Job ID = 10714498 sra ファイルのダウンロード中... Completed: 948756K bytes transferred in 13 seconds (583733K 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 14884254 spots for /home/okishinya/chipatlas/results/ce10/SRX4085415/SRR7167444.sra Written 14884254 spots for /home/okishinya/chipatlas/results/ce10/SRX4085415/SRR7167444.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: 00:09:25 14884254 reads; of these: 14884254 (100.00%) were paired; of these: 11395232 (76.56%) aligned concordantly 0 times 3032126 (20.37%) aligned concordantly exactly 1 time 456896 (3.07%) aligned concordantly >1 times ---- 11395232 pairs aligned concordantly 0 times; of these: 213995 (1.88%) aligned discordantly 1 time ---- 11181237 pairs aligned 0 times concordantly or discordantly; of these: 22362474 mates make up the pairs; of these: 15506637 (69.34%) aligned 0 times 6067530 (27.13%) aligned exactly 1 time 788307 (3.53%) aligned >1 times 47.91% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 237648 / 3575468 = 0.0665 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 13:10:56: # Command line: callpeak -t SRX4085415.bam -f BAM -g ce -n SRX4085415.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4085415.05 # format = BAM # ChIP-seq file = ['SRX4085415.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 13:10:56: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:56: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:10:56: # Command line: callpeak -t SRX4085415.bam -f BAM -g ce -n SRX4085415.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4085415.10 # format = BAM # ChIP-seq file = ['SRX4085415.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 13:10:56: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:56: # Command line: callpeak -t SRX4085415.bam -f BAM -g ce -n SRX4085415.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4085415.20 # format = BAM # ChIP-seq file = ['SRX4085415.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 13:10:56: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:10:56: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:10:56: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:11:02: 1000000 INFO @ Sun, 03 Jun 2018 13:11:03: 1000000 INFO @ Sun, 03 Jun 2018 13:11:03: 1000000 INFO @ Sun, 03 Jun 2018 13:11:08: 2000000 INFO @ Sun, 03 Jun 2018 13:11:09: 2000000 INFO @ Sun, 03 Jun 2018 13:11:09: 2000000 INFO @ Sun, 03 Jun 2018 13:11:14: 3000000 INFO @ Sun, 03 Jun 2018 13:11:15: 3000000 INFO @ Sun, 03 Jun 2018 13:11:15: 3000000 INFO @ Sun, 03 Jun 2018 13:11:20: 4000000 INFO @ Sun, 03 Jun 2018 13:11:21: 4000000 INFO @ Sun, 03 Jun 2018 13:11:21: 4000000 INFO @ Sun, 03 Jun 2018 13:11:26: 5000000 INFO @ Sun, 03 Jun 2018 13:11:27: 5000000 INFO @ Sun, 03 Jun 2018 13:11:27: 5000000 INFO @ Sun, 03 Jun 2018 13:11:32: 6000000 INFO @ Sun, 03 Jun 2018 13:11:34: 6000000 INFO @ Sun, 03 Jun 2018 13:11:34: 6000000 INFO @ Sun, 03 Jun 2018 13:11:38: 7000000 INFO @ Sun, 03 Jun 2018 13:11:40: 7000000 INFO @ Sun, 03 Jun 2018 13:11:40: 7000000 INFO @ Sun, 03 Jun 2018 13:11:44: 8000000 INFO @ Sun, 03 Jun 2018 13:11:46: 8000000 INFO @ Sun, 03 Jun 2018 13:11:46: 8000000 INFO @ Sun, 03 Jun 2018 13:11:50: 9000000 INFO @ Sun, 03 Jun 2018 13:11:52: 9000000 INFO @ Sun, 03 Jun 2018 13:11:52: 9000000 INFO @ Sun, 03 Jun 2018 13:11:56: 10000000 INFO @ Sun, 03 Jun 2018 13:11:58: 10000000 INFO @ Sun, 03 Jun 2018 13:11:58: 10000000 INFO @ Sun, 03 Jun 2018 13:12:01: 11000000 INFO @ Sun, 03 Jun 2018 13:12:04: 11000000 INFO @ Sun, 03 Jun 2018 13:12:04: 11000000 INFO @ Sun, 03 Jun 2018 13:12:07: 12000000 INFO @ Sun, 03 Jun 2018 13:12:10: 12000000 INFO @ Sun, 03 Jun 2018 13:12:10: 12000000 INFO @ Sun, 03 Jun 2018 13:12:13: 13000000 INFO @ Sun, 03 Jun 2018 13:12:16: 13000000 INFO @ Sun, 03 Jun 2018 13:12:16: 13000000 INFO @ Sun, 03 Jun 2018 13:12:17: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:17: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:17: #1 total tags in treatment: 3255204 INFO @ Sun, 03 Jun 2018 13:12:17: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:17: #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 13:12:17: #1 tags after filtering in treatment: 3058018 INFO @ Sun, 03 Jun 2018 13:12:17: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:12:17: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:17: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:18: #2 number of paired peaks: 186 WARNING @ Sun, 03 Jun 2018 13:12:18: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:18: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:18: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:18: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:18: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:18: #2 predicted fragment length is 93 bps INFO @ Sun, 03 Jun 2018 13:12:18: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Sun, 03 Jun 2018 13:12:18: #2.2 Generate R script for model : SRX4085415.05_model.r WARNING @ Sun, 03 Jun 2018 13:12:18: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:18: #2 You may need to consider one of the other alternative d(s): 93,140,166 WARNING @ Sun, 03 Jun 2018 13:12:18: #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 13:12:18: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:21: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:21: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:21: #1 total tags in treatment: 3255204 INFO @ Sun, 03 Jun 2018 13:12:21: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:21: #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 13:12:21: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 13:12:21: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 13:12:21: #1 total tags in treatment: 3255204 INFO @ Sun, 03 Jun 2018 13:12:21: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:12:21: #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 13:12:21: #1 tags after filtering in treatment: 3058018 INFO @ Sun, 03 Jun 2018 13:12:21: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:12:21: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:21: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:21: #1 tags after filtering in treatment: 3058018 INFO @ Sun, 03 Jun 2018 13:12:21: #1 Redundant rate of treatment: 0.06 INFO @ Sun, 03 Jun 2018 13:12:21: #1 finished! INFO @ Sun, 03 Jun 2018 13:12:21: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:12:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:12:21: #2 number of paired peaks: 186 WARNING @ Sun, 03 Jun 2018 13:12:21: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:21: #2 number of paired peaks: 186 WARNING @ Sun, 03 Jun 2018 13:12:21: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 03 Jun 2018 13:12:21: start model_add_line... INFO @ Sun, 03 Jun 2018 13:12:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:21: start X-correlation... INFO @ Sun, 03 Jun 2018 13:12:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:21: end of X-cor INFO @ Sun, 03 Jun 2018 13:12:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:21: #2 finished! INFO @ Sun, 03 Jun 2018 13:12:21: #2 predicted fragment length is 93 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2 predicted fragment length is 93 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2 alternative fragment length(s) may be 93,140,166 bps INFO @ Sun, 03 Jun 2018 13:12:21: #2.2 Generate R script for model : SRX4085415.10_model.r INFO @ Sun, 03 Jun 2018 13:12:21: #2.2 Generate R script for model : SRX4085415.20_model.r WARNING @ Sun, 03 Jun 2018 13:12:21: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:21: #2 You may need to consider one of the other alternative d(s): 93,140,166 WARNING @ Sun, 03 Jun 2018 13:12:21: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:12:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 03 Jun 2018 13:12:21: #2 You may need to consider one of the other alternative d(s): 93,140,166 INFO @ Sun, 03 Jun 2018 13:12:21: #3 Call peaks... WARNING @ Sun, 03 Jun 2018 13:12:21: #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 13:12:21: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:12:25: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:12:29: #4 Write output xls file... SRX4085415.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:29: #4 Write peak in narrowPeak format file... SRX4085415.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:29: #4 Write summits bed file... SRX4085415.05_summits.bed INFO @ Sun, 03 Jun 2018 13:12:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write output xls file... SRX4085415.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write peak in narrowPeak format file... SRX4085415.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write summits bed file... SRX4085415.20_summits.bed INFO @ Sun, 03 Jun 2018 13:12:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write output xls file... SRX4085415.10_peaks.xls CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write peak in narrowPeak format file... SRX4085415.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:12:32: #4 Write summits bed file... SRX4085415.10_summits.bed INFO @ Sun, 03 Jun 2018 13:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (167 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。