file = ['SRX1149358.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 00:09:05: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:09:05: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:09:05: # Command line: callpeak -t SRX1149358.bam -f BAM -g dm -n SRX1149358.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1149358.05 # format = BAM # ChIP-seq file = ['SRX1149358.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 00:09:05: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:09:05: # Command line: callpeak -t SRX1149358.bam -f BAM -g dm -n SRX1149358.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1149358.10 # format = BAM # ChIP-seq file = ['SRX1149358.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 00:09:05: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:09:05: #1 read tag files... INFO @ Mon, 05 Jun 2017 00:09:05: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 00:09:12: 1000000 INFO @ Mon, 05 Jun 2017 00:09:12: 1000000 INFO @ Mon, 05 Jun 2017 00:09:12: 1000000 INFO @ Mon, 05 Jun 2017 00:09:18: 2000000 INFO @ Mon, 05 Jun 2017 00:09:18: 2000000 INFO @ Mon, 05 Jun 2017 00:09:18: 2000000 INFO @ Mon, 05 Jun 2017 00:09:24: 3000000 INFO @ Mon, 05 Jun 2017 00:09:25: 3000000 INFO @ Mon, 05 Jun 2017 00:09:25: 3000000 INFO @ Mon, 05 Jun 2017 00:09:28: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:09:28: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:09:28: #1 total tags in treatment: 3694647 INFO @ Mon, 05 Jun 2017 00:09:28: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:09:28: #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 00:09:29: #1 tags after filtering in treatment: 3694367 INFO @ Mon, 05 Jun 2017 00:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:09:29: #1 finished! INFO @ Mon, 05 Jun 2017 00:09:29: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:09:29: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:09:29: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:09:29: #1 total tags in treatment: 3694647 INFO @ Mon, 05 Jun 2017 00:09:29: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:09:29: #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 00:09:29: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 00:09:29: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 00:09:29: #1 total tags in treatment: 3694647 INFO @ Mon, 05 Jun 2017 00:09:29: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 00:09:29: #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 00:09:29: #2 number of paired peaks: 472 WARNING @ Mon, 05 Jun 2017 00:09:29: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 05 Jun 2017 00:09:29: start model_add_line... INFO @ Mon, 05 Jun 2017 00:09:30: #1 tags after filtering in treatment: 3694367 INFO @ Mon, 05 Jun 2017 00:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:09:30: #1 finished! INFO @ Mon, 05 Jun 2017 00:09:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:09:30: #1 tags after filtering in treatment: 3694367 INFO @ Mon, 05 Jun 2017 00:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 00:09:30: #1 finished! INFO @ Mon, 05 Jun 2017 00:09:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 00:09:31: #2 number of paired peaks: 472 WARNING @ Mon, 05 Jun 2017 00:09:31: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 05 Jun 2017 00:09:31: start model_add_line... INFO @ Mon, 05 Jun 2017 00:09:31: start X-correlation... INFO @ Mon, 05 Jun 2017 00:09:31: end of X-cor INFO @ Mon, 05 Jun 2017 00:09:31: #2 finished! INFO @ Mon, 05 Jun 2017 00:09:31: #2 predicted fragment length is 59 bps INFO @ Mon, 05 Jun 2017 00:09:31: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 05 Jun 2017 00:09:31: #2.2 Generate R script for model : SRX1149358.20_model.r WARNING @ Mon, 05 Jun 2017 00:09:31: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:09:31: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 05 Jun 2017 00:09:31: #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 00:09:31: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:09:31: #2 number of paired peaks: 472 WARNING @ Mon, 05 Jun 2017 00:09:31: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Mon, 05 Jun 2017 00:09:31: start model_add_line... INFO @ Mon, 05 Jun 2017 00:09:32: start X-correlation... INFO @ Mon, 05 Jun 2017 00:09:32: end of X-cor INFO @ Mon, 05 Jun 2017 00:09:32: #2 finished! INFO @ Mon, 05 Jun 2017 00:09:32: #2 predicted fragment length is 59 bps INFO @ Mon, 05 Jun 2017 00:09:32: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 05 Jun 2017 00:09:32: #2.2 Generate R script for model : SRX1149358.10_model.r WARNING @ Mon, 05 Jun 2017 00:09:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:09:32: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 05 Jun 2017 00:09:32: #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 00:09:32: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:09:32: start X-correlation... INFO @ Mon, 05 Jun 2017 00:09:32: end of X-cor INFO @ Mon, 05 Jun 2017 00:09:32: #2 finished! INFO @ Mon, 05 Jun 2017 00:09:32: #2 predicted fragment length is 59 bps INFO @ Mon, 05 Jun 2017 00:09:32: #2 alternative fragment length(s) may be 59 bps INFO @ Mon, 05 Jun 2017 00:09:32: #2.2 Generate R script for model : SRX1149358.05_model.r WARNING @ Mon, 05 Jun 2017 00:09:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 05 Jun 2017 00:09:32: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Mon, 05 Jun 2017 00:09:32: #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 00:09:32: #3 Call peaks... INFO @ Mon, 05 Jun 2017 00:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 00:09:52: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:09:54: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:09:55: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 00:10:09: #4 Write output xls file... SRX1149358.20_peaks.xls INFO @ Mon, 05 Jun 2017 00:10:09: #4 Write peak in narrowPeak format file... SRX1149358.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:10:09: #4 Write summits bed file... SRX1149358.20_summits.bed INFO @ Mon, 05 Jun 2017 00:10:09: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:10:10: #4 Write output xls file... SRX1149358.10_peaks.xls INFO @ Mon, 05 Jun 2017 00:10:10: #4 Write peak in narrowPeak format file... SRX1149358.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:10:10: #4 Write summits bed file... SRX1149358.10_summits.bed INFO @ Mon, 05 Jun 2017 00:10:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 00:10:13: #4 Write output xls file... SRX1149358.05_peaks.xls INFO @ Mon, 05 Jun 2017 00:10:13: #4 Write peak in narrowPeak format file... SRX1149358.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 00:10:13: #4 Write summits bed file... SRX1149358.05_summits.bed INFO @ Mon, 05 Jun 2017 00:10:13: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (653 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。