Job ID = 10714505 sra ファイルのダウンロード中... Completed: 1106877K bytes transferred in 14 seconds (631506K 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 17365888 spots for /home/okishinya/chipatlas/results/ce10/SRX4085421/SRR7167450.sra Written 17365888 spots for /home/okishinya/chipatlas/results/ce10/SRX4085421/SRR7167450.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: 00:13:38 17365888 reads; of these: 17365888 (100.00%) were paired; of these: 9090909 (52.35%) aligned concordantly 0 times 6994911 (40.28%) aligned concordantly exactly 1 time 1280068 (7.37%) aligned concordantly >1 times ---- 9090909 pairs aligned concordantly 0 times; of these: 405939 (4.47%) aligned discordantly 1 time ---- 8684970 pairs aligned 0 times concordantly or discordantly; of these: 17369940 mates make up the pairs; of these: 12513283 (72.04%) aligned 0 times 4300508 (24.76%) aligned exactly 1 time 556149 (3.20%) aligned >1 times 63.97% overall alignment rate Time searching: 00:13:38 Overall time: 00:13:38 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] 699195 / 8533271 = 0.0819 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 13:22:39: # Command line: callpeak -t SRX4085421.bam -f BAM -g ce -n SRX4085421.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085421.20 # format = BAM # ChIP-seq file = ['SRX4085421.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 13:22:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:39: # Command line: callpeak -t SRX4085421.bam -f BAM -g ce -n SRX4085421.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085421.10 # format = BAM # ChIP-seq file = ['SRX4085421.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 13:22:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:39: # Command line: callpeak -t SRX4085421.bam -f BAM -g ce -n SRX4085421.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085421.05 # format = BAM # ChIP-seq file = ['SRX4085421.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 13:22:39: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:22:39: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:22:46: 1000000 INFO @ Sun, 03 Jun 2018 13:22:46: 1000000 INFO @ Sun, 03 Jun 2018 13:22:46: 1000000 INFO @ Sun, 03 Jun 2018 13:22:53: 2000000 INFO @ Sun, 03 Jun 2018 13:22:53: 2000000 INFO @ Sun, 03 Jun 2018 13:22:53: 2000000 INFO @ Sun, 03 Jun 2018 13:22:59: 3000000 INFO @ Sun, 03 Jun 2018 13:22:59: 3000000 INFO @ Sun, 03 Jun 2018 13:23:01: 3000000 INFO @ Sun, 03 Jun 2018 13:23:06: 4000000 INFO @ Sun, 03 Jun 2018 13:23:06: 4000000 INFO @ Sun, 03 Jun 2018 13:23:08: 4000000 INFO @ Sun, 03 Jun 2018 13:23:12: 5000000 INFO @ Sun, 03 Jun 2018 13:23:12: 5000000 INFO @ Sun, 03 Jun 2018 13:23:15: 5000000 INFO @ Sun, 03 Jun 2018 13:23:19: 6000000 INFO @ Sun, 03 Jun 2018 13:23:19: 6000000 INFO @ Sun, 03 Jun 2018 13:23:22: 6000000 INFO @ Sun, 03 Jun 2018 13:23:25: 7000000 INFO @ Sun, 03 Jun 2018 13:23:25: 7000000 INFO @ Sun, 03 Jun 2018 13:23:30: 7000000 INFO @ Sun, 03 Jun 2018 13:23:32: 8000000 INFO @ Sun, 03 Jun 2018 13:23:32: 8000000 INFO @ Sun, 03 Jun 2018 13:23:37: 8000000 INFO @ Sun, 03 Jun 2018 13:23:39: 9000000 INFO @ Sun, 03 Jun 2018 13:23:39: 9000000 INFO @ Sun, 03 Jun 2018 13:23:44: 9000000 INFO @ Sun, 03 Jun 2018 13:23:46: 10000000 INFO @ Sun, 03 Jun 2018 13:23:46: 10000000 INFO @ Sun, 03 Jun 2018 13:23:51: 10000000 INFO @ Sun, 03 Jun 2018 13:23:52: 11000000 INFO @ Sun, 03 Jun 2018 13:23:52: 11000000 INFO @ Sun, 03 Jun 2018 13:23:58: 11000000 INFO @ Sun, 03 Jun 2018 13:23:59: 12000000 INFO @ Sun, 03 Jun 2018 13:23:59: 12000000 INFO @ Sun, 03 Jun 2018 13:24:05: 12000000 INFO @ Sun, 03 Jun 2018 13:24:06: 13000000 INFO @ Sun, 03 Jun 2018 13:24:06: 13000000 INFO @ Sun, 03 Jun 2018 13:24:12: 13000000 INFO @ Sun, 03 Jun 2018 13:24:12: 14000000 INFO @ Sun, 03 Jun 2018 13:24:12: 14000000 INFO @ Sun, 03 Jun 2018 13:24:19: 15000000 INFO @ Sun, 03 Jun 2018 13:24:19: 15000000 INFO @ Sun, 03 Jun 2018 13:24:19: 14000000 INFO @ Sun, 03 Jun 2018 13:24:26: 16000000 INFO @ Sun, 03 Jun 2018 13:24:26: 16000000 INFO @ Sun, 03 Jun 2018 13:24:26: 15000000 INFO @ Sun, 03 Jun 2018 13:24:33: 17000000 INFO @ Sun, 03 Jun 2018 13:24:33: 17000000 INFO @ Sun, 03 Jun 2018 13:24:33: 16000000 INFO @ Sun, 03 Jun 2018 13:24:39: 18000000 INFO @ Sun, 03 Jun 2018 13:24:39: 18000000 INFO @ Sun, 03 Jun 2018 13:24:40: 17000000 INFO @ Sun, 03 Jun 2018 13:24:46: 19000000 INFO @ Sun, 03 Jun 2018 13:24:46: 19000000 INFO @ Sun, 03 Jun 2018 13:24:47: 18000000 INFO @ Sun, 03 Jun 2018 13:24:52: 20000000 INFO @ Sun, 03 Jun 2018 13:24:52: 20000000 INFO @ Sun, 03 Jun 2018 13:24:54: 19000000 INFO @ Sun, 03 Jun 2018 13:24:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:57: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:57: #1 total tags in treatment: 7595390 INFO @ Sun, 03 Jun 2018 13:24:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:57: #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 13:24:57: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:24:57: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:24:57: #1 total tags in treatment: 7595390 INFO @ Sun, 03 Jun 2018 13:24:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:24:57: #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 13:24:57: #1 tags after filtering in treatment: 6587272 INFO @ Sun, 03 Jun 2018 13:24:57: #1 tags after filtering in treatment: 6587272 INFO @ Sun, 03 Jun 2018 13:24:57: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:24:57: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:24:57: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:57: #1 finished! INFO @ Sun, 03 Jun 2018 13:24:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:57: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:24:58: #2 number of paired peaks: 535 WARNING @ Sun, 03 Jun 2018 13:24:58: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:58: #2 number of paired peaks: 535 WARNING @ Sun, 03 Jun 2018 13:24:58: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Sun, 03 Jun 2018 13:24:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:24:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:58: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:24:58: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:24:58: #2.2 Generate R script for model : SRX4085421.20_model.r INFO @ Sun, 03 Jun 2018 13:24:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:24:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:24:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:24:58: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:24:58: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:24:58: #2.2 Generate R script for model : SRX4085421.10_model.r WARNING @ Sun, 03 Jun 2018 13:24:58: #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 13:24:58: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:24:58: #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 13:24:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:58: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Jun 2018 13:24:58: #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 13:24:58: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:24:58: #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 13:24:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:01: 20000000 INFO @ Sun, 03 Jun 2018 13:25:06: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:25:06: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:25:06: #1 total tags in treatment: 7595390 INFO @ Sun, 03 Jun 2018 13:25:06: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:25:06: #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 13:25:06: #1 tags after filtering in treatment: 6587272 INFO @ Sun, 03 Jun 2018 13:25:06: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 03 Jun 2018 13:25:06: #1 finished! INFO @ Sun, 03 Jun 2018 13:25:06: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:25:07: #2 number of paired peaks: 535 WARNING @ Sun, 03 Jun 2018 13:25:07: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Sun, 03 Jun 2018 13:25:07: start model_add_line... INFO @ Sun, 03 Jun 2018 13:25:07: start X-correlation... INFO @ Sun, 03 Jun 2018 13:25:07: end of X-cor INFO @ Sun, 03 Jun 2018 13:25:07: #2 finished! INFO @ Sun, 03 Jun 2018 13:25:07: #2 predicted fragment length is 94 bps INFO @ Sun, 03 Jun 2018 13:25:07: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 03 Jun 2018 13:25:07: #2.2 Generate R script for model : SRX4085421.05_model.r WARNING @ Sun, 03 Jun 2018 13:25:07: #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 13:25:07: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 03 Jun 2018 13:25:07: #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 13:25:07: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:25:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:25:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:14: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:21: #4 Write output xls file... SRX4085421.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:21: #4 Write peak in narrowPeak format file... SRX4085421.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:21: #4 Write summits bed file... SRX4085421.20_summits.bed INFO @ Sun, 03 Jun 2018 13:25:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (916 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:25:23: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:25:24: #4 Write output xls file... SRX4085421.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:24: #4 Write peak in narrowPeak format file... SRX4085421.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:24: #4 Write summits bed file... SRX4085421.10_summits.bed INFO @ Sun, 03 Jun 2018 13:25:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:25:32: #4 Write output xls file... SRX4085421.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:25:32: #4 Write peak in narrowPeak format file... SRX4085421.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:25:32: #4 Write summits bed file... SRX4085421.05_summits.bed INFO @ Sun, 03 Jun 2018 13:25:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3631 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。