Job ID = 9029746 sra ファイルのダウンロード中... Completed: 370605K bytes transferred in 6 seconds (486474K 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 20109 0 20109 0 0 2587 0 --:--:-- 0:00:07 --:--:-- 14678 100 49069 0 49069 0 0 5595 0 --:--:-- 0:00:08 --:--:-- 20747 100 58845 0 58845 0 0 6648 0 --:--:-- 0:00:08 --:--:-- 24047 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 7786981 spots for /home/okishinya/chipatlas/results/dm3/SRX202833/SRR611194.sra Written 7786981 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: 00:02:29 7786981 reads; of these: 7786981 (100.00%) were unpaired; of these: 3263816 (41.91%) aligned 0 times 3751232 (48.17%) aligned exactly 1 time 771933 (9.91%) aligned >1 times 58.09% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 243160 / 4523165 = 0.0538 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 15:05:39: # Command line: callpeak -t SRX202833.bam -f BAM -g dm -n SRX202833.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX202833.10 # format = BAM # ChIP-seq file = ['SRX202833.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 15:05:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:05:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:05:39: # Command line: callpeak -t SRX202833.bam -f BAM -g dm -n SRX202833.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX202833.20 # format = BAM # ChIP-seq file = ['SRX202833.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 15:05:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:05:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:05:39: # Command line: callpeak -t SRX202833.bam -f BAM -g dm -n SRX202833.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX202833.05 # format = BAM # ChIP-seq file = ['SRX202833.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 15:05:39: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:05:39: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:05:47: 1000000 INFO @ Sat, 03 Jun 2017 15:05:47: 1000000 INFO @ Sat, 03 Jun 2017 15:05:47: 1000000 INFO @ Sat, 03 Jun 2017 15:05:55: 2000000 INFO @ Sat, 03 Jun 2017 15:05:55: 2000000 INFO @ Sat, 03 Jun 2017 15:05:55: 2000000 INFO @ Sat, 03 Jun 2017 15:06:02: 3000000 INFO @ Sat, 03 Jun 2017 15:06:02: 3000000 INFO @ Sat, 03 Jun 2017 15:06:02: 3000000 INFO @ Sat, 03 Jun 2017 15:06:10: 4000000 INFO @ Sat, 03 Jun 2017 15:06:10: 4000000 INFO @ Sat, 03 Jun 2017 15:06:10: 4000000 INFO @ Sat, 03 Jun 2017 15:06:12: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 15:06:12: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 15:06:12: #1 total tags in treatment: 4280005 INFO @ Sat, 03 Jun 2017 15:06:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:06:12: #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 15:06:12: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 15:06:12: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 15:06:12: #1 total tags in treatment: 4280005 INFO @ Sat, 03 Jun 2017 15:06:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:06:12: #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 15:06:12: #1 tag size is determined as 75 bps INFO @ Sat, 03 Jun 2017 15:06:12: #1 tag size = 75 INFO @ Sat, 03 Jun 2017 15:06:12: #1 total tags in treatment: 4280005 INFO @ Sat, 03 Jun 2017 15:06:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:06:12: #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 15:06:12: #1 tags after filtering in treatment: 4279390 INFO @ Sat, 03 Jun 2017 15:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:06:12: #1 finished! INFO @ Sat, 03 Jun 2017 15:06:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:06:12: #1 tags after filtering in treatment: 4279390 INFO @ Sat, 03 Jun 2017 15:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:06:12: #1 finished! INFO @ Sat, 03 Jun 2017 15:06:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:06:12: #1 tags after filtering in treatment: 4279390 INFO @ Sat, 03 Jun 2017 15:06:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:06:12: #1 finished! INFO @ Sat, 03 Jun 2017 15:06:12: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:06:13: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 15:06:13: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 15:06:13: start model_add_line... INFO @ Sat, 03 Jun 2017 15:06:13: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 15:06:13: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 15:06:13: start model_add_line... INFO @ Sat, 03 Jun 2017 15:06:13: #2 number of paired peaks: 105 WARNING @ Sat, 03 Jun 2017 15:06:13: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Sat, 03 Jun 2017 15:06:13: start model_add_line... INFO @ Sat, 03 Jun 2017 15:06:14: start X-correlation... INFO @ Sat, 03 Jun 2017 15:06:14: end of X-cor INFO @ Sat, 03 Jun 2017 15:06:14: #2 finished! INFO @ Sat, 03 Jun 2017 15:06:14: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2.2 Generate R script for model : SRX202833.05_model.r WARNING @ Sat, 03 Jun 2017 15:06:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:06:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Jun 2017 15:06:14: #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 15:06:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:06:14: start X-correlation... INFO @ Sat, 03 Jun 2017 15:06:14: start X-correlation... INFO @ Sat, 03 Jun 2017 15:06:14: end of X-cor INFO @ Sat, 03 Jun 2017 15:06:14: #2 finished! INFO @ Sat, 03 Jun 2017 15:06:14: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2.2 Generate R script for model : SRX202833.20_model.r INFO @ Sat, 03 Jun 2017 15:06:14: end of X-cor INFO @ Sat, 03 Jun 2017 15:06:14: #2 finished! INFO @ Sat, 03 Jun 2017 15:06:14: #2 predicted fragment length is 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2 alternative fragment length(s) may be 73 bps INFO @ Sat, 03 Jun 2017 15:06:14: #2.2 Generate R script for model : SRX202833.10_model.r WARNING @ Sat, 03 Jun 2017 15:06:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:06:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Jun 2017 15:06:14: #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 15:06:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:06:14: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 03 Jun 2017 15:06:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:06:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Sat, 03 Jun 2017 15:06:14: #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 15:06:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:06:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:06:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:06:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:06:41: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:06:56: #4 Write output xls file... SRX202833.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:06:56: #4 Write peak in narrowPeak format file... SRX202833.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:06:56: #4 Write summits bed file... SRX202833.20_summits.bed INFO @ Sat, 03 Jun 2017 15:06:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write output xls file... SRX202833.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write peak in narrowPeak format file... SRX202833.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write summits bed file... SRX202833.10_summits.bed INFO @ Sat, 03 Jun 2017 15:07:00: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write output xls file... SRX202833.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write peak in narrowPeak format file... SRX202833.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:07:00: #4 Write summits bed file... SRX202833.05_summits.bed INFO @ Sat, 03 Jun 2017 15:07:00: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (618 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。