Job ID = 11293649 sra ファイルのダウンロード中... Completed: 388979K bytes transferred in 9 seconds (326037K 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: SINGLE fastq に変換中... Read 17561934 spots for /home/okishinya/chipatlas/results/ce10/SRX4344460/SRR7474919.sra Written 17561934 spots for /home/okishinya/chipatlas/results/ce10/SRX4344460/SRR7474919.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: 00:04:09 17561934 reads; of these: 17561934 (100.00%) were unpaired; of these: 1409623 (8.03%) aligned 0 times 13619296 (77.55%) aligned exactly 1 time 2533015 (14.42%) aligned >1 times 91.97% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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_rmdupse_core] 6765660 / 16152311 = 0.4189 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, 04 Nov 2018 17:55:14: # Command line: callpeak -t SRX4344460.bam -f BAM -g ce -n SRX4344460.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4344460.20 # format = BAM # ChIP-seq file = ['SRX4344460.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, 04 Nov 2018 17:55:14: # Command line: callpeak -t SRX4344460.bam -f BAM -g ce -n SRX4344460.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4344460.05 # format = BAM # ChIP-seq file = ['SRX4344460.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, 04 Nov 2018 17:55:14: # Command line: callpeak -t SRX4344460.bam -f BAM -g ce -n SRX4344460.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4344460.10 # format = BAM # ChIP-seq file = ['SRX4344460.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, 04 Nov 2018 17:55:14: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:14: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:14: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:55:14: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:14: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:14: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:55:20: 1000000 INFO @ Sun, 04 Nov 2018 17:55:20: 1000000 INFO @ Sun, 04 Nov 2018 17:55:20: 1000000 INFO @ Sun, 04 Nov 2018 17:55:26: 2000000 INFO @ Sun, 04 Nov 2018 17:55:27: 2000000 INFO @ Sun, 04 Nov 2018 17:55:27: 2000000 INFO @ Sun, 04 Nov 2018 17:55:33: 3000000 INFO @ Sun, 04 Nov 2018 17:55:33: 3000000 INFO @ Sun, 04 Nov 2018 17:55:33: 3000000 INFO @ Sun, 04 Nov 2018 17:55:39: 4000000 INFO @ Sun, 04 Nov 2018 17:55:39: 4000000 INFO @ Sun, 04 Nov 2018 17:55:40: 4000000 INFO @ Sun, 04 Nov 2018 17:55:45: 5000000 INFO @ Sun, 04 Nov 2018 17:55:46: 5000000 INFO @ Sun, 04 Nov 2018 17:55:46: 5000000 INFO @ Sun, 04 Nov 2018 17:55:52: 6000000 INFO @ Sun, 04 Nov 2018 17:55:52: 6000000 INFO @ Sun, 04 Nov 2018 17:55:53: 6000000 INFO @ Sun, 04 Nov 2018 17:55:58: 7000000 INFO @ Sun, 04 Nov 2018 17:55:59: 7000000 INFO @ Sun, 04 Nov 2018 17:55:59: 7000000 INFO @ Sun, 04 Nov 2018 17:56:04: 8000000 INFO @ Sun, 04 Nov 2018 17:56:05: 8000000 INFO @ Sun, 04 Nov 2018 17:56:06: 8000000 INFO @ Sun, 04 Nov 2018 17:56:12: 9000000 INFO @ Sun, 04 Nov 2018 17:56:12: 9000000 INFO @ Sun, 04 Nov 2018 17:56:13: 9000000 INFO @ Sun, 04 Nov 2018 17:56:15: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:56:15: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:56:15: #1 total tags in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:15: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:15: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:56:15: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:56:15: #1 total tags in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:15: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:15: #1 tags after filtering in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:15: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:15: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:15: #1 tags after filtering in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:15: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:15: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:16: #1 tag size is determined as 50 bps INFO @ Sun, 04 Nov 2018 17:56:16: #1 tag size = 50 INFO @ Sun, 04 Nov 2018 17:56:16: #1 total tags in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:16: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:56:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:56:16: #1 tags after filtering in treatment: 9386651 INFO @ Sun, 04 Nov 2018 17:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:56:16: #1 finished! INFO @ Sun, 04 Nov 2018 17:56:16: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:56:16: #2 number of paired peaks: 465 WARNING @ Sun, 04 Nov 2018 17:56:16: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 04 Nov 2018 17:56:16: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:16: #2 number of paired peaks: 465 WARNING @ Sun, 04 Nov 2018 17:56:16: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 04 Nov 2018 17:56:16: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:16: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:16: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:16: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:16: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:16: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:16: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:56:16: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:16: #2 alternative fragment length(s) may be 3,53,549,569 bps INFO @ Sun, 04 Nov 2018 17:56:16: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:56:16: #2.2 Generate R script for model : SRX4344460.20_model.r INFO @ Sun, 04 Nov 2018 17:56:16: #2 alternative fragment length(s) may be 3,53,549,569 bps INFO @ Sun, 04 Nov 2018 17:56:16: #2.2 Generate R script for model : SRX4344460.05_model.r WARNING @ Sun, 04 Nov 2018 17:56:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:56:16: #2 You may need to consider one of the other alternative d(s): 3,53,549,569 WARNING @ Sun, 04 Nov 2018 17:56:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:56:16: #3 Call peaks... WARNING @ Sun, 04 Nov 2018 17:56:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:56:16: #2 You may need to consider one of the other alternative d(s): 3,53,549,569 WARNING @ Sun, 04 Nov 2018 17:56:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:56:16: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:17: #2 number of paired peaks: 465 WARNING @ Sun, 04 Nov 2018 17:56:17: Fewer paired peaks (465) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 465 pairs to build model! INFO @ Sun, 04 Nov 2018 17:56:17: start model_add_line... INFO @ Sun, 04 Nov 2018 17:56:17: start X-correlation... INFO @ Sun, 04 Nov 2018 17:56:17: end of X-cor INFO @ Sun, 04 Nov 2018 17:56:17: #2 finished! INFO @ Sun, 04 Nov 2018 17:56:17: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:56:17: #2 alternative fragment length(s) may be 3,53,549,569 bps INFO @ Sun, 04 Nov 2018 17:56:17: #2.2 Generate R script for model : SRX4344460.10_model.r WARNING @ Sun, 04 Nov 2018 17:56:17: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:56:17: #2 You may need to consider one of the other alternative d(s): 3,53,549,569 WARNING @ Sun, 04 Nov 2018 17:56:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:56:17: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:56:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write output xls file... SRX4344460.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write peak in narrowPeak format file... SRX4344460.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write summits bed file... SRX4344460.10_summits.bed INFO @ Sun, 04 Nov 2018 17:56:49: Done! INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write output xls file... SRX4344460.05_peaks.xls pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 2 millis INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write peak in narrowPeak format file... SRX4344460.05_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:49: #4 Write summits bed file... SRX4344460.05_summits.bed INFO @ Sun, 04 Nov 2018 17:56:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1043 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:56:50: #4 Write output xls file... SRX4344460.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:56:50: #4 Write peak in narrowPeak format file... SRX4344460.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:56:50: #4 Write summits bed file... SRX4344460.20_summits.bed INFO @ Sun, 04 Nov 2018 17:56:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (237 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。