Job ID = 10480684 sra ファイルのダウンロード中... Completed: 743703K bytes transferred in 16 seconds (375675K 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 23172272 spots for /home/okishinya/chipatlas/results/dm3/SRX3068955/SRR5907431.sra Written 23172272 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:06 23172272 reads; of these: 23172272 (100.00%) were unpaired; of these: 8563965 (36.96%) aligned 0 times 11732330 (50.63%) aligned exactly 1 time 2875977 (12.41%) aligned >1 times 63.04% overall alignment rate Time searching: 00:06:07 Overall time: 00:06:07 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] 4744863 / 14608307 = 0.3248 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 07:45:24: # Command line: callpeak -t SRX3068955.bam -f BAM -g dm -n SRX3068955.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068955.10 # format = BAM # ChIP-seq file = ['SRX3068955.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 07:45:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:45:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:45:24: # Command line: callpeak -t SRX3068955.bam -f BAM -g dm -n SRX3068955.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068955.05 # format = BAM # ChIP-seq file = ['SRX3068955.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 07:45:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:45:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:45:24: # Command line: callpeak -t SRX3068955.bam -f BAM -g dm -n SRX3068955.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068955.20 # format = BAM # ChIP-seq file = ['SRX3068955.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 07:45:24: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:45:24: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:45:30: 1000000 INFO @ Fri, 16 Mar 2018 07:45:30: 1000000 INFO @ Fri, 16 Mar 2018 07:45:30: 1000000 INFO @ Fri, 16 Mar 2018 07:45:37: 2000000 INFO @ Fri, 16 Mar 2018 07:45:37: 2000000 INFO @ Fri, 16 Mar 2018 07:45:37: 2000000 INFO @ Fri, 16 Mar 2018 07:45:44: 3000000 INFO @ Fri, 16 Mar 2018 07:45:44: 3000000 INFO @ Fri, 16 Mar 2018 07:45:44: 3000000 INFO @ Fri, 16 Mar 2018 07:45:50: 4000000 INFO @ Fri, 16 Mar 2018 07:45:50: 4000000 INFO @ Fri, 16 Mar 2018 07:45:51: 4000000 INFO @ Fri, 16 Mar 2018 07:45:57: 5000000 INFO @ Fri, 16 Mar 2018 07:45:57: 5000000 INFO @ Fri, 16 Mar 2018 07:45:58: 5000000 INFO @ Fri, 16 Mar 2018 07:46:03: 6000000 INFO @ Fri, 16 Mar 2018 07:46:04: 6000000 INFO @ Fri, 16 Mar 2018 07:46:05: 6000000 INFO @ Fri, 16 Mar 2018 07:46:10: 7000000 INFO @ Fri, 16 Mar 2018 07:46:11: 7000000 INFO @ Fri, 16 Mar 2018 07:46:12: 7000000 INFO @ Fri, 16 Mar 2018 07:46:17: 8000000 INFO @ Fri, 16 Mar 2018 07:46:18: 8000000 INFO @ Fri, 16 Mar 2018 07:46:19: 8000000 INFO @ Fri, 16 Mar 2018 07:46:23: 9000000 INFO @ Fri, 16 Mar 2018 07:46:26: 9000000 INFO @ Fri, 16 Mar 2018 07:46:27: 9000000 INFO @ Fri, 16 Mar 2018 07:46:29: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:29: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:29: #1 total tags in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:29: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:29: #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 07:46:29: #1 tags after filtering in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:29: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:29: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:30: #2 number of paired peaks: 480 WARNING @ Fri, 16 Mar 2018 07:46:30: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Fri, 16 Mar 2018 07:46:30: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:30: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:30: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:30: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:30: #2 predicted fragment length is 95 bps INFO @ Fri, 16 Mar 2018 07:46:30: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 16 Mar 2018 07:46:30: #2.2 Generate R script for model : SRX3068955.20_model.r WARNING @ Fri, 16 Mar 2018 07:46:30: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:46:30: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 16 Mar 2018 07:46:30: #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 07:46:30: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:32: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:32: #1 total tags in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:32: #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 07:46:32: #1 tags after filtering in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:33: #2 number of paired peaks: 480 WARNING @ Fri, 16 Mar 2018 07:46:33: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Fri, 16 Mar 2018 07:46:33: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:33: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:33: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:33: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:33: #2 predicted fragment length is 95 bps INFO @ Fri, 16 Mar 2018 07:46:33: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 16 Mar 2018 07:46:33: #2.2 Generate R script for model : SRX3068955.10_model.r WARNING @ Fri, 16 Mar 2018 07:46:33: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:46:33: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 16 Mar 2018 07:46:33: #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 07:46:33: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:33: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:33: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:33: #1 total tags in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:33: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:33: #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 07:46:33: #1 tags after filtering in treatment: 9863444 INFO @ Fri, 16 Mar 2018 07:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:33: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:33: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:34: #2 number of paired peaks: 480 WARNING @ Fri, 16 Mar 2018 07:46:34: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Fri, 16 Mar 2018 07:46:34: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:34: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:34: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:34: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:34: #2 predicted fragment length is 95 bps INFO @ Fri, 16 Mar 2018 07:46:34: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 16 Mar 2018 07:46:34: #2.2 Generate R script for model : SRX3068955.05_model.r WARNING @ Fri, 16 Mar 2018 07:46:34: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 07:46:34: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 16 Mar 2018 07:46:34: #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 07:46:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:51: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:46:56: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:46:57: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:04: #4 Write output xls file... SRX3068955.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:04: #4 Write peak in narrowPeak format file... SRX3068955.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:04: #4 Write summits bed file... SRX3068955.20_summits.bed INFO @ Fri, 16 Mar 2018 07:47:04: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1256 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:08: #4 Write output xls file... SRX3068955.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:08: #4 Write peak in narrowPeak format file... SRX3068955.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:09: #4 Write summits bed file... SRX3068955.05_summits.bed INFO @ Fri, 16 Mar 2018 07:47:09: Done! INFO @ Fri, 16 Mar 2018 07:47:09: #4 Write output xls file... SRX3068955.10_peaks.xls pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5733 records, 4 fields): 8 millis INFO @ Fri, 16 Mar 2018 07:47:09: #4 Write peak in narrowPeak format file... SRX3068955.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:09: #4 Write summits bed file... SRX3068955.10_summits.bed INFO @ Fri, 16 Mar 2018 07:47:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2938 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。