Job ID = 11597694 sra ファイルのダウンロード中... Completed: 1838270K bytes transferred in 18 seconds (793957K 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: PAIRED fastq に変換中... Read 16090837 spots for /home/okishinya/chipatlas/results/ce10/SRX5064642/SRR8246578.sra Written 16090837 spots for /home/okishinya/chipatlas/results/ce10/SRX5064642/SRR8246578.sra 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: 00:38:04 16090837 reads; of these: 16090837 (100.00%) were paired; of these: 590742 (3.67%) aligned concordantly 0 times 14466067 (89.90%) aligned concordantly exactly 1 time 1034028 (6.43%) aligned concordantly >1 times ---- 590742 pairs aligned concordantly 0 times; of these: 234097 (39.63%) aligned discordantly 1 time ---- 356645 pairs aligned 0 times concordantly or discordantly; of these: 713290 mates make up the pairs; of these: 553567 (77.61%) aligned 0 times 112355 (15.75%) aligned exactly 1 time 47368 (6.64%) aligned >1 times 98.28% overall alignment rate Time searching: 00:38:04 Overall time: 00:38:04 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 24 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 4486058 / 15716527 = 0.2854 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 @ Wed, 30 Jan 2019 15:14:30: # Command line: callpeak -t SRX5064642.bam -f BAM -g ce -n SRX5064642.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX5064642.10 # format = BAM # ChIP-seq file = ['SRX5064642.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 @ Wed, 30 Jan 2019 15:14:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:14:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:14:30: # Command line: callpeak -t SRX5064642.bam -f BAM -g ce -n SRX5064642.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX5064642.05 # format = BAM # ChIP-seq file = ['SRX5064642.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 @ Wed, 30 Jan 2019 15:14:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:14:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:14:30: # Command line: callpeak -t SRX5064642.bam -f BAM -g ce -n SRX5064642.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX5064642.20 # format = BAM # ChIP-seq file = ['SRX5064642.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 @ Wed, 30 Jan 2019 15:14:30: #1 read tag files... INFO @ Wed, 30 Jan 2019 15:14:30: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 15:14:40: 1000000 INFO @ Wed, 30 Jan 2019 15:14:42: 1000000 INFO @ Wed, 30 Jan 2019 15:14:42: 1000000 INFO @ Wed, 30 Jan 2019 15:14:49: 2000000 INFO @ Wed, 30 Jan 2019 15:14:52: 2000000 INFO @ Wed, 30 Jan 2019 15:14:52: 2000000 INFO @ Wed, 30 Jan 2019 15:14:58: 3000000 INFO @ Wed, 30 Jan 2019 15:15:04: 3000000 INFO @ Wed, 30 Jan 2019 15:15:04: 3000000 INFO @ Wed, 30 Jan 2019 15:15:12: 4000000 INFO @ Wed, 30 Jan 2019 15:15:16: 4000000 INFO @ Wed, 30 Jan 2019 15:15:16: 4000000 INFO @ Wed, 30 Jan 2019 15:15:25: 5000000 INFO @ Wed, 30 Jan 2019 15:15:28: 5000000 INFO @ Wed, 30 Jan 2019 15:15:28: 5000000 INFO @ Wed, 30 Jan 2019 15:15:35: 6000000 INFO @ Wed, 30 Jan 2019 15:15:39: 6000000 INFO @ Wed, 30 Jan 2019 15:15:39: 6000000 INFO @ Wed, 30 Jan 2019 15:15:45: 7000000 INFO @ Wed, 30 Jan 2019 15:15:50: 7000000 INFO @ Wed, 30 Jan 2019 15:15:50: 7000000 INFO @ Wed, 30 Jan 2019 15:15:56: 8000000 INFO @ Wed, 30 Jan 2019 15:16:01: 8000000 INFO @ Wed, 30 Jan 2019 15:16:01: 8000000 INFO @ Wed, 30 Jan 2019 15:16:06: 9000000 INFO @ Wed, 30 Jan 2019 15:16:12: 9000000 INFO @ Wed, 30 Jan 2019 15:16:12: 9000000 INFO @ Wed, 30 Jan 2019 15:16:17: 10000000 INFO @ Wed, 30 Jan 2019 15:16:23: 10000000 INFO @ Wed, 30 Jan 2019 15:16:23: 10000000 INFO @ Wed, 30 Jan 2019 15:16:28: 11000000 INFO @ Wed, 30 Jan 2019 15:16:33: 11000000 INFO @ Wed, 30 Jan 2019 15:16:34: 11000000 INFO @ Wed, 30 Jan 2019 15:16:40: 12000000 INFO @ Wed, 30 Jan 2019 15:16:44: 12000000 INFO @ Wed, 30 Jan 2019 15:16:48: 12000000 INFO @ Wed, 30 Jan 2019 15:16:51: 13000000 INFO @ Wed, 30 Jan 2019 15:16:54: 13000000 INFO @ Wed, 30 Jan 2019 15:17:01: 13000000 INFO @ Wed, 30 Jan 2019 15:17:03: 14000000 INFO @ Wed, 30 Jan 2019 15:17:05: 14000000 INFO @ Wed, 30 Jan 2019 15:17:14: 15000000 INFO @ Wed, 30 Jan 2019 15:17:14: 14000000 INFO @ Wed, 30 Jan 2019 15:17:16: 15000000 INFO @ Wed, 30 Jan 2019 15:17:25: 16000000 INFO @ Wed, 30 Jan 2019 15:17:27: 16000000 INFO @ Wed, 30 Jan 2019 15:17:28: 15000000 INFO @ Wed, 30 Jan 2019 15:17:37: 17000000 INFO @ Wed, 30 Jan 2019 15:17:38: 17000000 INFO @ Wed, 30 Jan 2019 15:17:40: 16000000 INFO @ Wed, 30 Jan 2019 15:17:48: 18000000 INFO @ Wed, 30 Jan 2019 15:17:49: 18000000 INFO @ Wed, 30 Jan 2019 15:17:52: 17000000 INFO @ Wed, 30 Jan 2019 15:17:59: 19000000 INFO @ Wed, 30 Jan 2019 15:18:01: 19000000 INFO @ Wed, 30 Jan 2019 15:18:05: 18000000 INFO @ Wed, 30 Jan 2019 15:18:11: 20000000 INFO @ Wed, 30 Jan 2019 15:18:14: 20000000 INFO @ Wed, 30 Jan 2019 15:18:16: 19000000 INFO @ Wed, 30 Jan 2019 15:18:23: 21000000 INFO @ Wed, 30 Jan 2019 15:18:27: 20000000 INFO @ Wed, 30 Jan 2019 15:18:28: 21000000 INFO @ Wed, 30 Jan 2019 15:18:36: 22000000 INFO @ Wed, 30 Jan 2019 15:18:39: 22000000 INFO @ Wed, 30 Jan 2019 15:18:40: 21000000 INFO @ Wed, 30 Jan 2019 15:18:44: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:18:44: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:18:44: #1 total tags in treatment: 11062869 INFO @ Wed, 30 Jan 2019 15:18:44: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:18:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:18:44: #1 tags after filtering in treatment: 9630274 INFO @ Wed, 30 Jan 2019 15:18:44: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 30 Jan 2019 15:18:44: #1 finished! INFO @ Wed, 30 Jan 2019 15:18:44: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:18:45: #2 number of paired peaks: 4086 INFO @ Wed, 30 Jan 2019 15:18:45: start model_add_line... INFO @ Wed, 30 Jan 2019 15:18:45: start X-correlation... INFO @ Wed, 30 Jan 2019 15:18:45: end of X-cor INFO @ Wed, 30 Jan 2019 15:18:45: #2 finished! INFO @ Wed, 30 Jan 2019 15:18:45: #2 predicted fragment length is 280 bps INFO @ Wed, 30 Jan 2019 15:18:45: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 30 Jan 2019 15:18:45: #2.2 Generate R script for model : SRX5064642.05_model.r WARNING @ Wed, 30 Jan 2019 15:18:45: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:18:45: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Wed, 30 Jan 2019 15:18:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:18:45: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:18:48: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:18:48: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:18:48: #1 total tags in treatment: 11062869 INFO @ Wed, 30 Jan 2019 15:18:48: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:18:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:18:48: #1 tags after filtering in treatment: 9630274 INFO @ Wed, 30 Jan 2019 15:18:48: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 30 Jan 2019 15:18:48: #1 finished! INFO @ Wed, 30 Jan 2019 15:18:48: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:18:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:18:49: #2 number of paired peaks: 4086 INFO @ Wed, 30 Jan 2019 15:18:49: start model_add_line... INFO @ Wed, 30 Jan 2019 15:18:49: start X-correlation... INFO @ Wed, 30 Jan 2019 15:18:49: end of X-cor INFO @ Wed, 30 Jan 2019 15:18:49: #2 finished! INFO @ Wed, 30 Jan 2019 15:18:49: #2 predicted fragment length is 280 bps INFO @ Wed, 30 Jan 2019 15:18:49: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 30 Jan 2019 15:18:49: #2.2 Generate R script for model : SRX5064642.20_model.r WARNING @ Wed, 30 Jan 2019 15:18:49: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:18:49: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Wed, 30 Jan 2019 15:18:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:18:49: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:18:51: 22000000 INFO @ Wed, 30 Jan 2019 15:18:58: #1 tag size is determined as 150 bps INFO @ Wed, 30 Jan 2019 15:18:58: #1 tag size = 150 INFO @ Wed, 30 Jan 2019 15:18:58: #1 total tags in treatment: 11062869 INFO @ Wed, 30 Jan 2019 15:18:58: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 15:18:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 15:18:58: #1 tags after filtering in treatment: 9630274 INFO @ Wed, 30 Jan 2019 15:18:58: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 30 Jan 2019 15:18:58: #1 finished! INFO @ Wed, 30 Jan 2019 15:18:58: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 15:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 15:18:59: #2 number of paired peaks: 4086 INFO @ Wed, 30 Jan 2019 15:18:59: start model_add_line... INFO @ Wed, 30 Jan 2019 15:18:59: start X-correlation... INFO @ Wed, 30 Jan 2019 15:18:59: end of X-cor INFO @ Wed, 30 Jan 2019 15:18:59: #2 finished! INFO @ Wed, 30 Jan 2019 15:18:59: #2 predicted fragment length is 280 bps INFO @ Wed, 30 Jan 2019 15:18:59: #2 alternative fragment length(s) may be 280 bps INFO @ Wed, 30 Jan 2019 15:18:59: #2.2 Generate R script for model : SRX5064642.10_model.r WARNING @ Wed, 30 Jan 2019 15:18:59: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 15:18:59: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Wed, 30 Jan 2019 15:18:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 15:18:59: #3 Call peaks... INFO @ Wed, 30 Jan 2019 15:18:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 15:19:21: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:19:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:19:37: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 15:19:37: #4 Write output xls file... SRX5064642.05_peaks.xls INFO @ Wed, 30 Jan 2019 15:19:38: #4 Write peak in narrowPeak format file... SRX5064642.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:19:38: #4 Write summits bed file... SRX5064642.05_summits.bed INFO @ Wed, 30 Jan 2019 15:19:38: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5633 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:19:41: #4 Write output xls file... SRX5064642.20_peaks.xls INFO @ Wed, 30 Jan 2019 15:19:41: #4 Write peak in narrowPeak format file... SRX5064642.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:19:41: #4 Write summits bed file... SRX5064642.20_summits.bed INFO @ Wed, 30 Jan 2019 15:19:41: Done! pass1 - making usageList (6 chroms): 5 millis pass2 - checking and writing primary data (3292 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 15:19:53: #4 Write output xls file... SRX5064642.10_peaks.xls INFO @ Wed, 30 Jan 2019 15:19:53: #4 Write peak in narrowPeak format file... SRX5064642.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 15:19:53: #4 Write summits bed file... SRX5064642.10_summits.bed INFO @ Wed, 30 Jan 2019 15:19:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4421 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。