Job ID = 10714387 sra ファイルのダウンロード中... Completed: 278984K bytes transferred in 9 seconds (253340K 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 13936847 spots for /home/okishinya/chipatlas/results/ce10/SRX4082347/SRR7164165.sra Written 13936847 spots for /home/okishinya/chipatlas/results/ce10/SRX4082347/SRR7164165.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: 00:03:33 13936847 reads; of these: 13936847 (100.00%) were unpaired; of these: 84630 (0.61%) aligned 0 times 12031576 (86.33%) aligned exactly 1 time 1820641 (13.06%) aligned >1 times 99.39% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 1417700 / 13852217 = 0.1023 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 12:35:37: # Command line: callpeak -t SRX4082347.bam -f BAM -g ce -n SRX4082347.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082347.10 # format = BAM # ChIP-seq file = ['SRX4082347.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 12:35:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:37: # Command line: callpeak -t SRX4082347.bam -f BAM -g ce -n SRX4082347.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082347.05 # format = BAM # ChIP-seq file = ['SRX4082347.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 12:35:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:37: # Command line: callpeak -t SRX4082347.bam -f BAM -g ce -n SRX4082347.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082347.20 # format = BAM # ChIP-seq file = ['SRX4082347.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 12:35:37: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:35:37: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:35:44: 1000000 INFO @ Sun, 03 Jun 2018 12:35:44: 1000000 INFO @ Sun, 03 Jun 2018 12:35:44: 1000000 INFO @ Sun, 03 Jun 2018 12:35:52: 2000000 INFO @ Sun, 03 Jun 2018 12:35:52: 2000000 INFO @ Sun, 03 Jun 2018 12:35:52: 2000000 INFO @ Sun, 03 Jun 2018 12:35:59: 3000000 INFO @ Sun, 03 Jun 2018 12:35:59: 3000000 INFO @ Sun, 03 Jun 2018 12:35:59: 3000000 INFO @ Sun, 03 Jun 2018 12:36:07: 4000000 INFO @ Sun, 03 Jun 2018 12:36:07: 4000000 INFO @ Sun, 03 Jun 2018 12:36:07: 4000000 INFO @ Sun, 03 Jun 2018 12:36:14: 5000000 INFO @ Sun, 03 Jun 2018 12:36:14: 5000000 INFO @ Sun, 03 Jun 2018 12:36:14: 5000000 INFO @ Sun, 03 Jun 2018 12:36:22: 6000000 INFO @ Sun, 03 Jun 2018 12:36:22: 6000000 INFO @ Sun, 03 Jun 2018 12:36:22: 6000000 INFO @ Sun, 03 Jun 2018 12:36:29: 7000000 INFO @ Sun, 03 Jun 2018 12:36:29: 7000000 INFO @ Sun, 03 Jun 2018 12:36:29: 7000000 INFO @ Sun, 03 Jun 2018 12:36:36: 8000000 INFO @ Sun, 03 Jun 2018 12:36:36: 8000000 INFO @ Sun, 03 Jun 2018 12:36:36: 8000000 INFO @ Sun, 03 Jun 2018 12:36:43: 9000000 INFO @ Sun, 03 Jun 2018 12:36:43: 9000000 INFO @ Sun, 03 Jun 2018 12:36:43: 9000000 INFO @ Sun, 03 Jun 2018 12:36:51: 10000000 INFO @ Sun, 03 Jun 2018 12:36:51: 10000000 INFO @ Sun, 03 Jun 2018 12:36:51: 10000000 INFO @ Sun, 03 Jun 2018 12:36:58: 11000000 INFO @ Sun, 03 Jun 2018 12:36:58: 11000000 INFO @ Sun, 03 Jun 2018 12:36:58: 11000000 INFO @ Sun, 03 Jun 2018 12:37:05: 12000000 INFO @ Sun, 03 Jun 2018 12:37:05: 12000000 INFO @ Sun, 03 Jun 2018 12:37:05: 12000000 INFO @ Sun, 03 Jun 2018 12:37:09: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:09: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:09: #1 total tags in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:09: #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 12:37:09: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:09: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:09: #1 total tags in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:09: #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 12:37:09: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 12:37:09: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 12:37:09: #1 total tags in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:37:09: #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 12:37:09: #1 tags after filtering in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:09: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:09: #1 tags after filtering in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:09: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:09: #1 tags after filtering in treatment: 12434517 INFO @ Sun, 03 Jun 2018 12:37:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:37:09: #1 finished! INFO @ Sun, 03 Jun 2018 12:37:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:37:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:37:10: #2 number of paired peaks: 129 WARNING @ Sun, 03 Jun 2018 12:37:10: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:10: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:10: #2 number of paired peaks: 129 WARNING @ Sun, 03 Jun 2018 12:37:10: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:10: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:10: #2 number of paired peaks: 129 WARNING @ Sun, 03 Jun 2018 12:37:10: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sun, 03 Jun 2018 12:37:10: start model_add_line... INFO @ Sun, 03 Jun 2018 12:37:10: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:10: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:10: start X-correlation... INFO @ Sun, 03 Jun 2018 12:37:10: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:10: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:10: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:10: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:10: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2 alternative fragment length(s) may be 3,47,485,487,507,571,577,593,597 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2 alternative fragment length(s) may be 3,47,485,487,507,571,577,593,597 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2.2 Generate R script for model : SRX4082347.10_model.r INFO @ Sun, 03 Jun 2018 12:37:10: #2.2 Generate R script for model : SRX4082347.20_model.r INFO @ Sun, 03 Jun 2018 12:37:10: end of X-cor INFO @ Sun, 03 Jun 2018 12:37:10: #2 finished! INFO @ Sun, 03 Jun 2018 12:37:10: #2 predicted fragment length is 47 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2 alternative fragment length(s) may be 3,47,485,487,507,571,577,593,597 bps INFO @ Sun, 03 Jun 2018 12:37:10: #2.2 Generate R script for model : SRX4082347.05_model.r WARNING @ Sun, 03 Jun 2018 12:37:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:10: #2 You may need to consider one of the other alternative d(s): 3,47,485,487,507,571,577,593,597 WARNING @ Sun, 03 Jun 2018 12:37:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:10: #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 12:37:10: #2 You may need to consider one of the other alternative d(s): 3,47,485,487,507,571,577,593,597 INFO @ Sun, 03 Jun 2018 12:37:10: #3 Call peaks... WARNING @ Sun, 03 Jun 2018 12:37:10: #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 12:37:10: #3 Call peaks... WARNING @ Sun, 03 Jun 2018 12:37:10: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:37:10: #2 You may need to consider one of the other alternative d(s): 3,47,485,487,507,571,577,593,597 WARNING @ Sun, 03 Jun 2018 12:37:10: #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 12:37:10: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:37:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:36: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:37:47: #4 Write output xls file... SRX4082347.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:47: #4 Write peak in narrowPeak format file... SRX4082347.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:47: #4 Write summits bed file... SRX4082347.10_summits.bed INFO @ Sun, 03 Jun 2018 12:37:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (239 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write output xls file... SRX4082347.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write peak in narrowPeak format file... SRX4082347.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write summits bed file... SRX4082347.05_summits.bed INFO @ Sun, 03 Jun 2018 12:37:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1080 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write output xls file... SRX4082347.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write peak in narrowPeak format file... SRX4082347.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:37:50: #4 Write summits bed file... SRX4082347.20_summits.bed INFO @ Sun, 03 Jun 2018 12:37:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (97 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。