Job ID = 10480661 sra ファイルのダウンロード中... Completed: 508458K bytes transferred in 55 seconds (74410K 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 15533607 spots for /home/okishinya/chipatlas/results/dm3/SRX2832097/SRR5573761.sra Written 15533607 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: 00:24:15 15533607 reads; of these: 15533607 (100.00%) were unpaired; of these: 379522 (2.44%) aligned 0 times 9885541 (63.64%) aligned exactly 1 time 5268544 (33.92%) aligned >1 times 97.56% overall alignment rate Time searching: 00:24:15 Overall time: 00:24:15 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] 4822897 / 15154085 = 0.3183 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 07:56:58: # Command line: callpeak -t SRX2832097.bam -f BAM -g dm -n SRX2832097.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2832097.05 # format = BAM # ChIP-seq file = ['SRX2832097.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 07:56:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:58: # Command line: callpeak -t SRX2832097.bam -f BAM -g dm -n SRX2832097.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2832097.10 # format = BAM # ChIP-seq file = ['SRX2832097.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 07:56:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:56:58: # Command line: callpeak -t SRX2832097.bam -f BAM -g dm -n SRX2832097.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2832097.20 # format = BAM # ChIP-seq file = ['SRX2832097.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 07:56:58: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:56:58: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:57:17: 1000000 INFO @ Fri, 16 Mar 2018 07:57:18: 1000000 INFO @ Fri, 16 Mar 2018 07:57:19: 1000000 INFO @ Fri, 16 Mar 2018 07:57:37: 2000000 INFO @ Fri, 16 Mar 2018 07:57:38: 2000000 INFO @ Fri, 16 Mar 2018 07:57:39: 2000000 INFO @ Fri, 16 Mar 2018 07:57:58: 3000000 INFO @ Fri, 16 Mar 2018 07:57:58: 3000000 INFO @ Fri, 16 Mar 2018 07:58:00: 3000000 INFO @ Fri, 16 Mar 2018 07:58:18: 4000000 INFO @ Fri, 16 Mar 2018 07:58:20: 4000000 INFO @ Fri, 16 Mar 2018 07:58:20: 4000000 INFO @ Fri, 16 Mar 2018 07:58:39: 5000000 INFO @ Fri, 16 Mar 2018 07:58:41: 5000000 INFO @ Fri, 16 Mar 2018 07:58:41: 5000000 INFO @ Fri, 16 Mar 2018 07:58:59: 6000000 INFO @ Fri, 16 Mar 2018 07:59:01: 6000000 INFO @ Fri, 16 Mar 2018 07:59:02: 6000000 INFO @ Fri, 16 Mar 2018 07:59:20: 7000000 INFO @ Fri, 16 Mar 2018 07:59:21: 7000000 INFO @ Fri, 16 Mar 2018 07:59:23: 7000000 INFO @ Fri, 16 Mar 2018 07:59:41: 8000000 INFO @ Fri, 16 Mar 2018 07:59:42: 8000000 INFO @ Fri, 16 Mar 2018 07:59:44: 8000000 INFO @ Fri, 16 Mar 2018 08:00:01: 9000000 INFO @ Fri, 16 Mar 2018 08:00:01: 9000000 INFO @ Fri, 16 Mar 2018 08:00:05: 9000000 INFO @ Fri, 16 Mar 2018 08:00:21: 10000000 INFO @ Fri, 16 Mar 2018 08:00:22: 10000000 INFO @ Fri, 16 Mar 2018 08:00:26: 10000000 INFO @ Fri, 16 Mar 2018 08:00:27: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 08:00:27: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 08:00:27: #1 total tags in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:27: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:00:27: #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 08:00:28: #1 tags after filtering in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:00:28: #1 finished! INFO @ Fri, 16 Mar 2018 08:00:28: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:00:29: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 08:00:29: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 08:00:29: #1 total tags in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:29: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:00:29: #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 08:00:30: #1 tags after filtering in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:00:30: #1 finished! INFO @ Fri, 16 Mar 2018 08:00:30: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:00:31: #2 number of paired peaks: 1829 INFO @ Fri, 16 Mar 2018 08:00:31: start model_add_line... INFO @ Fri, 16 Mar 2018 08:00:31: start X-correlation... INFO @ Fri, 16 Mar 2018 08:00:31: end of X-cor INFO @ Fri, 16 Mar 2018 08:00:31: #2 finished! INFO @ Fri, 16 Mar 2018 08:00:31: #2 predicted fragment length is 58 bps INFO @ Fri, 16 Mar 2018 08:00:31: #2 alternative fragment length(s) may be 4,58,564 bps INFO @ Fri, 16 Mar 2018 08:00:31: #2.2 Generate R script for model : SRX2832097.20_model.r WARNING @ Fri, 16 Mar 2018 08:00:31: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:00:31: #2 You may need to consider one of the other alternative d(s): 4,58,564 WARNING @ Fri, 16 Mar 2018 08:00:31: #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 08:00:31: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:00:33: #1 tag size is determined as 50 bps INFO @ Fri, 16 Mar 2018 08:00:33: #1 tag size = 50 INFO @ Fri, 16 Mar 2018 08:00:33: #1 total tags in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:33: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 08:00:33: #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 08:00:33: #2 number of paired peaks: 1829 INFO @ Fri, 16 Mar 2018 08:00:33: start model_add_line... INFO @ Fri, 16 Mar 2018 08:00:34: start X-correlation... INFO @ Fri, 16 Mar 2018 08:00:34: end of X-cor INFO @ Fri, 16 Mar 2018 08:00:34: #2 finished! INFO @ Fri, 16 Mar 2018 08:00:34: #2 predicted fragment length is 58 bps INFO @ Fri, 16 Mar 2018 08:00:34: #2 alternative fragment length(s) may be 4,58,564 bps INFO @ Fri, 16 Mar 2018 08:00:34: #2.2 Generate R script for model : SRX2832097.05_model.r WARNING @ Fri, 16 Mar 2018 08:00:34: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:00:34: #2 You may need to consider one of the other alternative d(s): 4,58,564 WARNING @ Fri, 16 Mar 2018 08:00:34: #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 08:00:34: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:00:34: #1 tags after filtering in treatment: 10331188 INFO @ Fri, 16 Mar 2018 08:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 08:00:34: #1 finished! INFO @ Fri, 16 Mar 2018 08:00:34: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 08:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 08:00:36: #2 number of paired peaks: 1829 INFO @ Fri, 16 Mar 2018 08:00:36: start model_add_line... INFO @ Fri, 16 Mar 2018 08:00:37: start X-correlation... INFO @ Fri, 16 Mar 2018 08:00:37: end of X-cor INFO @ Fri, 16 Mar 2018 08:00:37: #2 finished! INFO @ Fri, 16 Mar 2018 08:00:37: #2 predicted fragment length is 58 bps INFO @ Fri, 16 Mar 2018 08:00:37: #2 alternative fragment length(s) may be 4,58,564 bps INFO @ Fri, 16 Mar 2018 08:00:37: #2.2 Generate R script for model : SRX2832097.10_model.r WARNING @ Fri, 16 Mar 2018 08:00:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 16 Mar 2018 08:00:37: #2 You may need to consider one of the other alternative d(s): 4,58,564 WARNING @ Fri, 16 Mar 2018 08:00:37: #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 08:00:37: #3 Call peaks... INFO @ Fri, 16 Mar 2018 08:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 08:01:35: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:01:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:01:53: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write output xls file... SRX2832097.20_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write peak in narrowPeak format file... SRX2832097.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:08: #4 Write summits bed file... SRX2832097.20_summits.bed INFO @ Fri, 16 Mar 2018 08:02:08: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:02:16: #4 Write output xls file... SRX2832097.05_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:16: #4 Write peak in narrowPeak format file... SRX2832097.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:16: #4 Write summits bed file... SRX2832097.05_summits.bed INFO @ Fri, 16 Mar 2018 08:02:16: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (3596 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 08:02:34: #4 Write output xls file... SRX2832097.10_peaks.xls INFO @ Fri, 16 Mar 2018 08:02:34: #4 Write peak in narrowPeak format file... SRX2832097.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 08:02:34: #4 Write summits bed file... SRX2832097.10_summits.bed INFO @ Fri, 16 Mar 2018 08:02:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2570 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。