Job ID = 11170841 sra ファイルのダウンロード中... Completed: 933722K bytes transferred in 125 seconds (60952K 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 32777421 spots for /home/okishinya/chipatlas/results/ce10/SRX3583341/SRR6493997.sra Written 32777421 spots for /home/okishinya/chipatlas/results/ce10/SRX3583341/SRR6493997.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: 00:11:57 32777421 reads; of these: 32777421 (100.00%) were unpaired; of these: 710662 (2.17%) aligned 0 times 27923854 (85.19%) aligned exactly 1 time 4142905 (12.64%) aligned >1 times 97.83% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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 16 files... [bam_rmdupse_core] 6003357 / 32066759 = 0.1872 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 @ Sat, 08 Sep 2018 11:49:07: # Command line: callpeak -t SRX3583341.bam -f BAM -g ce -n SRX3583341.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3583341.10 # format = BAM # ChIP-seq file = ['SRX3583341.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 @ Sat, 08 Sep 2018 11:49:07: # Command line: callpeak -t SRX3583341.bam -f BAM -g ce -n SRX3583341.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3583341.05 # format = BAM # ChIP-seq file = ['SRX3583341.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 @ Sat, 08 Sep 2018 11:49:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:07: # Command line: callpeak -t SRX3583341.bam -f BAM -g ce -n SRX3583341.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3583341.20 # format = BAM # ChIP-seq file = ['SRX3583341.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 @ Sat, 08 Sep 2018 11:49:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:49:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:49:14: 1000000 INFO @ Sat, 08 Sep 2018 11:49:14: 1000000 INFO @ Sat, 08 Sep 2018 11:49:14: 1000000 INFO @ Sat, 08 Sep 2018 11:49:21: 2000000 INFO @ Sat, 08 Sep 2018 11:49:22: 2000000 INFO @ Sat, 08 Sep 2018 11:49:22: 2000000 INFO @ Sat, 08 Sep 2018 11:49:28: 3000000 INFO @ Sat, 08 Sep 2018 11:49:30: 3000000 INFO @ Sat, 08 Sep 2018 11:49:30: 3000000 INFO @ Sat, 08 Sep 2018 11:49:36: 4000000 INFO @ Sat, 08 Sep 2018 11:49:37: 4000000 INFO @ Sat, 08 Sep 2018 11:49:38: 4000000 INFO @ Sat, 08 Sep 2018 11:49:44: 5000000 INFO @ Sat, 08 Sep 2018 11:49:44: 5000000 INFO @ Sat, 08 Sep 2018 11:49:46: 5000000 INFO @ Sat, 08 Sep 2018 11:49:51: 6000000 INFO @ Sat, 08 Sep 2018 11:49:51: 6000000 INFO @ Sat, 08 Sep 2018 11:49:54: 6000000 INFO @ Sat, 08 Sep 2018 11:49:59: 7000000 INFO @ Sat, 08 Sep 2018 11:49:59: 7000000 INFO @ Sat, 08 Sep 2018 11:50:01: 7000000 INFO @ Sat, 08 Sep 2018 11:50:06: 8000000 INFO @ Sat, 08 Sep 2018 11:50:06: 8000000 INFO @ Sat, 08 Sep 2018 11:50:09: 8000000 INFO @ Sat, 08 Sep 2018 11:50:13: 9000000 INFO @ Sat, 08 Sep 2018 11:50:14: 9000000 INFO @ Sat, 08 Sep 2018 11:50:16: 9000000 INFO @ Sat, 08 Sep 2018 11:50:21: 10000000 INFO @ Sat, 08 Sep 2018 11:50:21: 10000000 INFO @ Sat, 08 Sep 2018 11:50:23: 10000000 INFO @ Sat, 08 Sep 2018 11:50:28: 11000000 INFO @ Sat, 08 Sep 2018 11:50:28: 11000000 INFO @ Sat, 08 Sep 2018 11:50:31: 11000000 INFO @ Sat, 08 Sep 2018 11:50:35: 12000000 INFO @ Sat, 08 Sep 2018 11:50:36: 12000000 INFO @ Sat, 08 Sep 2018 11:50:38: 12000000 INFO @ Sat, 08 Sep 2018 11:50:42: 13000000 INFO @ Sat, 08 Sep 2018 11:50:43: 13000000 INFO @ Sat, 08 Sep 2018 11:50:46: 13000000 INFO @ Sat, 08 Sep 2018 11:50:50: 14000000 INFO @ Sat, 08 Sep 2018 11:50:51: 14000000 INFO @ Sat, 08 Sep 2018 11:50:54: 14000000 INFO @ Sat, 08 Sep 2018 11:50:57: 15000000 INFO @ Sat, 08 Sep 2018 11:50:58: 15000000 INFO @ Sat, 08 Sep 2018 11:51:01: 15000000 INFO @ Sat, 08 Sep 2018 11:51:04: 16000000 INFO @ Sat, 08 Sep 2018 11:51:06: 16000000 INFO @ Sat, 08 Sep 2018 11:51:09: 16000000 INFO @ Sat, 08 Sep 2018 11:51:11: 17000000 INFO @ Sat, 08 Sep 2018 11:51:14: 17000000 INFO @ Sat, 08 Sep 2018 11:51:17: 17000000 INFO @ Sat, 08 Sep 2018 11:51:18: 18000000 INFO @ Sat, 08 Sep 2018 11:51:21: 18000000 INFO @ Sat, 08 Sep 2018 11:51:25: 18000000 INFO @ Sat, 08 Sep 2018 11:51:25: 19000000 INFO @ Sat, 08 Sep 2018 11:51:29: 19000000 INFO @ Sat, 08 Sep 2018 11:51:33: 19000000 INFO @ Sat, 08 Sep 2018 11:51:33: 20000000 INFO @ Sat, 08 Sep 2018 11:51:36: 20000000 INFO @ Sat, 08 Sep 2018 11:51:40: 21000000 INFO @ Sat, 08 Sep 2018 11:51:40: 20000000 INFO @ Sat, 08 Sep 2018 11:51:44: 21000000 INFO @ Sat, 08 Sep 2018 11:51:47: 22000000 INFO @ Sat, 08 Sep 2018 11:51:48: 21000000 INFO @ Sat, 08 Sep 2018 11:51:51: 22000000 INFO @ Sat, 08 Sep 2018 11:51:54: 23000000 INFO @ Sat, 08 Sep 2018 11:51:56: 22000000 INFO @ Sat, 08 Sep 2018 11:51:59: 23000000 INFO @ Sat, 08 Sep 2018 11:52:01: 24000000 INFO @ Sat, 08 Sep 2018 11:52:03: 23000000 INFO @ Sat, 08 Sep 2018 11:52:06: 24000000 INFO @ Sat, 08 Sep 2018 11:52:09: 25000000 INFO @ Sat, 08 Sep 2018 11:52:11: 24000000 INFO @ Sat, 08 Sep 2018 11:52:14: 25000000 INFO @ Sat, 08 Sep 2018 11:52:16: 26000000 INFO @ Sat, 08 Sep 2018 11:52:16: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:16: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:16: #1 total tags in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:16: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:17: #1 tags after filtering in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:17: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:17: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:18: 25000000 INFO @ Sat, 08 Sep 2018 11:52:19: #2 number of paired peaks: 453 WARNING @ Sat, 08 Sep 2018 11:52:19: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:19: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:19: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:19: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:19: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:19: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 11:52:19: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sat, 08 Sep 2018 11:52:19: #2.2 Generate R script for model : SRX3583341.10_model.r INFO @ Sat, 08 Sep 2018 11:52:19: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:52:21: 26000000 INFO @ Sat, 08 Sep 2018 11:52:22: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:22: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:22: #1 total tags in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:22: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:22: #1 tags after filtering in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:22: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:22: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:24: #2 number of paired peaks: 453 WARNING @ Sat, 08 Sep 2018 11:52:24: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:24: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:24: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:24: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:24: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:24: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 11:52:24: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sat, 08 Sep 2018 11:52:24: #2.2 Generate R script for model : SRX3583341.20_model.r INFO @ Sat, 08 Sep 2018 11:52:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:52:26: 26000000 INFO @ Sat, 08 Sep 2018 11:52:26: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:52:26: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:52:26: #1 total tags in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:52:27: #1 tags after filtering in treatment: 26063402 INFO @ Sat, 08 Sep 2018 11:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:52:27: #1 finished! INFO @ Sat, 08 Sep 2018 11:52:27: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:52:29: #2 number of paired peaks: 453 WARNING @ Sat, 08 Sep 2018 11:52:29: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sat, 08 Sep 2018 11:52:29: start model_add_line... INFO @ Sat, 08 Sep 2018 11:52:29: start X-correlation... INFO @ Sat, 08 Sep 2018 11:52:29: end of X-cor INFO @ Sat, 08 Sep 2018 11:52:29: #2 finished! INFO @ Sat, 08 Sep 2018 11:52:29: #2 predicted fragment length is 162 bps INFO @ Sat, 08 Sep 2018 11:52:29: #2 alternative fragment length(s) may be 4,162 bps INFO @ Sat, 08 Sep 2018 11:52:29: #2.2 Generate R script for model : SRX3583341.05_model.r INFO @ Sat, 08 Sep 2018 11:52:29: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:53:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:22: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:53:42: #4 Write output xls file... SRX3583341.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:42: #4 Write peak in narrowPeak format file... SRX3583341.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:42: #4 Write summits bed file... SRX3583341.10_summits.bed INFO @ Sat, 08 Sep 2018 11:53:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3721 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write output xls file... SRX3583341.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write peak in narrowPeak format file... SRX3583341.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:47: #4 Write summits bed file... SRX3583341.20_summits.bed INFO @ Sat, 08 Sep 2018 11:53:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2840 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:53:49: #4 Write output xls file... SRX3583341.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:53:49: #4 Write peak in narrowPeak format file... SRX3583341.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:53:49: #4 Write summits bed file... SRX3583341.05_summits.bed INFO @ Sat, 08 Sep 2018 11:53:49: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4805 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。