Job ID = 11597670 sra ファイルのダウンロード中... Completed: 1883573K bytes transferred in 26 seconds (593140K 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 13688347 spots for /home/okishinya/chipatlas/results/ce10/ERX1485064/ERR1414281.sra Written 13688347 spots for /home/okishinya/chipatlas/results/ce10/ERX1485064/ERR1414281.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: 00:34:15 13688347 reads; of these: 13688347 (100.00%) were paired; of these: 471865 (3.45%) aligned concordantly 0 times 9923364 (72.49%) aligned concordantly exactly 1 time 3293118 (24.06%) aligned concordantly >1 times ---- 471865 pairs aligned concordantly 0 times; of these: 67732 (14.35%) aligned discordantly 1 time ---- 404133 pairs aligned 0 times concordantly or discordantly; of these: 808266 mates make up the pairs; of these: 413097 (51.11%) aligned 0 times 211123 (26.12%) aligned exactly 1 time 184046 (22.77%) aligned >1 times 98.49% overall alignment rate Time searching: 00:34:15 Overall time: 00:34:16 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 12 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] 4248137 / 13240458 = 0.3208 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 21:43:35: # Command line: callpeak -t ERX1485064.bam -f BAM -g ce -n ERX1485064.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1485064.05 # format = BAM # ChIP-seq file = ['ERX1485064.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 21:43:35: # Command line: callpeak -t ERX1485064.bam -f BAM -g ce -n ERX1485064.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1485064.20 # format = BAM # ChIP-seq file = ['ERX1485064.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 21:43:35: # Command line: callpeak -t ERX1485064.bam -f BAM -g ce -n ERX1485064.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1485064.10 # format = BAM # ChIP-seq file = ['ERX1485064.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 21:43:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:43:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:43:35: #1 read tag files... INFO @ Wed, 30 Jan 2019 21:43:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:43:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:43:35: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 21:43:43: 1000000 INFO @ Wed, 30 Jan 2019 21:43:43: 1000000 INFO @ Wed, 30 Jan 2019 21:43:43: 1000000 INFO @ Wed, 30 Jan 2019 21:43:51: 2000000 INFO @ Wed, 30 Jan 2019 21:43:51: 2000000 INFO @ Wed, 30 Jan 2019 21:43:51: 2000000 INFO @ Wed, 30 Jan 2019 21:43:58: 3000000 INFO @ Wed, 30 Jan 2019 21:43:59: 3000000 INFO @ Wed, 30 Jan 2019 21:43:59: 3000000 INFO @ Wed, 30 Jan 2019 21:44:06: 4000000 INFO @ Wed, 30 Jan 2019 21:44:07: 4000000 INFO @ Wed, 30 Jan 2019 21:44:07: 4000000 INFO @ Wed, 30 Jan 2019 21:44:14: 5000000 INFO @ Wed, 30 Jan 2019 21:44:15: 5000000 INFO @ Wed, 30 Jan 2019 21:44:15: 5000000 INFO @ Wed, 30 Jan 2019 21:44:22: 6000000 INFO @ Wed, 30 Jan 2019 21:44:23: 6000000 INFO @ Wed, 30 Jan 2019 21:44:23: 6000000 INFO @ Wed, 30 Jan 2019 21:44:30: 7000000 INFO @ Wed, 30 Jan 2019 21:44:31: 7000000 INFO @ Wed, 30 Jan 2019 21:44:32: 7000000 INFO @ Wed, 30 Jan 2019 21:44:38: 8000000 INFO @ Wed, 30 Jan 2019 21:44:40: 8000000 INFO @ Wed, 30 Jan 2019 21:44:40: 8000000 INFO @ Wed, 30 Jan 2019 21:44:45: 9000000 INFO @ Wed, 30 Jan 2019 21:44:48: 9000000 INFO @ Wed, 30 Jan 2019 21:44:48: 9000000 INFO @ Wed, 30 Jan 2019 21:44:53: 10000000 INFO @ Wed, 30 Jan 2019 21:44:56: 10000000 INFO @ Wed, 30 Jan 2019 21:44:56: 10000000 INFO @ Wed, 30 Jan 2019 21:45:01: 11000000 INFO @ Wed, 30 Jan 2019 21:45:05: 11000000 INFO @ Wed, 30 Jan 2019 21:45:05: 11000000 INFO @ Wed, 30 Jan 2019 21:45:09: 12000000 INFO @ Wed, 30 Jan 2019 21:45:13: 12000000 INFO @ Wed, 30 Jan 2019 21:45:13: 12000000 INFO @ Wed, 30 Jan 2019 21:45:17: 13000000 INFO @ Wed, 30 Jan 2019 21:45:21: 13000000 INFO @ Wed, 30 Jan 2019 21:45:21: 13000000 INFO @ Wed, 30 Jan 2019 21:45:25: 14000000 INFO @ Wed, 30 Jan 2019 21:45:29: 14000000 INFO @ Wed, 30 Jan 2019 21:45:29: 14000000 INFO @ Wed, 30 Jan 2019 21:45:33: 15000000 INFO @ Wed, 30 Jan 2019 21:45:37: 15000000 INFO @ Wed, 30 Jan 2019 21:45:37: 15000000 INFO @ Wed, 30 Jan 2019 21:45:40: 16000000 INFO @ Wed, 30 Jan 2019 21:45:45: 16000000 INFO @ Wed, 30 Jan 2019 21:45:45: 16000000 INFO @ Wed, 30 Jan 2019 21:45:48: 17000000 INFO @ Wed, 30 Jan 2019 21:45:53: 17000000 INFO @ Wed, 30 Jan 2019 21:45:53: 17000000 INFO @ Wed, 30 Jan 2019 21:45:56: 18000000 INFO @ Wed, 30 Jan 2019 21:45:59: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 21:45:59: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 21:45:59: #1 total tags in treatment: 8979455 INFO @ Wed, 30 Jan 2019 21:45:59: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:45:59: #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 21:46:00: #1 tags after filtering in treatment: 7194247 INFO @ Wed, 30 Jan 2019 21:46:00: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 30 Jan 2019 21:46:00: #1 finished! INFO @ Wed, 30 Jan 2019 21:46:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:46:00: #2 number of paired peaks: 1404 INFO @ Wed, 30 Jan 2019 21:46:00: start model_add_line... INFO @ Wed, 30 Jan 2019 21:46:00: start X-correlation... INFO @ Wed, 30 Jan 2019 21:46:00: end of X-cor INFO @ Wed, 30 Jan 2019 21:46:00: #2 finished! INFO @ Wed, 30 Jan 2019 21:46:00: #2 predicted fragment length is 176 bps INFO @ Wed, 30 Jan 2019 21:46:00: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 30 Jan 2019 21:46:00: #2.2 Generate R script for model : ERX1485064.10_model.r WARNING @ Wed, 30 Jan 2019 21:46:00: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:46:00: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 30 Jan 2019 21:46:00: #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 21:46:00: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:46:01: 18000000 INFO @ Wed, 30 Jan 2019 21:46:01: 18000000 INFO @ Wed, 30 Jan 2019 21:46:05: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 21:46:05: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 21:46:05: #1 total tags in treatment: 8979455 INFO @ Wed, 30 Jan 2019 21:46:05: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:46:05: #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 21:46:05: #1 tag size is determined as 101 bps INFO @ Wed, 30 Jan 2019 21:46:05: #1 tag size = 101 INFO @ Wed, 30 Jan 2019 21:46:05: #1 total tags in treatment: 8979455 INFO @ Wed, 30 Jan 2019 21:46:05: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 21:46:05: #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 21:46:05: #1 tags after filtering in treatment: 7194247 INFO @ Wed, 30 Jan 2019 21:46:05: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 30 Jan 2019 21:46:05: #1 finished! INFO @ Wed, 30 Jan 2019 21:46:05: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:46:05: #1 tags after filtering in treatment: 7194247 INFO @ Wed, 30 Jan 2019 21:46:05: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 30 Jan 2019 21:46:05: #1 finished! INFO @ Wed, 30 Jan 2019 21:46:05: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 21:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 21:46:06: #2 number of paired peaks: 1404 INFO @ Wed, 30 Jan 2019 21:46:06: start model_add_line... INFO @ Wed, 30 Jan 2019 21:46:06: start X-correlation... INFO @ Wed, 30 Jan 2019 21:46:06: end of X-cor INFO @ Wed, 30 Jan 2019 21:46:06: #2 finished! INFO @ Wed, 30 Jan 2019 21:46:06: #2 predicted fragment length is 176 bps INFO @ Wed, 30 Jan 2019 21:46:06: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 30 Jan 2019 21:46:06: #2.2 Generate R script for model : ERX1485064.05_model.r WARNING @ Wed, 30 Jan 2019 21:46:06: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:46:06: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 30 Jan 2019 21:46:06: #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 21:46:06: #2 number of paired peaks: 1404 INFO @ Wed, 30 Jan 2019 21:46:06: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:46:06: start model_add_line... INFO @ Wed, 30 Jan 2019 21:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:46:06: start X-correlation... INFO @ Wed, 30 Jan 2019 21:46:06: end of X-cor INFO @ Wed, 30 Jan 2019 21:46:06: #2 finished! INFO @ Wed, 30 Jan 2019 21:46:06: #2 predicted fragment length is 176 bps INFO @ Wed, 30 Jan 2019 21:46:06: #2 alternative fragment length(s) may be 176 bps INFO @ Wed, 30 Jan 2019 21:46:06: #2.2 Generate R script for model : ERX1485064.20_model.r WARNING @ Wed, 30 Jan 2019 21:46:06: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 21:46:06: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Wed, 30 Jan 2019 21:46:06: #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 21:46:06: #3 Call peaks... INFO @ Wed, 30 Jan 2019 21:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 21:46:20: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:46:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:46:28: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 21:46:30: #4 Write output xls file... ERX1485064.10_peaks.xls INFO @ Wed, 30 Jan 2019 21:46:30: #4 Write peak in narrowPeak format file... ERX1485064.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:46:30: #4 Write summits bed file... ERX1485064.10_summits.bed INFO @ Wed, 30 Jan 2019 21:46:30: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (15183 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 21:46:37: #4 Write output xls file... ERX1485064.20_peaks.xls INFO @ Wed, 30 Jan 2019 21:46:37: #4 Write peak in narrowPeak format file... ERX1485064.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:46:37: #4 Write summits bed file... ERX1485064.20_summits.bed INFO @ Wed, 30 Jan 2019 21:46:37: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4661 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 21:46:38: #4 Write output xls file... ERX1485064.05_peaks.xls INFO @ Wed, 30 Jan 2019 21:46:38: #4 Write peak in narrowPeak format file... ERX1485064.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 21:46:38: #4 Write summits bed file... ERX1485064.05_summits.bed INFO @ Wed, 30 Jan 2019 21:46:38: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (24316 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。