Job ID = 10714458 sra ファイルのダウンロード中... Completed: 987392K bytes transferred in 26 seconds (302087K 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 15348796 spots for /home/okishinya/chipatlas/results/ce10/SRX4085374/SRR7167403.sra Written 15348796 spots for /home/okishinya/chipatlas/results/ce10/SRX4085374/SRR7167403.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: 00:12:29 15348796 reads; of these: 15348796 (100.00%) were paired; of these: 7048931 (45.92%) aligned concordantly 0 times 7034383 (45.83%) aligned concordantly exactly 1 time 1265482 (8.24%) aligned concordantly >1 times ---- 7048931 pairs aligned concordantly 0 times; of these: 398371 (5.65%) aligned discordantly 1 time ---- 6650560 pairs aligned 0 times concordantly or discordantly; of these: 13301120 mates make up the pairs; of these: 9428071 (70.88%) aligned 0 times 3360006 (25.26%) aligned exactly 1 time 513043 (3.86%) aligned >1 times 69.29% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 531586 / 8572798 = 0.0620 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 12:59:34: # Command line: callpeak -t SRX4085374.bam -f BAM -g ce -n SRX4085374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085374.20 # format = BAM # ChIP-seq file = ['SRX4085374.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 12:59:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:59:34: # Command line: callpeak -t SRX4085374.bam -f BAM -g ce -n SRX4085374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085374.10 # format = BAM # ChIP-seq file = ['SRX4085374.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 12:59:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:59:34: # Command line: callpeak -t SRX4085374.bam -f BAM -g ce -n SRX4085374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085374.05 # format = BAM # ChIP-seq file = ['SRX4085374.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 12:59:34: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:34: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:59:40: 1000000 INFO @ Sun, 03 Jun 2018 12:59:40: 1000000 INFO @ Sun, 03 Jun 2018 12:59:40: 1000000 INFO @ Sun, 03 Jun 2018 12:59:47: 2000000 INFO @ Sun, 03 Jun 2018 12:59:47: 2000000 INFO @ Sun, 03 Jun 2018 12:59:47: 2000000 INFO @ Sun, 03 Jun 2018 12:59:53: 3000000 INFO @ Sun, 03 Jun 2018 12:59:53: 3000000 INFO @ Sun, 03 Jun 2018 12:59:54: 3000000 INFO @ Sun, 03 Jun 2018 13:00:00: 4000000 INFO @ Sun, 03 Jun 2018 13:00:00: 4000000 INFO @ Sun, 03 Jun 2018 13:00:00: 4000000 INFO @ Sun, 03 Jun 2018 13:00:07: 5000000 INFO @ Sun, 03 Jun 2018 13:00:07: 5000000 INFO @ Sun, 03 Jun 2018 13:00:07: 5000000 INFO @ Sun, 03 Jun 2018 13:00:13: 6000000 INFO @ Sun, 03 Jun 2018 13:00:13: 6000000 INFO @ Sun, 03 Jun 2018 13:00:13: 6000000 INFO @ Sun, 03 Jun 2018 13:00:20: 7000000 INFO @ Sun, 03 Jun 2018 13:00:20: 7000000 INFO @ Sun, 03 Jun 2018 13:00:20: 7000000 INFO @ Sun, 03 Jun 2018 13:00:26: 8000000 INFO @ Sun, 03 Jun 2018 13:00:27: 8000000 INFO @ Sun, 03 Jun 2018 13:00:27: 8000000 INFO @ Sun, 03 Jun 2018 13:00:33: 9000000 INFO @ Sun, 03 Jun 2018 13:00:33: 9000000 INFO @ Sun, 03 Jun 2018 13:00:33: 9000000 INFO @ Sun, 03 Jun 2018 13:00:40: 10000000 INFO @ Sun, 03 Jun 2018 13:00:40: 10000000 INFO @ Sun, 03 Jun 2018 13:00:40: 10000000 INFO @ Sun, 03 Jun 2018 13:00:46: 11000000 INFO @ Sun, 03 Jun 2018 13:00:46: 11000000 INFO @ Sun, 03 Jun 2018 13:00:47: 11000000 INFO @ Sun, 03 Jun 2018 13:00:53: 12000000 INFO @ Sun, 03 Jun 2018 13:00:53: 12000000 INFO @ Sun, 03 Jun 2018 13:00:53: 12000000 INFO @ Sun, 03 Jun 2018 13:00:59: 13000000 INFO @ Sun, 03 Jun 2018 13:00:59: 13000000 INFO @ Sun, 03 Jun 2018 13:01:00: 13000000 INFO @ Sun, 03 Jun 2018 13:01:06: 14000000 INFO @ Sun, 03 Jun 2018 13:01:06: 14000000 INFO @ Sun, 03 Jun 2018 13:01:07: 14000000 INFO @ Sun, 03 Jun 2018 13:01:12: 15000000 INFO @ Sun, 03 Jun 2018 13:01:12: 15000000 INFO @ Sun, 03 Jun 2018 13:01:14: 15000000 INFO @ Sun, 03 Jun 2018 13:01:19: 16000000 INFO @ Sun, 03 Jun 2018 13:01:19: 16000000 INFO @ Sun, 03 Jun 2018 13:01:21: 16000000 INFO @ Sun, 03 Jun 2018 13:01:26: 17000000 INFO @ Sun, 03 Jun 2018 13:01:26: 17000000 INFO @ Sun, 03 Jun 2018 13:01:27: 17000000 INFO @ Sun, 03 Jun 2018 13:01:32: 18000000 INFO @ Sun, 03 Jun 2018 13:01:32: 18000000 INFO @ Sun, 03 Jun 2018 13:01:34: 18000000 INFO @ Sun, 03 Jun 2018 13:01:39: 19000000 INFO @ Sun, 03 Jun 2018 13:01:39: 19000000 INFO @ Sun, 03 Jun 2018 13:01:40: 19000000 INFO @ Sun, 03 Jun 2018 13:01:45: 20000000 INFO @ Sun, 03 Jun 2018 13:01:45: 20000000 INFO @ Sun, 03 Jun 2018 13:01:46: 20000000 INFO @ Sun, 03 Jun 2018 13:01:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:47: #1 total tags in treatment: 7786728 INFO @ Sun, 03 Jun 2018 13:01:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:47: #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 13:01:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:47: #1 total tags in treatment: 7786728 INFO @ Sun, 03 Jun 2018 13:01:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:47: #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 13:01:47: #1 tags after filtering in treatment: 6918351 INFO @ Sun, 03 Jun 2018 13:01:47: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:01:47: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:47: #1 tags after filtering in treatment: 6918351 INFO @ Sun, 03 Jun 2018 13:01:47: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:01:47: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:47: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:47: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:47: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:47: #1 total tags in treatment: 7786728 INFO @ Sun, 03 Jun 2018 13:01:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:47: #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 13:01:47: #2 number of paired peaks: 473 WARNING @ Sun, 03 Jun 2018 13:01:47: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:47: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:47: #2 number of paired peaks: 473 WARNING @ Sun, 03 Jun 2018 13:01:47: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:47: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:47: start X-correlation... INFO @ Sun, 03 Jun 2018 13:01:47: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:47: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:47: #2 predicted fragment length is 88 bps INFO @ Sun, 03 Jun 2018 13:01:47: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 03 Jun 2018 13:01:47: #2.2 Generate R script for model : SRX4085374.10_model.r WARNING @ Sun, 03 Jun 2018 13:01:47: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! INFO @ Sun, 03 Jun 2018 13:01:47: start X-correlation... WARNING @ Sun, 03 Jun 2018 13:01:47: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 03 Jun 2018 13:01:47: #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 13:01:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:01:47: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:47: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:47: #2 predicted fragment length is 88 bps INFO @ Sun, 03 Jun 2018 13:01:47: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 03 Jun 2018 13:01:47: #2.2 Generate R script for model : SRX4085374.20_model.r WARNING @ Sun, 03 Jun 2018 13:01:47: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:01:47: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 03 Jun 2018 13:01:47: #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 13:01:47: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:01:48: #1 tags after filtering in treatment: 6918351 INFO @ Sun, 03 Jun 2018 13:01:48: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 03 Jun 2018 13:01:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:48: #2 number of paired peaks: 473 WARNING @ Sun, 03 Jun 2018 13:01:48: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:48: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:48: start X-correlation... INFO @ Sun, 03 Jun 2018 13:01:48: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:48: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:48: #2 predicted fragment length is 88 bps INFO @ Sun, 03 Jun 2018 13:01:48: #2 alternative fragment length(s) may be 88 bps INFO @ Sun, 03 Jun 2018 13:01:48: #2.2 Generate R script for model : SRX4085374.05_model.r WARNING @ Sun, 03 Jun 2018 13:01:48: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:01:48: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Sun, 03 Jun 2018 13:01:48: #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 13:01:48: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:02:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:04: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write output xls file... SRX4085374.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write peak in narrowPeak format file... SRX4085374.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write summits bed file... SRX4085374.20_summits.bed INFO @ Sun, 03 Jun 2018 13:02:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write output xls file... SRX4085374.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write peak in narrowPeak format file... SRX4085374.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:12: #4 Write summits bed file... SRX4085374.10_summits.bed INFO @ Sun, 03 Jun 2018 13:02:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1657 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:14: #4 Write output xls file... SRX4085374.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:14: #4 Write peak in narrowPeak format file... SRX4085374.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:14: #4 Write summits bed file... SRX4085374.05_summits.bed INFO @ Sun, 03 Jun 2018 13:02:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2863 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。