Job ID = 9157188 sra ファイルのダウンロード中... Completed: 340227K bytes transferred in 6 seconds (456900K bits/sec), in 1 file, 2 directories. 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 16370602 spots for /home/okishinya/chipatlas/results/ce10/SRX2228905/SRR4380361.sra Written 16370602 spots total 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: 00:04:18 16370602 reads; of these: 16370602 (100.00%) were unpaired; of these: 121058 (0.74%) aligned 0 times 13575884 (82.93%) aligned exactly 1 time 2673660 (16.33%) aligned >1 times 99.26% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 1407294 / 16249544 = 0.0866 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 @ Tue, 27 Jun 2017 11:04:16: # Command line: callpeak -t SRX2228905.bam -f BAM -g ce -n SRX2228905.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2228905.05 # format = BAM # ChIP-seq file = ['SRX2228905.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 @ Tue, 27 Jun 2017 11:04:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:16: # Command line: callpeak -t SRX2228905.bam -f BAM -g ce -n SRX2228905.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2228905.20 # format = BAM # ChIP-seq file = ['SRX2228905.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 @ Tue, 27 Jun 2017 11:04:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:16: # Command line: callpeak -t SRX2228905.bam -f BAM -g ce -n SRX2228905.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2228905.10 # format = BAM # ChIP-seq file = ['SRX2228905.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 @ Tue, 27 Jun 2017 11:04:16: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:04:16: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:04:23: 1000000 INFO @ Tue, 27 Jun 2017 11:04:24: 1000000 INFO @ Tue, 27 Jun 2017 11:04:24: 1000000 INFO @ Tue, 27 Jun 2017 11:04:30: 2000000 INFO @ Tue, 27 Jun 2017 11:04:32: 2000000 INFO @ Tue, 27 Jun 2017 11:04:32: 2000000 INFO @ Tue, 27 Jun 2017 11:04:37: 3000000 INFO @ Tue, 27 Jun 2017 11:04:41: 3000000 INFO @ Tue, 27 Jun 2017 11:04:41: 3000000 INFO @ Tue, 27 Jun 2017 11:04:44: 4000000 INFO @ Tue, 27 Jun 2017 11:04:49: 4000000 INFO @ Tue, 27 Jun 2017 11:04:49: 4000000 INFO @ Tue, 27 Jun 2017 11:04:51: 5000000 INFO @ Tue, 27 Jun 2017 11:04:58: 5000000 INFO @ Tue, 27 Jun 2017 11:04:58: 5000000 INFO @ Tue, 27 Jun 2017 11:04:58: 6000000 INFO @ Tue, 27 Jun 2017 11:05:05: 7000000 INFO @ Tue, 27 Jun 2017 11:05:06: 6000000 INFO @ Tue, 27 Jun 2017 11:05:06: 6000000 INFO @ Tue, 27 Jun 2017 11:05:13: 8000000 INFO @ Tue, 27 Jun 2017 11:05:14: 7000000 INFO @ Tue, 27 Jun 2017 11:05:14: 7000000 INFO @ Tue, 27 Jun 2017 11:05:20: 9000000 INFO @ Tue, 27 Jun 2017 11:05:23: 8000000 INFO @ Tue, 27 Jun 2017 11:05:23: 8000000 INFO @ Tue, 27 Jun 2017 11:05:27: 10000000 INFO @ Tue, 27 Jun 2017 11:05:31: 9000000 INFO @ Tue, 27 Jun 2017 11:05:31: 9000000 INFO @ Tue, 27 Jun 2017 11:05:34: 11000000 INFO @ Tue, 27 Jun 2017 11:05:39: 10000000 INFO @ Tue, 27 Jun 2017 11:05:39: 10000000 INFO @ Tue, 27 Jun 2017 11:05:41: 12000000 INFO @ Tue, 27 Jun 2017 11:05:48: 13000000 INFO @ Tue, 27 Jun 2017 11:05:48: 11000000 INFO @ Tue, 27 Jun 2017 11:05:48: 11000000 INFO @ Tue, 27 Jun 2017 11:05:55: 14000000 INFO @ Tue, 27 Jun 2017 11:05:56: 12000000 INFO @ Tue, 27 Jun 2017 11:05:56: 12000000 INFO @ Tue, 27 Jun 2017 11:06:00: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:06:00: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:06:00: #1 total tags in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:00: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:06:01: #1 tags after filtering in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:01: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:02: #2 number of paired peaks: 254 WARNING @ Tue, 27 Jun 2017 11:06:02: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:02: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:02: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:02: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:02: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:02: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:06:02: #2 alternative fragment length(s) may be 1,49,565 bps INFO @ Tue, 27 Jun 2017 11:06:02: #2.2 Generate R script for model : SRX2228905.05_model.r WARNING @ Tue, 27 Jun 2017 11:06:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:02: #2 You may need to consider one of the other alternative d(s): 1,49,565 WARNING @ Tue, 27 Jun 2017 11:06:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:06:02: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:04: 13000000 INFO @ Tue, 27 Jun 2017 11:06:04: 13000000 INFO @ Tue, 27 Jun 2017 11:06:12: 14000000 INFO @ Tue, 27 Jun 2017 11:06:12: 14000000 INFO @ Tue, 27 Jun 2017 11:06:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:06:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:06:19: #1 total tags in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:06:19: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 11:06:19: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 11:06:19: #1 total tags in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:19: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:06:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:06:19: #1 tags after filtering in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:19: #1 tags after filtering in treatment: 14842250 INFO @ Tue, 27 Jun 2017 11:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:06:19: #1 finished! INFO @ Tue, 27 Jun 2017 11:06:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:06:20: #2 number of paired peaks: 254 WARNING @ Tue, 27 Jun 2017 11:06:20: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:20: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:20: #2 number of paired peaks: 254 WARNING @ Tue, 27 Jun 2017 11:06:20: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 27 Jun 2017 11:06:20: start model_add_line... INFO @ Tue, 27 Jun 2017 11:06:20: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:20: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:20: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:20: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:06:20: #2 alternative fragment length(s) may be 1,49,565 bps INFO @ Tue, 27 Jun 2017 11:06:20: #2.2 Generate R script for model : SRX2228905.10_model.r WARNING @ Tue, 27 Jun 2017 11:06:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:20: #2 You may need to consider one of the other alternative d(s): 1,49,565 WARNING @ Tue, 27 Jun 2017 11:06:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:06:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:20: start X-correlation... INFO @ Tue, 27 Jun 2017 11:06:20: end of X-cor INFO @ Tue, 27 Jun 2017 11:06:20: #2 finished! INFO @ Tue, 27 Jun 2017 11:06:20: #2 predicted fragment length is 49 bps INFO @ Tue, 27 Jun 2017 11:06:20: #2 alternative fragment length(s) may be 1,49,565 bps INFO @ Tue, 27 Jun 2017 11:06:20: #2.2 Generate R script for model : SRX2228905.20_model.r WARNING @ Tue, 27 Jun 2017 11:06:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:06:20: #2 You may need to consider one of the other alternative d(s): 1,49,565 WARNING @ Tue, 27 Jun 2017 11:06:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:06:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:06:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:06:33: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:06:48: #4 Write output xls file... SRX2228905.05_peaks.xls INFO @ Tue, 27 Jun 2017 11:06:48: #4 Write peak in narrowPeak format file... SRX2228905.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:06:48: #4 Write summits bed file... SRX2228905.05_summits.bed INFO @ Tue, 27 Jun 2017 11:06:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:06:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:06:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write output xls file... SRX2228905.10_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write peak in narrowPeak format file... SRX2228905.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write summits bed file... SRX2228905.10_summits.bed INFO @ Tue, 27 Jun 2017 11:07:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (413 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write output xls file... SRX2228905.20_peaks.xls INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write peak in narrowPeak format file... SRX2228905.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 11:07:05: #4 Write summits bed file... SRX2228905.20_summits.bed INFO @ Tue, 27 Jun 2017 11:07:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 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。