Job ID = 11597666 sra ファイルのダウンロード中... Completed: 282148K bytes transferred in 6 seconds (379108K bits/sec), in 1 file. 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... Read 12430706 spots for /home/okishinya/chipatlas/results/ce10/ERX1270343/ERR1198084.sra Written 12430706 spots for /home/okishinya/chipatlas/results/ce10/ERX1270343/ERR1198084.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:03:10 12430706 reads; of these: 12430706 (100.00%) were unpaired; of these: 1074325 (8.64%) aligned 0 times 9427546 (75.84%) aligned exactly 1 time 1928835 (15.52%) aligned >1 times 91.36% overall alignment rate Time searching: 00:03:10 Overall time: 00:03:10 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] 1973965 / 11356381 = 0.1738 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 @ Wed, 30 Jan 2019 14:22:27: # Command line: callpeak -t ERX1270343.bam -f BAM -g ce -n ERX1270343.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1270343.10 # format = BAM # ChIP-seq file = ['ERX1270343.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 # Paired-End mode is off INFO @ Wed, 30 Jan 2019 14:22:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:22:27: # Command line: callpeak -t ERX1270343.bam -f BAM -g ce -n ERX1270343.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1270343.05 # format = BAM # ChIP-seq file = ['ERX1270343.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 # Paired-End mode is off INFO @ Wed, 30 Jan 2019 14:22:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:22:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:22:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:22:27: # Command line: callpeak -t ERX1270343.bam -f BAM -g ce -n ERX1270343.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1270343.20 # format = BAM # ChIP-seq file = ['ERX1270343.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 # Paired-End mode is off INFO @ Wed, 30 Jan 2019 14:22:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:22:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:22:34: 1000000 INFO @ Wed, 30 Jan 2019 14:22:35: 1000000 INFO @ Wed, 30 Jan 2019 14:22:35: 1000000 INFO @ Wed, 30 Jan 2019 14:22:42: 2000000 INFO @ Wed, 30 Jan 2019 14:22:42: 2000000 INFO @ Wed, 30 Jan 2019 14:22:42: 2000000 INFO @ Wed, 30 Jan 2019 14:22:49: 3000000 INFO @ Wed, 30 Jan 2019 14:22:50: 3000000 INFO @ Wed, 30 Jan 2019 14:22:50: 3000000 INFO @ Wed, 30 Jan 2019 14:22:56: 4000000 INFO @ Wed, 30 Jan 2019 14:22:58: 4000000 INFO @ Wed, 30 Jan 2019 14:22:58: 4000000 INFO @ Wed, 30 Jan 2019 14:23:04: 5000000 INFO @ Wed, 30 Jan 2019 14:23:06: 5000000 INFO @ Wed, 30 Jan 2019 14:23:06: 5000000 INFO @ Wed, 30 Jan 2019 14:23:12: 6000000 INFO @ Wed, 30 Jan 2019 14:23:14: 6000000 INFO @ Wed, 30 Jan 2019 14:23:14: 6000000 INFO @ Wed, 30 Jan 2019 14:23:19: 7000000 INFO @ Wed, 30 Jan 2019 14:23:22: 7000000 INFO @ Wed, 30 Jan 2019 14:23:22: 7000000 INFO @ Wed, 30 Jan 2019 14:23:27: 8000000 INFO @ Wed, 30 Jan 2019 14:23:29: 8000000 INFO @ Wed, 30 Jan 2019 14:23:30: 8000000 INFO @ Wed, 30 Jan 2019 14:23:34: 9000000 INFO @ Wed, 30 Jan 2019 14:23:37: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:23:37: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:23:37: #1 total tags in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:37: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:23:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:23:37: 9000000 INFO @ Wed, 30 Jan 2019 14:23:37: #1 tags after filtering in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:23:37: #1 finished! INFO @ Wed, 30 Jan 2019 14:23:37: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:23:37: 9000000 INFO @ Wed, 30 Jan 2019 14:23:38: #2 number of paired peaks: 399 WARNING @ Wed, 30 Jan 2019 14:23:38: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 30 Jan 2019 14:23:38: start model_add_line... INFO @ Wed, 30 Jan 2019 14:23:38: start X-correlation... INFO @ Wed, 30 Jan 2019 14:23:38: end of X-cor INFO @ Wed, 30 Jan 2019 14:23:38: #2 finished! INFO @ Wed, 30 Jan 2019 14:23:38: #2 predicted fragment length is 51 bps INFO @ Wed, 30 Jan 2019 14:23:38: #2 alternative fragment length(s) may be 2,51,576 bps INFO @ Wed, 30 Jan 2019 14:23:38: #2.2 Generate R script for model : ERX1270343.10_model.r WARNING @ Wed, 30 Jan 2019 14:23:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:23:38: #2 You may need to consider one of the other alternative d(s): 2,51,576 WARNING @ Wed, 30 Jan 2019 14:23:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:23:38: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:23:40: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:23:40: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:23:40: #1 total tags in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:23:40: #1 tags after filtering in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:23:40: #1 finished! INFO @ Wed, 30 Jan 2019 14:23:40: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:23:40: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:23:40: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:23:40: #1 total tags in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:40: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:23:40: #1 tags after filtering in treatment: 9382416 INFO @ Wed, 30 Jan 2019 14:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:23:40: #1 finished! INFO @ Wed, 30 Jan 2019 14:23:40: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:23:40: #2 number of paired peaks: 399 WARNING @ Wed, 30 Jan 2019 14:23:40: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 30 Jan 2019 14:23:40: start model_add_line... INFO @ Wed, 30 Jan 2019 14:23:41: start X-correlation... INFO @ Wed, 30 Jan 2019 14:23:41: end of X-cor INFO @ Wed, 30 Jan 2019 14:23:41: #2 finished! INFO @ Wed, 30 Jan 2019 14:23:41: #2 predicted fragment length is 51 bps INFO @ Wed, 30 Jan 2019 14:23:41: #2 alternative fragment length(s) may be 2,51,576 bps INFO @ Wed, 30 Jan 2019 14:23:41: #2.2 Generate R script for model : ERX1270343.20_model.r WARNING @ Wed, 30 Jan 2019 14:23:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:23:41: #2 You may need to consider one of the other alternative d(s): 2,51,576 WARNING @ Wed, 30 Jan 2019 14:23:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:23:41: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:23:41: #2 number of paired peaks: 399 WARNING @ Wed, 30 Jan 2019 14:23:41: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Wed, 30 Jan 2019 14:23:41: start model_add_line... INFO @ Wed, 30 Jan 2019 14:23:41: start X-correlation... INFO @ Wed, 30 Jan 2019 14:23:41: end of X-cor INFO @ Wed, 30 Jan 2019 14:23:41: #2 finished! INFO @ Wed, 30 Jan 2019 14:23:41: #2 predicted fragment length is 51 bps INFO @ Wed, 30 Jan 2019 14:23:41: #2 alternative fragment length(s) may be 2,51,576 bps INFO @ Wed, 30 Jan 2019 14:23:41: #2.2 Generate R script for model : ERX1270343.05_model.r WARNING @ Wed, 30 Jan 2019 14:23:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:23:41: #2 You may need to consider one of the other alternative d(s): 2,51,576 WARNING @ Wed, 30 Jan 2019 14:23:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:23:41: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:24:00: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:24:00: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:24:00: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:24:10: #4 Write output xls file... ERX1270343.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:24:10: #4 Write peak in narrowPeak format file... ERX1270343.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:24:10: #4 Write summits bed file... ERX1270343.10_summits.bed INFO @ Wed, 30 Jan 2019 14:24:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (453 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write output xls file... ERX1270343.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write peak in narrowPeak format file... ERX1270343.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write summits bed file... ERX1270343.05_summits.bed INFO @ Wed, 30 Jan 2019 14:24:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (818 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write output xls file... ERX1270343.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write peak in narrowPeak format file... ERX1270343.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:24:12: #4 Write summits bed file... ERX1270343.20_summits.bed INFO @ Wed, 30 Jan 2019 14:24:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 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。