Job ID = 10480659 sra ファイルのダウンロード中... Completed: 298347K bytes transferred in 33 seconds (72697K 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 9010367 spots for /home/okishinya/chipatlas/results/dm3/SRX2832095/SRR5573759.sra Written 9010367 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: 00:03:47 9010367 reads; of these: 9010367 (100.00%) were unpaired; of these: 538721 (5.98%) aligned 0 times 4583110 (50.86%) aligned exactly 1 time 3888536 (43.16%) aligned >1 times 94.02% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 1239478 / 8471646 = 0.1463 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 07:25:55: # Command line: callpeak -t SRX2832095.bam -f BAM -g dm -n SRX2832095.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832095.20 # format = BAM # ChIP-seq file = ['SRX2832095.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 07:25:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:25:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:25:55: # Command line: callpeak -t SRX2832095.bam -f BAM -g dm -n SRX2832095.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832095.05 # format = BAM # ChIP-seq file = ['SRX2832095.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 07:25:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:25:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:25:55: # Command line: callpeak -t SRX2832095.bam -f BAM -g dm -n SRX2832095.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832095.10 # format = BAM # ChIP-seq file = ['SRX2832095.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 07:25:55: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:25:55: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:26:01: 1000000 INFO @ Fri, 16 Mar 2018 07:26:01: 1000000 INFO @ Fri, 16 Mar 2018 07:26:01: 1000000 INFO @ Fri, 16 Mar 2018 07:26:08: 2000000 INFO @ Fri, 16 Mar 2018 07:26:08: 2000000 INFO @ Fri, 16 Mar 2018 07:26:08: 2000000 INFO @ Fri, 16 Mar 2018 07:26:15: 3000000 INFO @ Fri, 16 Mar 2018 07:26:15: 3000000 INFO @ Fri, 16 Mar 2018 07:26:15: 3000000 INFO @ Fri, 16 Mar 2018 07:26:22: 4000000 INFO @ Fri, 16 Mar 2018 07:26:22: 4000000 INFO @ Fri, 16 Mar 2018 07:26:22: 4000000 INFO @ Fri, 16 Mar 2018 07:26:28: 5000000 INFO @ Fri, 16 Mar 2018 07:26:28: 5000000 INFO @ Fri, 16 Mar 2018 07:26:28: 5000000 INFO @ Fri, 16 Mar 2018 07:26:35: 6000000 INFO @ Fri, 16 Mar 2018 07:26:35: 6000000 INFO @ Fri, 16 Mar 2018 07:26:35: 6000000 INFO @ Fri, 16 Mar 2018 07:26:41: 7000000 INFO @ Fri, 16 Mar 2018 07:26:41: 7000000 INFO @ Fri, 16 Mar 2018 07:26:42: 7000000 INFO @ Fri, 16 Mar 2018 07:26:43: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:26:43: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:26:43: #1 total tags in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:26:43: #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 07:26:43: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:26:43: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:26:43: #1 total tags in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:26:43: #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 07:26:43: #1 tags after filtering in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:26:43: #1 tags after filtering in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:26:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:26:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:26:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:26:43: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 07:26:43: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 07:26:43: #1 total tags in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:26:43: #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 07:26:43: #1 tags after filtering in treatment: 7232168 INFO @ Fri, 16 Mar 2018 07:26:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:26:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:26:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:26:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:26:44: #2 number of paired peaks: 506 WARNING @ Fri, 16 Mar 2018 07:26:44: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Fri, 16 Mar 2018 07:26:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:26:44: #2 number of paired peaks: 506 WARNING @ Fri, 16 Mar 2018 07:26:44: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Fri, 16 Mar 2018 07:26:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:26:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:26:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:26:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:26:44: #2 predicted fragment length is 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2.2 Generate R script for model : SRX2832095.05_model.r WARNING @ Fri, 16 Mar 2018 07:26:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:26:44: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 16 Mar 2018 07:26:44: #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 07:26:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:26:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:26:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:26:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:26:44: #2 predicted fragment length is 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2.2 Generate R script for model : SRX2832095.20_model.r WARNING @ Fri, 16 Mar 2018 07:26:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:26:44: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 16 Mar 2018 07:26:44: #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 07:26:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:26:44: #2 number of paired peaks: 506 WARNING @ Fri, 16 Mar 2018 07:26:44: Fewer paired peaks (506) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 506 pairs to build model! INFO @ Fri, 16 Mar 2018 07:26:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:26:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:26:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:26:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:26:44: #2 predicted fragment length is 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2 alternative fragment length(s) may be 72 bps INFO @ Fri, 16 Mar 2018 07:26:44: #2.2 Generate R script for model : SRX2832095.10_model.r WARNING @ Fri, 16 Mar 2018 07:26:44: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:26:44: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Fri, 16 Mar 2018 07:26:44: #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 07:26:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:27:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:27:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:27:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:27:09: #4 Write output xls file... SRX2832095.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:27:09: #4 Write peak in narrowPeak format file... SRX2832095.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:27:09: #4 Write summits bed file... SRX2832095.05_summits.bed INFO @ Fri, 16 Mar 2018 07:27:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3174 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:27:10: #4 Write output xls file... SRX2832095.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:27:10: #4 Write peak in narrowPeak format file... SRX2832095.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:27:10: #4 Write summits bed file... SRX2832095.20_summits.bed INFO @ Fri, 16 Mar 2018 07:27:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:27:11: #4 Write output xls file... SRX2832095.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:27:11: #4 Write peak in narrowPeak format file... SRX2832095.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:27:11: #4 Write summits bed file... SRX2832095.10_summits.bed INFO @ Fri, 16 Mar 2018 07:27:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1130 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。