Job ID = 10845239 sra ファイルのダウンロード中... Completed: 98618K bytes transferred in 4 seconds (195559K 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 2176828 spots for /home/okishinya/chipatlas/results/dm3/SRX3937201/SRR7004621.sra Written 2176828 spots for /home/okishinya/chipatlas/results/dm3/SRX3937201/SRR7004621.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:18 2176828 reads; of these: 2176828 (100.00%) were unpaired; of these: 360209 (16.55%) aligned 0 times 1305085 (59.95%) aligned exactly 1 time 511534 (23.50%) aligned >1 times 83.45% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 38397 / 1816619 = 0.0211 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, 04 Jul 2018 09:33:20: # Command line: callpeak -t SRX3937201.bam -f BAM -g dm -n SRX3937201.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3937201.20 # format = BAM # ChIP-seq file = ['SRX3937201.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 # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:33:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:20: # Command line: callpeak -t SRX3937201.bam -f BAM -g dm -n SRX3937201.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3937201.10 # format = BAM # ChIP-seq file = ['SRX3937201.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 # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:33:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:20: # Command line: callpeak -t SRX3937201.bam -f BAM -g dm -n SRX3937201.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3937201.05 # format = BAM # ChIP-seq file = ['SRX3937201.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 # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:33:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:33:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:33:28: 1000000 INFO @ Wed, 04 Jul 2018 09:33:28: 1000000 INFO @ Wed, 04 Jul 2018 09:33:28: 1000000 INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size is determined as 92 bps INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size = 92 INFO @ Wed, 04 Jul 2018 09:33:35: #1 total tags in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:33:35: #1 tags after filtering in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:35: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #2 number of paired peaks: 252 WARNING @ Wed, 04 Jul 2018 09:33:35: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:35: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:35: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:35: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:35: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2.2 Generate R script for model : SRX3937201.05_model.r WARNING @ Wed, 04 Jul 2018 09:33:35: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:33:35: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size is determined as 92 bps INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size = 92 INFO @ Wed, 04 Jul 2018 09:33:35: #1 total tags in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size is determined as 92 bps INFO @ Wed, 04 Jul 2018 09:33:35: #1 tag size = 92 INFO @ Wed, 04 Jul 2018 09:33:35: #1 total tags in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:33:35: #1 tags after filtering in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:35: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #1 tags after filtering in treatment: 1778222 INFO @ Wed, 04 Jul 2018 09:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:33:35: #1 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #2 number of paired peaks: 252 WARNING @ Wed, 04 Jul 2018 09:33:35: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:35: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:35: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:35: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:35: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2.2 Generate R script for model : SRX3937201.20_model.r WARNING @ Wed, 04 Jul 2018 09:33:35: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:33:35: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:35: #2 number of paired peaks: 252 WARNING @ Wed, 04 Jul 2018 09:33:35: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Wed, 04 Jul 2018 09:33:35: start model_add_line... INFO @ Wed, 04 Jul 2018 09:33:35: start X-correlation... INFO @ Wed, 04 Jul 2018 09:33:35: end of X-cor INFO @ Wed, 04 Jul 2018 09:33:35: #2 finished! INFO @ Wed, 04 Jul 2018 09:33:35: #2 predicted fragment length is 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2 alternative fragment length(s) may be 97 bps INFO @ Wed, 04 Jul 2018 09:33:35: #2.2 Generate R script for model : SRX3937201.10_model.r WARNING @ Wed, 04 Jul 2018 09:33:35: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Wed, 04 Jul 2018 09:33:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:33:35: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:33:39: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:39: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:39: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:33:41: #4 Write output xls file... SRX3937201.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:41: #4 Write peak in narrowPeak format file... SRX3937201.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:41: #4 Write summits bed file... SRX3937201.05_summits.bed INFO @ Wed, 04 Jul 2018 09:33:41: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:33:41: #4 Write output xls file... SRX3937201.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:41: #4 Write peak in narrowPeak format file... SRX3937201.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:42: #4 Write summits bed file... SRX3937201.10_summits.bed INFO @ Wed, 04 Jul 2018 09:33:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (250 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:33:42: #4 Write output xls file... SRX3937201.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:33:42: #4 Write peak in narrowPeak format file... SRX3937201.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:33:42: #4 Write summits bed file... SRX3937201.20_summits.bed INFO @ Wed, 04 Jul 2018 09:33:42: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。