Job ID = 10714368 sra ファイルのダウンロード中... Completed: 765046K bytes transferred in 83 seconds (75129K 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 45543277 spots for /home/okishinya/chipatlas/results/ce10/SRX2985927/SRR5807077.sra Written 45543277 spots for /home/okishinya/chipatlas/results/ce10/SRX2985927/SRR5807077.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: 00:12:31 45543277 reads; of these: 45543277 (100.00%) were unpaired; of these: 1662635 (3.65%) aligned 0 times 33618468 (73.82%) aligned exactly 1 time 10262174 (22.53%) aligned >1 times 96.35% overall alignment rate Time searching: 00:12:31 Overall time: 00:12:31 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 20 files... [bam_rmdupse_core] 23579061 / 43880642 = 0.5373 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 12:51:27: # Command line: callpeak -t SRX2985927.bam -f BAM -g ce -n SRX2985927.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2985927.10 # format = BAM # ChIP-seq file = ['SRX2985927.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 12:51:27: # Command line: callpeak -t SRX2985927.bam -f BAM -g ce -n SRX2985927.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2985927.20 # format = BAM # ChIP-seq file = ['SRX2985927.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 12:51:27: # Command line: callpeak -t SRX2985927.bam -f BAM -g ce -n SRX2985927.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2985927.05 # format = BAM # ChIP-seq file = ['SRX2985927.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 12:51:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:51:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:51:27: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:51:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:51:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:51:27: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:51:33: 1000000 INFO @ Sun, 03 Jun 2018 12:51:33: 1000000 INFO @ Sun, 03 Jun 2018 12:51:33: 1000000 INFO @ Sun, 03 Jun 2018 12:51:40: 2000000 INFO @ Sun, 03 Jun 2018 12:51:40: 2000000 INFO @ Sun, 03 Jun 2018 12:51:40: 2000000 INFO @ Sun, 03 Jun 2018 12:51:46: 3000000 INFO @ Sun, 03 Jun 2018 12:51:46: 3000000 INFO @ Sun, 03 Jun 2018 12:51:46: 3000000 INFO @ Sun, 03 Jun 2018 12:51:52: 4000000 INFO @ Sun, 03 Jun 2018 12:51:52: 4000000 INFO @ Sun, 03 Jun 2018 12:51:52: 4000000 INFO @ Sun, 03 Jun 2018 12:51:57: 5000000 INFO @ Sun, 03 Jun 2018 12:51:58: 5000000 INFO @ Sun, 03 Jun 2018 12:51:58: 5000000 INFO @ Sun, 03 Jun 2018 12:52:03: 6000000 INFO @ Sun, 03 Jun 2018 12:52:04: 6000000 INFO @ Sun, 03 Jun 2018 12:52:04: 6000000 INFO @ Sun, 03 Jun 2018 12:52:09: 7000000 INFO @ Sun, 03 Jun 2018 12:52:10: 7000000 INFO @ Sun, 03 Jun 2018 12:52:10: 7000000 INFO @ Sun, 03 Jun 2018 12:52:17: 8000000 INFO @ Sun, 03 Jun 2018 12:52:17: 8000000 INFO @ Sun, 03 Jun 2018 12:52:17: 8000000 INFO @ Sun, 03 Jun 2018 12:52:23: 9000000 INFO @ Sun, 03 Jun 2018 12:52:23: 9000000 INFO @ Sun, 03 Jun 2018 12:52:25: 9000000 INFO @ Sun, 03 Jun 2018 12:52:30: 10000000 INFO @ Sun, 03 Jun 2018 12:52:30: 10000000 INFO @ Sun, 03 Jun 2018 12:52:34: 10000000 INFO @ Sun, 03 Jun 2018 12:52:37: 11000000 INFO @ Sun, 03 Jun 2018 12:52:37: 11000000 INFO @ Sun, 03 Jun 2018 12:52:42: 11000000 INFO @ Sun, 03 Jun 2018 12:52:44: 12000000 INFO @ Sun, 03 Jun 2018 12:52:44: 12000000 INFO @ Sun, 03 Jun 2018 12:52:50: 12000000 INFO @ Sun, 03 Jun 2018 12:52:51: 13000000 INFO @ Sun, 03 Jun 2018 12:52:51: 13000000 INFO @ Sun, 03 Jun 2018 12:52:58: 13000000 INFO @ Sun, 03 Jun 2018 12:52:58: 14000000 INFO @ Sun, 03 Jun 2018 12:52:58: 14000000 INFO @ Sun, 03 Jun 2018 12:53:05: 15000000 INFO @ Sun, 03 Jun 2018 12:53:05: 15000000 INFO @ Sun, 03 Jun 2018 12:53:06: 14000000 INFO @ Sun, 03 Jun 2018 12:53:12: 16000000 INFO @ Sun, 03 Jun 2018 12:53:12: 16000000 INFO @ Sun, 03 Jun 2018 12:53:14: 15000000 INFO @ Sun, 03 Jun 2018 12:53:19: 17000000 INFO @ Sun, 03 Jun 2018 12:53:19: 17000000 INFO @ Sun, 03 Jun 2018 12:53:23: 16000000 INFO @ Sun, 03 Jun 2018 12:53:26: 18000000 INFO @ Sun, 03 Jun 2018 12:53:26: 18000000 INFO @ Sun, 03 Jun 2018 12:53:31: 17000000 INFO @ Sun, 03 Jun 2018 12:53:33: 19000000 INFO @ Sun, 03 Jun 2018 12:53:33: 19000000 INFO @ Sun, 03 Jun 2018 12:53:39: 18000000 INFO @ Sun, 03 Jun 2018 12:53:40: 20000000 INFO @ Sun, 03 Jun 2018 12:53:40: 20000000 INFO @ Sun, 03 Jun 2018 12:53:42: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:53:42: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:53:42: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:53:42: #1 total tags in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:42: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:53:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:53:42: #1 total tags in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:42: #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 12:53:42: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:53:42: #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 12:53:42: #1 tags after filtering in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:42: #1 tags after filtering in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:53:42: #1 finished! INFO @ Sun, 03 Jun 2018 12:53:42: #1 finished! INFO @ Sun, 03 Jun 2018 12:53:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:53:42: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:53:44: #2 number of paired peaks: 432 WARNING @ Sun, 03 Jun 2018 12:53:44: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sun, 03 Jun 2018 12:53:44: start model_add_line... INFO @ Sun, 03 Jun 2018 12:53:44: start X-correlation... INFO @ Sun, 03 Jun 2018 12:53:44: #2 number of paired peaks: 432 WARNING @ Sun, 03 Jun 2018 12:53:44: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sun, 03 Jun 2018 12:53:44: start model_add_line... INFO @ Sun, 03 Jun 2018 12:53:44: end of X-cor INFO @ Sun, 03 Jun 2018 12:53:44: #2 finished! INFO @ Sun, 03 Jun 2018 12:53:44: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:53:44: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Sun, 03 Jun 2018 12:53:44: #2.2 Generate R script for model : SRX2985927.05_model.r WARNING @ Sun, 03 Jun 2018 12:53:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:53:44: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Sun, 03 Jun 2018 12:53:44: #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 12:53:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:53:44: start X-correlation... INFO @ Sun, 03 Jun 2018 12:53:44: end of X-cor INFO @ Sun, 03 Jun 2018 12:53:44: #2 finished! INFO @ Sun, 03 Jun 2018 12:53:44: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:53:44: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Sun, 03 Jun 2018 12:53:44: #2.2 Generate R script for model : SRX2985927.10_model.r WARNING @ Sun, 03 Jun 2018 12:53:44: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:53:44: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Sun, 03 Jun 2018 12:53:44: #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 12:53:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:53:47: 19000000 INFO @ Sun, 03 Jun 2018 12:53:55: 20000000 INFO @ Sun, 03 Jun 2018 12:53:58: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:53:58: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:53:58: #1 total tags in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:53:58: #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 12:53:58: #1 tags after filtering in treatment: 20301581 INFO @ Sun, 03 Jun 2018 12:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:53:58: #1 finished! INFO @ Sun, 03 Jun 2018 12:53:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:54:00: #2 number of paired peaks: 432 WARNING @ Sun, 03 Jun 2018 12:54:00: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Sun, 03 Jun 2018 12:54:00: start model_add_line... INFO @ Sun, 03 Jun 2018 12:54:00: start X-correlation... INFO @ Sun, 03 Jun 2018 12:54:00: end of X-cor INFO @ Sun, 03 Jun 2018 12:54:00: #2 finished! INFO @ Sun, 03 Jun 2018 12:54:00: #2 predicted fragment length is 1 bps INFO @ Sun, 03 Jun 2018 12:54:00: #2 alternative fragment length(s) may be 1,41,597 bps INFO @ Sun, 03 Jun 2018 12:54:00: #2.2 Generate R script for model : SRX2985927.20_model.r WARNING @ Sun, 03 Jun 2018 12:54:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 12:54:00: #2 You may need to consider one of the other alternative d(s): 1,41,597 WARNING @ Sun, 03 Jun 2018 12:54:00: #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 12:54:00: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:54:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:54:21: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:54:35: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:54:35: #4 Write output xls file... SRX2985927.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:54:35: #4 Write peak in narrowPeak format file... SRX2985927.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:54:35: #4 Write summits bed file... SRX2985927.05_summits.bed INFO @ Sun, 03 Jun 2018 12:54:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:54:37: #4 Write output xls file... SRX2985927.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:54:37: #4 Write peak in narrowPeak format file... SRX2985927.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:54:37: #4 Write summits bed file... SRX2985927.10_summits.bed INFO @ Sun, 03 Jun 2018 12:54:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:54:52: #4 Write output xls file... SRX2985927.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:54:52: #4 Write peak in narrowPeak format file... SRX2985927.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:54:52: #4 Write summits bed file... SRX2985927.20_summits.bed INFO @ Sun, 03 Jun 2018 12:54:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。