Job ID = 10320338 sra ファイルのダウンロード中... Completed: 570171K bytes transferred in 37 seconds (124199K 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 37136316 spots for /home/okishinya/chipatlas/results/dm3/SRX3166314/SRR6012932.sra Written 37136316 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: 00:13:08 37136316 reads; of these: 37136316 (100.00%) were unpaired; of these: 16640148 (44.81%) aligned 0 times 6417003 (17.28%) aligned exactly 1 time 14079165 (37.91%) aligned >1 times 55.19% overall alignment rate Time searching: 00:13:08 Overall time: 00:13:08 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 12 files... [bam_rmdupse_core] 4954488 / 20496168 = 0.2417 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 @ Thu, 11 Jan 2018 02:24:45: # Command line: callpeak -t SRX3166314.bam -f BAM -g dm -n SRX3166314.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3166314.10 # format = BAM # ChIP-seq file = ['SRX3166314.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 @ Thu, 11 Jan 2018 02:24:45: # Command line: callpeak -t SRX3166314.bam -f BAM -g dm -n SRX3166314.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3166314.20 # format = BAM # ChIP-seq file = ['SRX3166314.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 @ Thu, 11 Jan 2018 02:24:45: # Command line: callpeak -t SRX3166314.bam -f BAM -g dm -n SRX3166314.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3166314.05 # format = BAM # ChIP-seq file = ['SRX3166314.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 @ Thu, 11 Jan 2018 02:24:45: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:24:45: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:24:45: #1 read tag files... INFO @ Thu, 11 Jan 2018 02:24:45: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:24:45: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:24:45: #1 read treatment tags... INFO @ Thu, 11 Jan 2018 02:24:51: 1000000 INFO @ Thu, 11 Jan 2018 02:24:51: 1000000 INFO @ Thu, 11 Jan 2018 02:24:51: 1000000 INFO @ Thu, 11 Jan 2018 02:24:58: 2000000 INFO @ Thu, 11 Jan 2018 02:24:58: 2000000 INFO @ Thu, 11 Jan 2018 02:24:58: 2000000 INFO @ Thu, 11 Jan 2018 02:25:04: 3000000 INFO @ Thu, 11 Jan 2018 02:25:04: 3000000 INFO @ Thu, 11 Jan 2018 02:25:05: 3000000 INFO @ Thu, 11 Jan 2018 02:25:10: 4000000 INFO @ Thu, 11 Jan 2018 02:25:10: 4000000 INFO @ Thu, 11 Jan 2018 02:25:11: 4000000 INFO @ Thu, 11 Jan 2018 02:25:17: 5000000 INFO @ Thu, 11 Jan 2018 02:25:17: 5000000 INFO @ Thu, 11 Jan 2018 02:25:18: 5000000 INFO @ Thu, 11 Jan 2018 02:25:23: 6000000 INFO @ Thu, 11 Jan 2018 02:25:23: 6000000 INFO @ Thu, 11 Jan 2018 02:25:25: 6000000 INFO @ Thu, 11 Jan 2018 02:25:29: 7000000 INFO @ Thu, 11 Jan 2018 02:25:30: 7000000 INFO @ Thu, 11 Jan 2018 02:25:31: 7000000 INFO @ Thu, 11 Jan 2018 02:25:36: 8000000 INFO @ Thu, 11 Jan 2018 02:25:36: 8000000 INFO @ Thu, 11 Jan 2018 02:25:38: 8000000 INFO @ Thu, 11 Jan 2018 02:25:42: 9000000 INFO @ Thu, 11 Jan 2018 02:25:43: 9000000 INFO @ Thu, 11 Jan 2018 02:25:45: 9000000 INFO @ Thu, 11 Jan 2018 02:25:48: 10000000 INFO @ Thu, 11 Jan 2018 02:25:49: 10000000 INFO @ Thu, 11 Jan 2018 02:25:51: 10000000 INFO @ Thu, 11 Jan 2018 02:25:55: 11000000 INFO @ Thu, 11 Jan 2018 02:25:55: 11000000 INFO @ Thu, 11 Jan 2018 02:25:58: 11000000 INFO @ Thu, 11 Jan 2018 02:26:01: 12000000 INFO @ Thu, 11 Jan 2018 02:26:02: 12000000 INFO @ Thu, 11 Jan 2018 02:26:04: 12000000 INFO @ Thu, 11 Jan 2018 02:26:08: 13000000 INFO @ Thu, 11 Jan 2018 02:26:09: 13000000 INFO @ Thu, 11 Jan 2018 02:26:11: 13000000 INFO @ Thu, 11 Jan 2018 02:26:14: 14000000 INFO @ Thu, 11 Jan 2018 02:26:15: 14000000 INFO @ Thu, 11 Jan 2018 02:26:18: 14000000 INFO @ Thu, 11 Jan 2018 02:26:21: 15000000 INFO @ Thu, 11 Jan 2018 02:26:22: 15000000 INFO @ Thu, 11 Jan 2018 02:26:24: 15000000 INFO @ Thu, 11 Jan 2018 02:26:24: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:26:24: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:26:24: #1 total tags in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:24: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:26:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:26:25: #1 tags after filtering in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:26:25: #1 finished! INFO @ Thu, 11 Jan 2018 02:26:25: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:26:25: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:26:25: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:26:25: #1 total tags in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:25: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:26:26: #1 tags after filtering in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:26:26: #1 finished! INFO @ Thu, 11 Jan 2018 02:26:26: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:26:26: #2 number of paired peaks: 2686 INFO @ Thu, 11 Jan 2018 02:26:26: start model_add_line... INFO @ Thu, 11 Jan 2018 02:26:27: start X-correlation... INFO @ Thu, 11 Jan 2018 02:26:27: end of X-cor INFO @ Thu, 11 Jan 2018 02:26:27: #2 finished! INFO @ Thu, 11 Jan 2018 02:26:27: #2 predicted fragment length is 59 bps INFO @ Thu, 11 Jan 2018 02:26:27: #2 alternative fragment length(s) may be 3,59 bps INFO @ Thu, 11 Jan 2018 02:26:27: #2.2 Generate R script for model : SRX3166314.20_model.r WARNING @ Thu, 11 Jan 2018 02:26:27: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:26:27: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Thu, 11 Jan 2018 02:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:26:27: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:26:27: #2 number of paired peaks: 2686 INFO @ Thu, 11 Jan 2018 02:26:27: start model_add_line... INFO @ Thu, 11 Jan 2018 02:26:27: start X-correlation... INFO @ Thu, 11 Jan 2018 02:26:27: end of X-cor INFO @ Thu, 11 Jan 2018 02:26:27: #2 finished! INFO @ Thu, 11 Jan 2018 02:26:27: #2 predicted fragment length is 59 bps INFO @ Thu, 11 Jan 2018 02:26:27: #2 alternative fragment length(s) may be 3,59 bps INFO @ Thu, 11 Jan 2018 02:26:27: #2.2 Generate R script for model : SRX3166314.10_model.r WARNING @ Thu, 11 Jan 2018 02:26:27: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:26:27: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Thu, 11 Jan 2018 02:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:26:27: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:26:28: #1 tag size is determined as 51 bps INFO @ Thu, 11 Jan 2018 02:26:28: #1 tag size = 51 INFO @ Thu, 11 Jan 2018 02:26:28: #1 total tags in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:28: #1 user defined the maximum tags... INFO @ Thu, 11 Jan 2018 02:26:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 11 Jan 2018 02:26:28: #1 tags after filtering in treatment: 15541680 INFO @ Thu, 11 Jan 2018 02:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 11 Jan 2018 02:26:28: #1 finished! INFO @ Thu, 11 Jan 2018 02:26:28: #2 Build Peak Model... INFO @ Thu, 11 Jan 2018 02:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 11 Jan 2018 02:26:30: #2 number of paired peaks: 2686 INFO @ Thu, 11 Jan 2018 02:26:30: start model_add_line... INFO @ Thu, 11 Jan 2018 02:26:30: start X-correlation... INFO @ Thu, 11 Jan 2018 02:26:30: end of X-cor INFO @ Thu, 11 Jan 2018 02:26:30: #2 finished! INFO @ Thu, 11 Jan 2018 02:26:30: #2 predicted fragment length is 59 bps INFO @ Thu, 11 Jan 2018 02:26:30: #2 alternative fragment length(s) may be 3,59 bps INFO @ Thu, 11 Jan 2018 02:26:30: #2.2 Generate R script for model : SRX3166314.05_model.r WARNING @ Thu, 11 Jan 2018 02:26:30: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 11 Jan 2018 02:26:30: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Thu, 11 Jan 2018 02:26:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 11 Jan 2018 02:26:30: #3 Call peaks... INFO @ Thu, 11 Jan 2018 02:26:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 11 Jan 2018 02:27:00: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:27:01: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:27:02: #3 Call peaks for each chromosome... INFO @ Thu, 11 Jan 2018 02:27:17: #4 Write output xls file... SRX3166314.20_peaks.xls INFO @ Thu, 11 Jan 2018 02:27:17: #4 Write peak in narrowPeak format file... SRX3166314.20_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:27:17: #4 Write summits bed file... SRX3166314.20_summits.bed INFO @ Thu, 11 Jan 2018 02:27:17: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1431 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:27:19: #4 Write output xls file... SRX3166314.10_peaks.xls INFO @ Thu, 11 Jan 2018 02:27:19: #4 Write peak in narrowPeak format file... SRX3166314.10_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:27:19: #4 Write summits bed file... SRX3166314.10_summits.bed INFO @ Thu, 11 Jan 2018 02:27:19: Done! INFO @ Thu, 11 Jan 2018 02:27:19: #4 Write output xls file... SRX3166314.05_peaks.xls pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5909 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 11 Jan 2018 02:27:20: #4 Write peak in narrowPeak format file... SRX3166314.05_peaks.narrowPeak INFO @ Thu, 11 Jan 2018 02:27:20: #4 Write summits bed file... SRX3166314.05_summits.bed INFO @ Thu, 11 Jan 2018 02:27:20: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14340 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。