Job ID = 10480735 sra ファイルのダウンロード中... Completed: 301345K bytes transferred in 7 seconds (312710K 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... Written 10169173 spots for /home/okishinya/chipatlas/results/dm3/SRX3380794/SRR6278157.sra Written 10169173 spots total 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: 00:03:53 10169173 reads; of these: 10169173 (100.00%) were unpaired; of these: 310948 (3.06%) aligned 0 times 7385943 (72.63%) aligned exactly 1 time 2472282 (24.31%) aligned >1 times 96.94% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 532286 / 9858225 = 0.0540 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 @ Fri, 16 Mar 2018 07:52:01: # Command line: callpeak -t SRX3380794.bam -f BAM -g dm -n SRX3380794.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3380794.20 # format = BAM # ChIP-seq file = ['SRX3380794.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 @ Fri, 16 Mar 2018 07:52:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:01: # Command line: callpeak -t SRX3380794.bam -f BAM -g dm -n SRX3380794.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3380794.10 # format = BAM # ChIP-seq file = ['SRX3380794.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 @ Fri, 16 Mar 2018 07:52:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:01: # Command line: callpeak -t SRX3380794.bam -f BAM -g dm -n SRX3380794.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3380794.05 # format = BAM # ChIP-seq file = ['SRX3380794.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 @ Fri, 16 Mar 2018 07:52:01: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:52:01: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:52:11: 1000000 INFO @ Fri, 16 Mar 2018 07:52:11: 1000000 INFO @ Fri, 16 Mar 2018 07:52:11: 1000000 INFO @ Fri, 16 Mar 2018 07:52:19: 2000000 INFO @ Fri, 16 Mar 2018 07:52:19: 2000000 INFO @ Fri, 16 Mar 2018 07:52:19: 2000000 INFO @ Fri, 16 Mar 2018 07:52:27: 3000000 INFO @ Fri, 16 Mar 2018 07:52:27: 3000000 INFO @ Fri, 16 Mar 2018 07:52:27: 3000000 INFO @ Fri, 16 Mar 2018 07:52:35: 4000000 INFO @ Fri, 16 Mar 2018 07:52:35: 4000000 INFO @ Fri, 16 Mar 2018 07:52:35: 4000000 INFO @ Fri, 16 Mar 2018 07:52:43: 5000000 INFO @ Fri, 16 Mar 2018 07:52:43: 5000000 INFO @ Fri, 16 Mar 2018 07:52:43: 5000000 INFO @ Fri, 16 Mar 2018 07:52:51: 6000000 INFO @ Fri, 16 Mar 2018 07:52:51: 6000000 INFO @ Fri, 16 Mar 2018 07:52:51: 6000000 INFO @ Fri, 16 Mar 2018 07:52:58: 7000000 INFO @ Fri, 16 Mar 2018 07:52:58: 7000000 INFO @ Fri, 16 Mar 2018 07:52:58: 7000000 INFO @ Fri, 16 Mar 2018 07:53:05: 8000000 INFO @ Fri, 16 Mar 2018 07:53:05: 8000000 INFO @ Fri, 16 Mar 2018 07:53:05: 8000000 INFO @ Fri, 16 Mar 2018 07:53:11: 9000000 INFO @ Fri, 16 Mar 2018 07:53:13: 9000000 INFO @ Fri, 16 Mar 2018 07:53:13: 9000000 INFO @ Fri, 16 Mar 2018 07:53:14: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:14: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:14: #1 total tags in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:14: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:14: #1 tags after filtering in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:14: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:14: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:14: #2 number of paired peaks: 207 WARNING @ Fri, 16 Mar 2018 07:53:14: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Fri, 16 Mar 2018 07:53:14: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:14: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:14: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:14: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:14: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:53:14: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 16 Mar 2018 07:53:14: #2.2 Generate R script for model : SRX3380794.20_model.r WARNING @ Fri, 16 Mar 2018 07:53:14: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:53:14: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 16 Mar 2018 07:53:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:53:14: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:15: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:15: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:15: #1 total tags in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:15: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:15: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:53:15: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:53:15: #1 total tags in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:15: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:53:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:53:15: #1 tags after filtering in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:15: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:15: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:15: #1 tags after filtering in treatment: 9325939 INFO @ Fri, 16 Mar 2018 07:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:53:15: #1 finished! INFO @ Fri, 16 Mar 2018 07:53:15: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:53:16: #2 number of paired peaks: 207 WARNING @ Fri, 16 Mar 2018 07:53:16: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Fri, 16 Mar 2018 07:53:16: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:16: #2 number of paired peaks: 207 WARNING @ Fri, 16 Mar 2018 07:53:16: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Fri, 16 Mar 2018 07:53:16: start model_add_line... INFO @ Fri, 16 Mar 2018 07:53:16: start X-correlation... INFO @ Fri, 16 Mar 2018 07:53:16: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:16: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:16: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:53:16: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 16 Mar 2018 07:53:16: #2.2 Generate R script for model : SRX3380794.10_model.r INFO @ Fri, 16 Mar 2018 07:53:16: start X-correlation... WARNING @ Fri, 16 Mar 2018 07:53:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:53:16: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 16 Mar 2018 07:53:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:53:16: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:16: end of X-cor INFO @ Fri, 16 Mar 2018 07:53:16: #2 finished! INFO @ Fri, 16 Mar 2018 07:53:16: #2 predicted fragment length is 51 bps INFO @ Fri, 16 Mar 2018 07:53:16: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 16 Mar 2018 07:53:16: #2.2 Generate R script for model : SRX3380794.05_model.r WARNING @ Fri, 16 Mar 2018 07:53:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:53:16: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 16 Mar 2018 07:53:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 16 Mar 2018 07:53:16: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:53:35: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:36: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:37: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:53:46: #4 Write output xls file... SRX3380794.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:46: #4 Write peak in narrowPeak format file... SRX3380794.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:46: #4 Write summits bed file... SRX3380794.20_summits.bed INFO @ Fri, 16 Mar 2018 07:53:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (791 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write output xls file... SRX3380794.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write peak in narrowPeak format file... SRX3380794.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write summits bed file... SRX3380794.05_summits.bed INFO @ Fri, 16 Mar 2018 07:53:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1412 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write output xls file... SRX3380794.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write peak in narrowPeak format file... SRX3380794.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:53:48: #4 Write summits bed file... SRX3380794.10_summits.bed INFO @ Fri, 16 Mar 2018 07:53:48: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1145 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。