Job ID = 9370837 sra ファイルのダウンロード中... Completed: 1097568K bytes transferred in 16 seconds (542370K 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: PAIRED fastq に変換中... Written 6456079 spots for /home/okishinya/chipatlas/results/dm3/SRX1958587/SRR3928901.sra Written 6456079 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: 01:06:49 6456079 reads; of these: 6456079 (100.00%) were paired; of these: 412814 (6.39%) aligned concordantly 0 times 4284441 (66.36%) aligned concordantly exactly 1 time 1758824 (27.24%) aligned concordantly >1 times ---- 412814 pairs aligned concordantly 0 times; of these: 12451 (3.02%) aligned discordantly 1 time ---- 400363 pairs aligned 0 times concordantly or discordantly; of these: 800726 mates make up the pairs; of these: 575559 (71.88%) aligned 0 times 131273 (16.39%) aligned exactly 1 time 93894 (11.73%) aligned >1 times 95.54% overall alignment rate Time searching: 01:06:49 Overall time: 01:06:49 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 216766 / 5716627 = 0.0379 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, 04 Aug 2017 14:46:16: # Command line: callpeak -t SRX1958587.bam -f BAM -g dm -n SRX1958587.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958587.05 # format = BAM # ChIP-seq file = ['SRX1958587.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, 04 Aug 2017 14:46:16: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:46:16: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:46:16: # Command line: callpeak -t SRX1958587.bam -f BAM -g dm -n SRX1958587.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958587.20 # format = BAM # ChIP-seq file = ['SRX1958587.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, 04 Aug 2017 14:46:16: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:46:16: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:46:16: # Command line: callpeak -t SRX1958587.bam -f BAM -g dm -n SRX1958587.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958587.10 # format = BAM # ChIP-seq file = ['SRX1958587.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, 04 Aug 2017 14:46:16: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:46:16: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:46:37: 1000000 INFO @ Fri, 04 Aug 2017 14:46:41: 1000000 INFO @ Fri, 04 Aug 2017 14:46:47: 1000000 INFO @ Fri, 04 Aug 2017 14:46:57: 2000000 INFO @ Fri, 04 Aug 2017 14:47:05: 2000000 INFO @ Fri, 04 Aug 2017 14:47:16: 3000000 INFO @ Fri, 04 Aug 2017 14:47:20: 2000000 INFO @ Fri, 04 Aug 2017 14:47:28: 3000000 INFO @ Fri, 04 Aug 2017 14:47:35: 4000000 INFO @ Fri, 04 Aug 2017 14:47:52: 4000000 INFO @ Fri, 04 Aug 2017 14:47:53: 3000000 INFO @ Fri, 04 Aug 2017 14:47:54: 5000000 INFO @ Fri, 04 Aug 2017 14:48:11: 6000000 INFO @ Fri, 04 Aug 2017 14:48:15: 5000000 INFO @ Fri, 04 Aug 2017 14:48:23: 4000000 INFO @ Fri, 04 Aug 2017 14:48:28: 7000000 INFO @ Fri, 04 Aug 2017 14:48:39: 6000000 INFO @ Fri, 04 Aug 2017 14:48:47: 8000000 INFO @ Fri, 04 Aug 2017 14:48:52: 5000000 INFO @ Fri, 04 Aug 2017 14:49:04: 9000000 INFO @ Fri, 04 Aug 2017 14:49:05: 7000000 INFO @ Fri, 04 Aug 2017 14:49:21: 6000000 INFO @ Fri, 04 Aug 2017 14:49:23: 10000000 INFO @ Fri, 04 Aug 2017 14:49:29: 8000000 INFO @ Fri, 04 Aug 2017 14:49:41: 11000000 INFO @ Fri, 04 Aug 2017 14:49:50: 7000000 INFO @ Fri, 04 Aug 2017 14:49:57: 9000000 INFO @ Fri, 04 Aug 2017 14:49:58: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:49:58: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:49:58: #1 total tags in treatment: 5826551 INFO @ Fri, 04 Aug 2017 14:49:58: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:49:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:49:58: #1 tags after filtering in treatment: 5540781 INFO @ Fri, 04 Aug 2017 14:49:58: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 14:49:58: #1 finished! INFO @ Fri, 04 Aug 2017 14:49:58: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:49:58: #2 number of paired peaks: 1208 INFO @ Fri, 04 Aug 2017 14:49:58: start model_add_line... INFO @ Fri, 04 Aug 2017 14:49:59: start X-correlation... INFO @ Fri, 04 Aug 2017 14:49:59: end of X-cor INFO @ Fri, 04 Aug 2017 14:49:59: #2 finished! INFO @ Fri, 04 Aug 2017 14:49:59: #2 predicted fragment length is 197 bps INFO @ Fri, 04 Aug 2017 14:49:59: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 04 Aug 2017 14:49:59: #2.2 Generate R script for model : SRX1958587.05_model.r WARNING @ Fri, 04 Aug 2017 14:49:59: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:49:59: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 04 Aug 2017 14:49:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:49:59: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:50:17: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:50:21: 8000000 INFO @ Fri, 04 Aug 2017 14:50:25: 10000000 INFO @ Fri, 04 Aug 2017 14:50:27: #4 Write output xls file... SRX1958587.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:50:27: #4 Write peak in narrowPeak format file... SRX1958587.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:50:27: #4 Write summits bed file... SRX1958587.05_summits.bed INFO @ Fri, 04 Aug 2017 14:50:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2353 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:50:54: 9000000 INFO @ Fri, 04 Aug 2017 14:50:56: 11000000 INFO @ Fri, 04 Aug 2017 14:51:24: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:51:24: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:51:24: #1 total tags in treatment: 5826551 INFO @ Fri, 04 Aug 2017 14:51:24: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:51:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:51:24: #1 tags after filtering in treatment: 5540781 INFO @ Fri, 04 Aug 2017 14:51:24: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 14:51:24: #1 finished! INFO @ Fri, 04 Aug 2017 14:51:24: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:51:24: 10000000 INFO @ Fri, 04 Aug 2017 14:51:25: #2 number of paired peaks: 1208 INFO @ Fri, 04 Aug 2017 14:51:25: start model_add_line... INFO @ Fri, 04 Aug 2017 14:51:25: start X-correlation... INFO @ Fri, 04 Aug 2017 14:51:25: end of X-cor INFO @ Fri, 04 Aug 2017 14:51:25: #2 finished! INFO @ Fri, 04 Aug 2017 14:51:25: #2 predicted fragment length is 197 bps INFO @ Fri, 04 Aug 2017 14:51:25: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 04 Aug 2017 14:51:25: #2.2 Generate R script for model : SRX1958587.10_model.r WARNING @ Fri, 04 Aug 2017 14:51:25: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:51:25: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 04 Aug 2017 14:51:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:51:25: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:51:44: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:51:53: 11000000 INFO @ Fri, 04 Aug 2017 14:51:55: #4 Write output xls file... SRX1958587.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:51:55: #4 Write peak in narrowPeak format file... SRX1958587.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:51:55: #4 Write summits bed file... SRX1958587.10_summits.bed INFO @ Fri, 04 Aug 2017 14:51:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1378 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:52:20: #1 tag size is determined as 150 bps INFO @ Fri, 04 Aug 2017 14:52:20: #1 tag size = 150 INFO @ Fri, 04 Aug 2017 14:52:20: #1 total tags in treatment: 5826551 INFO @ Fri, 04 Aug 2017 14:52:20: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:52:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:52:20: #1 tags after filtering in treatment: 5540781 INFO @ Fri, 04 Aug 2017 14:52:20: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 04 Aug 2017 14:52:20: #1 finished! INFO @ Fri, 04 Aug 2017 14:52:20: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:52:21: #2 number of paired peaks: 1208 INFO @ Fri, 04 Aug 2017 14:52:21: start model_add_line... INFO @ Fri, 04 Aug 2017 14:52:21: start X-correlation... INFO @ Fri, 04 Aug 2017 14:52:21: end of X-cor INFO @ Fri, 04 Aug 2017 14:52:21: #2 finished! INFO @ Fri, 04 Aug 2017 14:52:21: #2 predicted fragment length is 197 bps INFO @ Fri, 04 Aug 2017 14:52:21: #2 alternative fragment length(s) may be 197 bps INFO @ Fri, 04 Aug 2017 14:52:21: #2.2 Generate R script for model : SRX1958587.20_model.r WARNING @ Fri, 04 Aug 2017 14:52:21: #2 Since the d (197) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:52:21: #2 You may need to consider one of the other alternative d(s): 197 WARNING @ Fri, 04 Aug 2017 14:52:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:52:21: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:52:41: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:52:51: #4 Write output xls file... SRX1958587.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:52:51: #4 Write peak in narrowPeak format file... SRX1958587.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:52:51: #4 Write summits bed file... SRX1958587.20_summits.bed INFO @ Fri, 04 Aug 2017 14:52:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (741 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。