Job ID = 10714463 sra ファイルのダウンロード中... Completed: 989394K bytes transferred in 85 seconds (94299K 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 15617541 spots for /home/okishinya/chipatlas/results/ce10/SRX4085379/SRR7167408.sra Written 15617541 spots for /home/okishinya/chipatlas/results/ce10/SRX4085379/SRR7167408.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: 00:12:00 15617541 reads; of these: 15617541 (100.00%) were paired; of these: 10034576 (64.25%) aligned concordantly 0 times 4859697 (31.12%) aligned concordantly exactly 1 time 723268 (4.63%) aligned concordantly >1 times ---- 10034576 pairs aligned concordantly 0 times; of these: 385562 (3.84%) aligned discordantly 1 time ---- 9649014 pairs aligned 0 times concordantly or discordantly; of these: 19298028 mates make up the pairs; of these: 13450784 (69.70%) aligned 0 times 5181712 (26.85%) aligned exactly 1 time 665532 (3.45%) aligned >1 times 56.94% overall alignment rate Time searching: 00:12:00 Overall time: 00:12:00 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] 329612 / 5820044 = 0.0566 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 12:59:57: # Command line: callpeak -t SRX4085379.bam -f BAM -g ce -n SRX4085379.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085379.10 # format = BAM # ChIP-seq file = ['SRX4085379.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 12:59:57: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:57: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:59:57: # Command line: callpeak -t SRX4085379.bam -f BAM -g ce -n SRX4085379.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085379.05 # format = BAM # ChIP-seq file = ['SRX4085379.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 12:59:57: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:57: # Command line: callpeak -t SRX4085379.bam -f BAM -g ce -n SRX4085379.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085379.20 # format = BAM # ChIP-seq file = ['SRX4085379.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 12:59:57: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:59:57: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:59:57: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:00:03: 1000000 INFO @ Sun, 03 Jun 2018 13:00:03: 1000000 INFO @ Sun, 03 Jun 2018 13:00:03: 1000000 INFO @ Sun, 03 Jun 2018 13:00:09: 2000000 INFO @ Sun, 03 Jun 2018 13:00:10: 2000000 INFO @ Sun, 03 Jun 2018 13:00:10: 2000000 INFO @ Sun, 03 Jun 2018 13:00:15: 3000000 INFO @ Sun, 03 Jun 2018 13:00:17: 3000000 INFO @ Sun, 03 Jun 2018 13:00:17: 3000000 INFO @ Sun, 03 Jun 2018 13:00:21: 4000000 INFO @ Sun, 03 Jun 2018 13:00:24: 4000000 INFO @ Sun, 03 Jun 2018 13:00:24: 4000000 INFO @ Sun, 03 Jun 2018 13:00:27: 5000000 INFO @ Sun, 03 Jun 2018 13:00:31: 5000000 INFO @ Sun, 03 Jun 2018 13:00:32: 5000000 INFO @ Sun, 03 Jun 2018 13:00:33: 6000000 INFO @ Sun, 03 Jun 2018 13:00:39: 6000000 INFO @ Sun, 03 Jun 2018 13:00:39: 6000000 INFO @ Sun, 03 Jun 2018 13:00:39: 7000000 INFO @ Sun, 03 Jun 2018 13:00:45: 7000000 INFO @ Sun, 03 Jun 2018 13:00:45: 7000000 INFO @ Sun, 03 Jun 2018 13:00:46: 8000000 INFO @ Sun, 03 Jun 2018 13:00:52: 8000000 INFO @ Sun, 03 Jun 2018 13:00:52: 9000000 INFO @ Sun, 03 Jun 2018 13:00:52: 8000000 INFO @ Sun, 03 Jun 2018 13:00:58: 9000000 INFO @ Sun, 03 Jun 2018 13:00:59: 10000000 INFO @ Sun, 03 Jun 2018 13:00:59: 9000000 INFO @ Sun, 03 Jun 2018 13:01:05: 10000000 INFO @ Sun, 03 Jun 2018 13:01:05: 11000000 INFO @ Sun, 03 Jun 2018 13:01:06: 10000000 INFO @ Sun, 03 Jun 2018 13:01:11: 11000000 INFO @ Sun, 03 Jun 2018 13:01:12: 12000000 INFO @ Sun, 03 Jun 2018 13:01:13: 11000000 INFO @ Sun, 03 Jun 2018 13:01:18: 12000000 INFO @ Sun, 03 Jun 2018 13:01:19: 13000000 INFO @ Sun, 03 Jun 2018 13:01:19: 12000000 INFO @ Sun, 03 Jun 2018 13:01:25: 13000000 INFO @ Sun, 03 Jun 2018 13:01:25: 14000000 INFO @ Sun, 03 Jun 2018 13:01:26: 13000000 INFO @ Sun, 03 Jun 2018 13:01:31: 14000000 INFO @ Sun, 03 Jun 2018 13:01:32: 15000000 INFO @ Sun, 03 Jun 2018 13:01:33: 14000000 INFO @ Sun, 03 Jun 2018 13:01:37: 15000000 INFO @ Sun, 03 Jun 2018 13:01:38: 16000000 INFO @ Sun, 03 Jun 2018 13:01:39: 15000000 INFO @ Sun, 03 Jun 2018 13:01:43: 17000000 INFO @ Sun, 03 Jun 2018 13:01:44: 16000000 INFO @ Sun, 03 Jun 2018 13:01:44: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:44: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:44: #1 total tags in treatment: 5266244 INFO @ Sun, 03 Jun 2018 13:01:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:44: #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 13:01:44: #1 tags after filtering in treatment: 4824510 INFO @ Sun, 03 Jun 2018 13:01:44: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:01:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:45: #2 number of paired peaks: 340 WARNING @ Sun, 03 Jun 2018 13:01:45: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:45: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:45: start X-correlation... INFO @ Sun, 03 Jun 2018 13:01:45: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:45: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:45: #2 predicted fragment length is 72 bps INFO @ Sun, 03 Jun 2018 13:01:45: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 03 Jun 2018 13:01:45: #2.2 Generate R script for model : SRX4085379.20_model.r WARNING @ Sun, 03 Jun 2018 13:01:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:01:45: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 03 Jun 2018 13:01:45: #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 13:01:45: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:01:45: 16000000 INFO @ Sun, 03 Jun 2018 13:01:49: 17000000 INFO @ Sun, 03 Jun 2018 13:01:50: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:50: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:50: #1 total tags in treatment: 5266244 INFO @ Sun, 03 Jun 2018 13:01:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:50: #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 13:01:50: #1 tags after filtering in treatment: 4824510 INFO @ Sun, 03 Jun 2018 13:01:50: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:01:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:51: 17000000 INFO @ Sun, 03 Jun 2018 13:01:51: #2 number of paired peaks: 340 WARNING @ Sun, 03 Jun 2018 13:01:51: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:51: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:51: start X-correlation... INFO @ Sun, 03 Jun 2018 13:01:51: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:51: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:51: #2 predicted fragment length is 72 bps INFO @ Sun, 03 Jun 2018 13:01:51: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 03 Jun 2018 13:01:51: #2.2 Generate R script for model : SRX4085379.10_model.r WARNING @ Sun, 03 Jun 2018 13:01:51: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:01:51: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 03 Jun 2018 13:01:51: #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 13:01:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:01:51: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:01:51: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:01:51: #1 total tags in treatment: 5266244 INFO @ Sun, 03 Jun 2018 13:01:51: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:01:51: #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 13:01:51: #1 tags after filtering in treatment: 4824510 INFO @ Sun, 03 Jun 2018 13:01:51: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 03 Jun 2018 13:01:51: #1 finished! INFO @ Sun, 03 Jun 2018 13:01:51: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:01:52: #2 number of paired peaks: 340 WARNING @ Sun, 03 Jun 2018 13:01:52: Fewer paired peaks (340) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 340 pairs to build model! INFO @ Sun, 03 Jun 2018 13:01:52: start model_add_line... INFO @ Sun, 03 Jun 2018 13:01:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:01:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:01:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:01:52: #2 predicted fragment length is 72 bps INFO @ Sun, 03 Jun 2018 13:01:52: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 03 Jun 2018 13:01:52: #2.2 Generate R script for model : SRX4085379.05_model.r WARNING @ Sun, 03 Jun 2018 13:01:52: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:01:52: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 03 Jun 2018 13:01:52: #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 13:01:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:01:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:01:56: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:02: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:02: #4 Write output xls file... SRX4085379.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:02: #4 Write peak in narrowPeak format file... SRX4085379.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:02: #4 Write summits bed file... SRX4085379.20_summits.bed INFO @ Sun, 03 Jun 2018 13:02:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:03: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write output xls file... SRX4085379.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write peak in narrowPeak format file... SRX4085379.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write summits bed file... SRX4085379.10_summits.bed INFO @ Sun, 03 Jun 2018 13:02:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write output xls file... SRX4085379.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write peak in narrowPeak format file... SRX4085379.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:02:09: #4 Write summits bed file... SRX4085379.05_summits.bed INFO @ Sun, 03 Jun 2018 13:02:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1475 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。