Job ID = 10714493 sra ファイルのダウンロード中... Completed: 1356748K bytes transferred in 18 seconds (592057K 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 20844202 spots for /home/okishinya/chipatlas/results/ce10/SRX4085410/SRR7167439.sra Written 20844202 spots for /home/okishinya/chipatlas/results/ce10/SRX4085410/SRR7167439.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: 00:12:17 20844202 reads; of these: 20844202 (100.00%) were paired; of these: 14111215 (67.70%) aligned concordantly 0 times 5782922 (27.74%) aligned concordantly exactly 1 time 950065 (4.56%) aligned concordantly >1 times ---- 14111215 pairs aligned concordantly 0 times; of these: 313327 (2.22%) aligned discordantly 1 time ---- 13797888 pairs aligned 0 times concordantly or discordantly; of these: 27595776 mates make up the pairs; of these: 22144087 (80.24%) aligned 0 times 4875162 (17.67%) aligned exactly 1 time 576527 (2.09%) aligned >1 times 46.88% overall alignment rate Time searching: 00:12:18 Overall time: 00:12:18 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 8 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] 1847509 / 6940180 = 0.2662 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 @ Sun, 03 Jun 2018 13:13:02: # Command line: callpeak -t SRX4085410.bam -f BAM -g ce -n SRX4085410.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085410.05 # format = BAM # ChIP-seq file = ['SRX4085410.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 @ Sun, 03 Jun 2018 13:13:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:13:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:13:02: # Command line: callpeak -t SRX4085410.bam -f BAM -g ce -n SRX4085410.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085410.20 # format = BAM # ChIP-seq file = ['SRX4085410.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 @ Sun, 03 Jun 2018 13:13:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:13:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:13:02: # Command line: callpeak -t SRX4085410.bam -f BAM -g ce -n SRX4085410.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085410.10 # format = BAM # ChIP-seq file = ['SRX4085410.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 @ Sun, 03 Jun 2018 13:13:02: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:13:02: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:13:07: 1000000 INFO @ Sun, 03 Jun 2018 13:13:08: 1000000 INFO @ Sun, 03 Jun 2018 13:13:08: 1000000 INFO @ Sun, 03 Jun 2018 13:13:13: 2000000 INFO @ Sun, 03 Jun 2018 13:13:14: 2000000 INFO @ Sun, 03 Jun 2018 13:13:14: 2000000 INFO @ Sun, 03 Jun 2018 13:13:19: 3000000 INFO @ Sun, 03 Jun 2018 13:13:20: 3000000 INFO @ Sun, 03 Jun 2018 13:13:20: 3000000 INFO @ Sun, 03 Jun 2018 13:13:25: 4000000 INFO @ Sun, 03 Jun 2018 13:13:25: 4000000 INFO @ Sun, 03 Jun 2018 13:13:25: 4000000 INFO @ Sun, 03 Jun 2018 13:13:30: 5000000 INFO @ Sun, 03 Jun 2018 13:13:31: 5000000 INFO @ Sun, 03 Jun 2018 13:13:31: 5000000 INFO @ Sun, 03 Jun 2018 13:13:36: 6000000 INFO @ Sun, 03 Jun 2018 13:13:37: 6000000 INFO @ Sun, 03 Jun 2018 13:13:37: 6000000 INFO @ Sun, 03 Jun 2018 13:13:42: 7000000 INFO @ Sun, 03 Jun 2018 13:13:43: 7000000 INFO @ Sun, 03 Jun 2018 13:13:43: 7000000 INFO @ Sun, 03 Jun 2018 13:13:47: 8000000 INFO @ Sun, 03 Jun 2018 13:13:49: 8000000 INFO @ Sun, 03 Jun 2018 13:13:49: 8000000 INFO @ Sun, 03 Jun 2018 13:13:53: 9000000 INFO @ Sun, 03 Jun 2018 13:13:55: 9000000 INFO @ Sun, 03 Jun 2018 13:13:55: 9000000 INFO @ Sun, 03 Jun 2018 13:13:59: 10000000 INFO @ Sun, 03 Jun 2018 13:14:01: 10000000 INFO @ Sun, 03 Jun 2018 13:14:01: 10000000 INFO @ Sun, 03 Jun 2018 13:14:05: 11000000 INFO @ Sun, 03 Jun 2018 13:14:07: 11000000 INFO @ Sun, 03 Jun 2018 13:14:07: 11000000 INFO @ Sun, 03 Jun 2018 13:14:10: 12000000 INFO @ Sun, 03 Jun 2018 13:14:13: 12000000 INFO @ Sun, 03 Jun 2018 13:14:13: 12000000 INFO @ Sun, 03 Jun 2018 13:14:16: 13000000 INFO @ Sun, 03 Jun 2018 13:14:19: 13000000 INFO @ Sun, 03 Jun 2018 13:14:19: 13000000 INFO @ Sun, 03 Jun 2018 13:14:22: 14000000 INFO @ Sun, 03 Jun 2018 13:14:25: 14000000 INFO @ Sun, 03 Jun 2018 13:14:25: 14000000 INFO @ Sun, 03 Jun 2018 13:14:28: 15000000 INFO @ Sun, 03 Jun 2018 13:14:30: 15000000 INFO @ Sun, 03 Jun 2018 13:14:30: 15000000 INFO @ Sun, 03 Jun 2018 13:14:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:32: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:32: #1 total tags in treatment: 4957182 INFO @ Sun, 03 Jun 2018 13:14:32: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:32: #1 tags after filtering in treatment: 4332108 INFO @ Sun, 03 Jun 2018 13:14:32: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:14:32: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:32: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:33: #2 number of paired peaks: 518 WARNING @ Sun, 03 Jun 2018 13:14:33: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:33: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:33: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:33: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:33: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:33: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:14:33: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:14:33: #2.2 Generate R script for model : SRX4085410.05_model.r WARNING @ Sun, 03 Jun 2018 13:14:33: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:33: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:14:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:33: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:34: #1 total tags in treatment: 4957182 INFO @ Sun, 03 Jun 2018 13:14:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:34: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:14:34: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:14:34: #1 total tags in treatment: 4957182 INFO @ Sun, 03 Jun 2018 13:14:34: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:14:34: #1 tags after filtering in treatment: 4332108 INFO @ Sun, 03 Jun 2018 13:14:34: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:14:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:34: #1 tags after filtering in treatment: 4332108 INFO @ Sun, 03 Jun 2018 13:14:34: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:14:34: #1 finished! INFO @ Sun, 03 Jun 2018 13:14:34: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:14:35: #2 number of paired peaks: 518 WARNING @ Sun, 03 Jun 2018 13:14:35: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:35: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:35: #2 number of paired peaks: 518 WARNING @ Sun, 03 Jun 2018 13:14:35: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 03 Jun 2018 13:14:35: start model_add_line... INFO @ Sun, 03 Jun 2018 13:14:35: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:35: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:35: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:35: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:14:35: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:14:35: #2.2 Generate R script for model : SRX4085410.20_model.r WARNING @ Sun, 03 Jun 2018 13:14:35: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:35: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:14:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:35: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:35: start X-correlation... INFO @ Sun, 03 Jun 2018 13:14:35: end of X-cor INFO @ Sun, 03 Jun 2018 13:14:35: #2 finished! INFO @ Sun, 03 Jun 2018 13:14:35: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:14:35: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:14:35: #2.2 Generate R script for model : SRX4085410.10_model.r WARNING @ Sun, 03 Jun 2018 13:14:35: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:14:35: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:14:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:14:35: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:14:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:46: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:14:49: #4 Write output xls file... SRX4085410.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:49: #4 Write peak in narrowPeak format file... SRX4085410.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:49: #4 Write summits bed file... SRX4085410.05_summits.bed INFO @ Sun, 03 Jun 2018 13:14:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2247 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:14:50: #4 Write output xls file... SRX4085410.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:50: #4 Write peak in narrowPeak format file... SRX4085410.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:50: #4 Write summits bed file... SRX4085410.10_summits.bed INFO @ Sun, 03 Jun 2018 13:14:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1212 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:14:51: #4 Write output xls file... SRX4085410.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:14:51: #4 Write peak in narrowPeak format file... SRX4085410.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:14:51: #4 Write summits bed file... SRX4085410.20_summits.bed INFO @ Sun, 03 Jun 2018 13:14:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。