Job ID = 11597665 sra ファイルのダウンロード中... Completed: 485778K bytes transferred in 8 seconds (472306K 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 21538826 spots for /home/okishinya/chipatlas/results/ce10/ERX1270342/ERR1198083.sra Written 21538826 spots for /home/okishinya/chipatlas/results/ce10/ERX1270342/ERR1198083.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: 00:05:33 21538826 reads; of these: 21538826 (100.00%) were unpaired; of these: 288183 (1.34%) aligned 0 times 17832951 (82.79%) aligned exactly 1 time 3417692 (15.87%) aligned >1 times 98.66% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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 12 files... [bam_rmdupse_core] 1893286 / 21250643 = 0.0891 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 @ Wed, 30 Jan 2019 14:27:58: # Command line: callpeak -t ERX1270342.bam -f BAM -g ce -n ERX1270342.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1270342.10 # format = BAM # ChIP-seq file = ['ERX1270342.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 @ Wed, 30 Jan 2019 14:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:27:58: # Command line: callpeak -t ERX1270342.bam -f BAM -g ce -n ERX1270342.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1270342.20 # format = BAM # ChIP-seq file = ['ERX1270342.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 @ Wed, 30 Jan 2019 14:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:27:58: # Command line: callpeak -t ERX1270342.bam -f BAM -g ce -n ERX1270342.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1270342.05 # format = BAM # ChIP-seq file = ['ERX1270342.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 @ Wed, 30 Jan 2019 14:27:58: #1 read tag files... INFO @ Wed, 30 Jan 2019 14:27:58: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 14:28:05: 1000000 INFO @ Wed, 30 Jan 2019 14:28:05: 1000000 INFO @ Wed, 30 Jan 2019 14:28:05: 1000000 INFO @ Wed, 30 Jan 2019 14:28:11: 2000000 INFO @ Wed, 30 Jan 2019 14:28:11: 2000000 INFO @ Wed, 30 Jan 2019 14:28:11: 2000000 INFO @ Wed, 30 Jan 2019 14:28:17: 3000000 INFO @ Wed, 30 Jan 2019 14:28:17: 3000000 INFO @ Wed, 30 Jan 2019 14:28:18: 3000000 INFO @ Wed, 30 Jan 2019 14:28:23: 4000000 INFO @ Wed, 30 Jan 2019 14:28:23: 4000000 INFO @ Wed, 30 Jan 2019 14:28:24: 4000000 INFO @ Wed, 30 Jan 2019 14:28:29: 5000000 INFO @ Wed, 30 Jan 2019 14:28:30: 5000000 INFO @ Wed, 30 Jan 2019 14:28:31: 5000000 INFO @ Wed, 30 Jan 2019 14:28:35: 6000000 INFO @ Wed, 30 Jan 2019 14:28:36: 6000000 INFO @ Wed, 30 Jan 2019 14:28:38: 6000000 INFO @ Wed, 30 Jan 2019 14:28:41: 7000000 INFO @ Wed, 30 Jan 2019 14:28:42: 7000000 INFO @ Wed, 30 Jan 2019 14:28:44: 7000000 INFO @ Wed, 30 Jan 2019 14:28:48: 8000000 INFO @ Wed, 30 Jan 2019 14:28:48: 8000000 INFO @ Wed, 30 Jan 2019 14:28:51: 8000000 INFO @ Wed, 30 Jan 2019 14:28:54: 9000000 INFO @ Wed, 30 Jan 2019 14:28:55: 9000000 INFO @ Wed, 30 Jan 2019 14:28:57: 9000000 INFO @ Wed, 30 Jan 2019 14:29:00: 10000000 INFO @ Wed, 30 Jan 2019 14:29:01: 10000000 INFO @ Wed, 30 Jan 2019 14:29:04: 10000000 INFO @ Wed, 30 Jan 2019 14:29:06: 11000000 INFO @ Wed, 30 Jan 2019 14:29:07: 11000000 INFO @ Wed, 30 Jan 2019 14:29:10: 11000000 INFO @ Wed, 30 Jan 2019 14:29:12: 12000000 INFO @ Wed, 30 Jan 2019 14:29:14: 12000000 INFO @ Wed, 30 Jan 2019 14:29:16: 12000000 INFO @ Wed, 30 Jan 2019 14:29:19: 13000000 INFO @ Wed, 30 Jan 2019 14:29:20: 13000000 INFO @ Wed, 30 Jan 2019 14:29:22: 13000000 INFO @ Wed, 30 Jan 2019 14:29:25: 14000000 INFO @ Wed, 30 Jan 2019 14:29:26: 14000000 INFO @ Wed, 30 Jan 2019 14:29:29: 14000000 INFO @ Wed, 30 Jan 2019 14:29:32: 15000000 INFO @ Wed, 30 Jan 2019 14:29:32: 15000000 INFO @ Wed, 30 Jan 2019 14:29:36: 15000000 INFO @ Wed, 30 Jan 2019 14:29:38: 16000000 INFO @ Wed, 30 Jan 2019 14:29:39: 16000000 INFO @ Wed, 30 Jan 2019 14:29:42: 16000000 INFO @ Wed, 30 Jan 2019 14:29:45: 17000000 INFO @ Wed, 30 Jan 2019 14:29:45: 17000000 INFO @ Wed, 30 Jan 2019 14:29:49: 17000000 INFO @ Wed, 30 Jan 2019 14:29:51: 18000000 INFO @ Wed, 30 Jan 2019 14:29:51: 18000000 INFO @ Wed, 30 Jan 2019 14:29:55: 18000000 INFO @ Wed, 30 Jan 2019 14:29:57: 19000000 INFO @ Wed, 30 Jan 2019 14:29:57: 19000000 INFO @ Wed, 30 Jan 2019 14:29:59: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:29:59: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:29:59: #1 total tags in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:29:59: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:29:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:30:00: #1 tags after filtering in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:30:00: #1 finished! INFO @ Wed, 30 Jan 2019 14:30:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:30:00: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:30:00: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:30:00: #1 total tags in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:30:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:30:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:30:00: #1 tags after filtering in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:30:00: #1 finished! INFO @ Wed, 30 Jan 2019 14:30:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:30:01: #2 number of paired peaks: 201 WARNING @ Wed, 30 Jan 2019 14:30:01: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 30 Jan 2019 14:30:01: start model_add_line... INFO @ Wed, 30 Jan 2019 14:30:01: #2 number of paired peaks: 201 WARNING @ Wed, 30 Jan 2019 14:30:01: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 30 Jan 2019 14:30:01: start model_add_line... INFO @ Wed, 30 Jan 2019 14:30:02: start X-correlation... INFO @ Wed, 30 Jan 2019 14:30:02: end of X-cor INFO @ Wed, 30 Jan 2019 14:30:02: #2 finished! INFO @ Wed, 30 Jan 2019 14:30:02: #2 predicted fragment length is 1 bps INFO @ Wed, 30 Jan 2019 14:30:02: #2 alternative fragment length(s) may be 1,46,549,574 bps INFO @ Wed, 30 Jan 2019 14:30:02: #2.2 Generate R script for model : ERX1270342.05_model.r WARNING @ Wed, 30 Jan 2019 14:30:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:30:02: #2 You may need to consider one of the other alternative d(s): 1,46,549,574 WARNING @ Wed, 30 Jan 2019 14:30:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:30:02: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:30:02: start X-correlation... INFO @ Wed, 30 Jan 2019 14:30:02: end of X-cor INFO @ Wed, 30 Jan 2019 14:30:02: #2 finished! INFO @ Wed, 30 Jan 2019 14:30:02: #2 predicted fragment length is 1 bps INFO @ Wed, 30 Jan 2019 14:30:02: #2 alternative fragment length(s) may be 1,46,549,574 bps INFO @ Wed, 30 Jan 2019 14:30:02: #2.2 Generate R script for model : ERX1270342.10_model.r INFO @ Wed, 30 Jan 2019 14:30:02: 19000000 WARNING @ Wed, 30 Jan 2019 14:30:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:30:02: #2 You may need to consider one of the other alternative d(s): 1,46,549,574 WARNING @ Wed, 30 Jan 2019 14:30:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:30:02: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:30:04: #1 tag size is determined as 49 bps INFO @ Wed, 30 Jan 2019 14:30:04: #1 tag size = 49 INFO @ Wed, 30 Jan 2019 14:30:04: #1 total tags in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:30:04: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 14:30:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 14:30:04: #1 tags after filtering in treatment: 19357357 INFO @ Wed, 30 Jan 2019 14:30:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 14:30:04: #1 finished! INFO @ Wed, 30 Jan 2019 14:30:04: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 14:30:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 14:30:06: #2 number of paired peaks: 201 WARNING @ Wed, 30 Jan 2019 14:30:06: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Wed, 30 Jan 2019 14:30:06: start model_add_line... INFO @ Wed, 30 Jan 2019 14:30:06: start X-correlation... INFO @ Wed, 30 Jan 2019 14:30:06: end of X-cor INFO @ Wed, 30 Jan 2019 14:30:06: #2 finished! INFO @ Wed, 30 Jan 2019 14:30:06: #2 predicted fragment length is 1 bps INFO @ Wed, 30 Jan 2019 14:30:06: #2 alternative fragment length(s) may be 1,46,549,574 bps INFO @ Wed, 30 Jan 2019 14:30:06: #2.2 Generate R script for model : ERX1270342.20_model.r WARNING @ Wed, 30 Jan 2019 14:30:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 14:30:06: #2 You may need to consider one of the other alternative d(s): 1,46,549,574 WARNING @ Wed, 30 Jan 2019 14:30:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 14:30:06: #3 Call peaks... INFO @ Wed, 30 Jan 2019 14:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 14:30:36: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:30:38: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:30:38: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write output xls file... ERX1270342.10_peaks.xls INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write peak in narrowPeak format file... ERX1270342.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write summits bed file... ERX1270342.10_summits.bed INFO @ Wed, 30 Jan 2019 14:30:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write output xls file... ERX1270342.20_peaks.xls INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write peak in narrowPeak format file... ERX1270342.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:30:54: #4 Write summits bed file... ERX1270342.20_summits.bed INFO @ Wed, 30 Jan 2019 14:30:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 14:30:55: #4 Write output xls file... ERX1270342.05_peaks.xls INFO @ Wed, 30 Jan 2019 14:30:55: #4 Write peak in narrowPeak format file... ERX1270342.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 14:30:55: #4 Write summits bed file... ERX1270342.05_summits.bed INFO @ Wed, 30 Jan 2019 14:30:55: 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。