Job ID = 10714473 sra ファイルのダウンロード中... Completed: 1079179K bytes transferred in 18 seconds (484205K 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 17707544 spots for /home/okishinya/chipatlas/results/ce10/SRX4085389/SRR7167418.sra Written 17707544 spots for /home/okishinya/chipatlas/results/ce10/SRX4085389/SRR7167418.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:00 17707544 reads; of these: 17707544 (100.00%) were paired; of these: 7739060 (43.70%) aligned concordantly 0 times 8776393 (49.56%) aligned concordantly exactly 1 time 1192091 (6.73%) aligned concordantly >1 times ---- 7739060 pairs aligned concordantly 0 times; of these: 433319 (5.60%) aligned discordantly 1 time ---- 7305741 pairs aligned 0 times concordantly or discordantly; of these: 14611482 mates make up the pairs; of these: 10424295 (71.34%) aligned 0 times 3662067 (25.06%) aligned exactly 1 time 525120 (3.59%) aligned >1 times 70.57% overall alignment rate Time searching: 00:14:01 Overall time: 00:14:01 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] 1119151 / 10203369 = 0.1097 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 13:04:38: # Command line: callpeak -t SRX4085389.bam -f BAM -g ce -n SRX4085389.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085389.05 # format = BAM # ChIP-seq file = ['SRX4085389.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 13:04:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:38: # Command line: callpeak -t SRX4085389.bam -f BAM -g ce -n SRX4085389.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085389.10 # format = BAM # ChIP-seq file = ['SRX4085389.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 13:04:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:38: # Command line: callpeak -t SRX4085389.bam -f BAM -g ce -n SRX4085389.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085389.20 # format = BAM # ChIP-seq file = ['SRX4085389.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 13:04:38: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:04:38: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:04:45: 1000000 INFO @ Sun, 03 Jun 2018 13:04:45: 1000000 INFO @ Sun, 03 Jun 2018 13:04:45: 1000000 INFO @ Sun, 03 Jun 2018 13:04:51: 2000000 INFO @ Sun, 03 Jun 2018 13:04:53: 2000000 INFO @ Sun, 03 Jun 2018 13:04:53: 2000000 INFO @ Sun, 03 Jun 2018 13:04:57: 3000000 INFO @ Sun, 03 Jun 2018 13:05:00: 3000000 INFO @ Sun, 03 Jun 2018 13:05:00: 3000000 INFO @ Sun, 03 Jun 2018 13:05:03: 4000000 INFO @ Sun, 03 Jun 2018 13:05:07: 4000000 INFO @ Sun, 03 Jun 2018 13:05:07: 4000000 INFO @ Sun, 03 Jun 2018 13:05:09: 5000000 INFO @ Sun, 03 Jun 2018 13:05:14: 5000000 INFO @ Sun, 03 Jun 2018 13:05:14: 5000000 INFO @ Sun, 03 Jun 2018 13:05:16: 6000000 INFO @ Sun, 03 Jun 2018 13:05:21: 6000000 INFO @ Sun, 03 Jun 2018 13:05:21: 6000000 INFO @ Sun, 03 Jun 2018 13:05:22: 7000000 INFO @ Sun, 03 Jun 2018 13:05:28: 7000000 INFO @ Sun, 03 Jun 2018 13:05:28: 7000000 INFO @ Sun, 03 Jun 2018 13:05:28: 8000000 INFO @ Sun, 03 Jun 2018 13:05:34: 8000000 INFO @ Sun, 03 Jun 2018 13:05:34: 8000000 INFO @ Sun, 03 Jun 2018 13:05:35: 9000000 INFO @ Sun, 03 Jun 2018 13:05:41: 10000000 INFO @ Sun, 03 Jun 2018 13:05:41: 9000000 INFO @ Sun, 03 Jun 2018 13:05:41: 9000000 INFO @ Sun, 03 Jun 2018 13:05:47: 11000000 INFO @ Sun, 03 Jun 2018 13:05:48: 10000000 INFO @ Sun, 03 Jun 2018 13:05:48: 10000000 INFO @ Sun, 03 Jun 2018 13:05:54: 12000000 INFO @ Sun, 03 Jun 2018 13:05:55: 11000000 INFO @ Sun, 03 Jun 2018 13:05:55: 11000000 INFO @ Sun, 03 Jun 2018 13:06:00: 13000000 INFO @ Sun, 03 Jun 2018 13:06:02: 12000000 INFO @ Sun, 03 Jun 2018 13:06:02: 12000000 INFO @ Sun, 03 Jun 2018 13:06:06: 14000000 INFO @ Sun, 03 Jun 2018 13:06:09: 13000000 INFO @ Sun, 03 Jun 2018 13:06:09: 13000000 INFO @ Sun, 03 Jun 2018 13:06:12: 15000000 INFO @ Sun, 03 Jun 2018 13:06:16: 14000000 INFO @ Sun, 03 Jun 2018 13:06:16: 14000000 INFO @ Sun, 03 Jun 2018 13:06:19: 16000000 INFO @ Sun, 03 Jun 2018 13:06:23: 15000000 INFO @ Sun, 03 Jun 2018 13:06:23: 15000000 INFO @ Sun, 03 Jun 2018 13:06:25: 17000000 INFO @ Sun, 03 Jun 2018 13:06:29: 16000000 INFO @ Sun, 03 Jun 2018 13:06:29: 16000000 INFO @ Sun, 03 Jun 2018 13:06:31: 18000000 INFO @ Sun, 03 Jun 2018 13:06:36: 17000000 INFO @ Sun, 03 Jun 2018 13:06:36: 17000000 INFO @ Sun, 03 Jun 2018 13:06:38: 19000000 INFO @ Sun, 03 Jun 2018 13:06:43: 18000000 INFO @ Sun, 03 Jun 2018 13:06:43: 18000000 INFO @ Sun, 03 Jun 2018 13:06:44: 20000000 INFO @ Sun, 03 Jun 2018 13:06:50: 19000000 INFO @ Sun, 03 Jun 2018 13:06:50: 19000000 INFO @ Sun, 03 Jun 2018 13:06:50: 21000000 INFO @ Sun, 03 Jun 2018 13:06:56: 20000000 INFO @ Sun, 03 Jun 2018 13:06:56: 20000000 INFO @ Sun, 03 Jun 2018 13:06:57: 22000000 INFO @ Sun, 03 Jun 2018 13:07:01: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:01: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:01: #1 total tags in treatment: 8874652 INFO @ Sun, 03 Jun 2018 13:07:01: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:01: #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 13:07:02: #1 tags after filtering in treatment: 8067744 INFO @ Sun, 03 Jun 2018 13:07:02: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:07:02: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:02: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:02: #2 number of paired peaks: 175 WARNING @ Sun, 03 Jun 2018 13:07:02: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:02: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:02: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:02: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:02: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:02: #2 predicted fragment length is 73 bps INFO @ Sun, 03 Jun 2018 13:07:02: #2 alternative fragment length(s) may be 4,73,100,121,144,587 bps INFO @ Sun, 03 Jun 2018 13:07:02: #2.2 Generate R script for model : SRX4085389.20_model.r WARNING @ Sun, 03 Jun 2018 13:07:02: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:07:02: #2 You may need to consider one of the other alternative d(s): 4,73,100,121,144,587 WARNING @ Sun, 03 Jun 2018 13:07:02: #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 13:07:02: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:07:03: 21000000 INFO @ Sun, 03 Jun 2018 13:07:03: 21000000 INFO @ Sun, 03 Jun 2018 13:07:10: 22000000 INFO @ Sun, 03 Jun 2018 13:07:10: 22000000 INFO @ Sun, 03 Jun 2018 13:07:15: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:15: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:15: #1 total tags in treatment: 8874652 INFO @ Sun, 03 Jun 2018 13:07:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:15: #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 13:07:15: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:07:15: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:07:15: #1 total tags in treatment: 8874652 INFO @ Sun, 03 Jun 2018 13:07:15: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:07:15: #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 13:07:15: #1 tags after filtering in treatment: 8067744 INFO @ Sun, 03 Jun 2018 13:07:15: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:07:15: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:15: #1 tags after filtering in treatment: 8067744 INFO @ Sun, 03 Jun 2018 13:07:15: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 03 Jun 2018 13:07:15: #1 finished! INFO @ Sun, 03 Jun 2018 13:07:15: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:07:16: #2 number of paired peaks: 175 WARNING @ Sun, 03 Jun 2018 13:07:16: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:16: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:16: #2 number of paired peaks: 175 WARNING @ Sun, 03 Jun 2018 13:07:16: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sun, 03 Jun 2018 13:07:16: start model_add_line... INFO @ Sun, 03 Jun 2018 13:07:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:16: #2 predicted fragment length is 73 bps INFO @ Sun, 03 Jun 2018 13:07:16: #2 alternative fragment length(s) may be 4,73,100,121,144,587 bps INFO @ Sun, 03 Jun 2018 13:07:16: #2.2 Generate R script for model : SRX4085389.10_model.r INFO @ Sun, 03 Jun 2018 13:07:16: start X-correlation... INFO @ Sun, 03 Jun 2018 13:07:16: end of X-cor INFO @ Sun, 03 Jun 2018 13:07:16: #2 finished! INFO @ Sun, 03 Jun 2018 13:07:16: #2 predicted fragment length is 73 bps INFO @ Sun, 03 Jun 2018 13:07:16: #2 alternative fragment length(s) may be 4,73,100,121,144,587 bps INFO @ Sun, 03 Jun 2018 13:07:16: #2.2 Generate R script for model : SRX4085389.05_model.r WARNING @ Sun, 03 Jun 2018 13:07:16: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:07:16: #2 You may need to consider one of the other alternative d(s): 4,73,100,121,144,587 WARNING @ Sun, 03 Jun 2018 13:07:16: #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 13:07:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:16: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Jun 2018 13:07:16: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:07:16: #2 You may need to consider one of the other alternative d(s): 4,73,100,121,144,587 WARNING @ Sun, 03 Jun 2018 13:07:16: #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 13:07:16: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:07:20: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:07:29: #4 Write output xls file... SRX4085389.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:07:29: #4 Write peak in narrowPeak format file... SRX4085389.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:07:29: #4 Write summits bed file... SRX4085389.20_summits.bed INFO @ Sun, 03 Jun 2018 13:07:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:07:33: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:07:33: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:07:42: #4 Write output xls file... SRX4085389.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:07:42: #4 Write peak in narrowPeak format file... SRX4085389.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:07:42: #4 Write summits bed file... SRX4085389.10_summits.bed INFO @ Sun, 03 Jun 2018 13:07:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (202 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:07:43: #4 Write output xls file... SRX4085389.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:07:43: #4 Write peak in narrowPeak format file... SRX4085389.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:07:43: #4 Write summits bed file... SRX4085389.05_summits.bed INFO @ Sun, 03 Jun 2018 13:07:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。