Job ID = 11170825 sra ファイルのダウンロード中... Completed: 748665K bytes transferred in 57 seconds (106754K 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 25911671 spots for /home/okishinya/chipatlas/results/ce10/SRX3043418/SRR5875902.sra Written 25911671 spots for /home/okishinya/chipatlas/results/ce10/SRX3043418/SRR5875902.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: 00:09:11 25911671 reads; of these: 25911671 (100.00%) were unpaired; of these: 1708595 (6.59%) aligned 0 times 21706219 (83.77%) aligned exactly 1 time 2496857 (9.64%) aligned >1 times 93.41% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 5441118 / 24203076 = 0.2248 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 11:42:19: # Command line: callpeak -t SRX3043418.bam -f BAM -g ce -n SRX3043418.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3043418.05 # format = BAM # ChIP-seq file = ['SRX3043418.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 11:42:19: # Command line: callpeak -t SRX3043418.bam -f BAM -g ce -n SRX3043418.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3043418.20 # format = BAM # ChIP-seq file = ['SRX3043418.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 11:42:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:19: # Command line: callpeak -t SRX3043418.bam -f BAM -g ce -n SRX3043418.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3043418.10 # format = BAM # ChIP-seq file = ['SRX3043418.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 11:42:19: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:19: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:26: 1000000 INFO @ Sat, 08 Sep 2018 11:42:26: 1000000 INFO @ Sat, 08 Sep 2018 11:42:26: 1000000 INFO @ Sat, 08 Sep 2018 11:42:32: 2000000 INFO @ Sat, 08 Sep 2018 11:42:33: 2000000 INFO @ Sat, 08 Sep 2018 11:42:33: 2000000 INFO @ Sat, 08 Sep 2018 11:42:39: 3000000 INFO @ Sat, 08 Sep 2018 11:42:40: 3000000 INFO @ Sat, 08 Sep 2018 11:42:40: 3000000 INFO @ Sat, 08 Sep 2018 11:42:46: 4000000 INFO @ Sat, 08 Sep 2018 11:42:47: 4000000 INFO @ Sat, 08 Sep 2018 11:42:47: 4000000 INFO @ Sat, 08 Sep 2018 11:42:53: 5000000 INFO @ Sat, 08 Sep 2018 11:42:54: 5000000 INFO @ Sat, 08 Sep 2018 11:42:54: 5000000 INFO @ Sat, 08 Sep 2018 11:42:59: 6000000 INFO @ Sat, 08 Sep 2018 11:43:01: 6000000 INFO @ Sat, 08 Sep 2018 11:43:01: 6000000 INFO @ Sat, 08 Sep 2018 11:43:06: 7000000 INFO @ Sat, 08 Sep 2018 11:43:08: 7000000 INFO @ Sat, 08 Sep 2018 11:43:08: 7000000 INFO @ Sat, 08 Sep 2018 11:43:13: 8000000 INFO @ Sat, 08 Sep 2018 11:43:15: 8000000 INFO @ Sat, 08 Sep 2018 11:43:15: 8000000 INFO @ Sat, 08 Sep 2018 11:43:20: 9000000 INFO @ Sat, 08 Sep 2018 11:43:22: 9000000 INFO @ Sat, 08 Sep 2018 11:43:22: 9000000 INFO @ Sat, 08 Sep 2018 11:43:26: 10000000 INFO @ Sat, 08 Sep 2018 11:43:29: 10000000 INFO @ Sat, 08 Sep 2018 11:43:30: 10000000 INFO @ Sat, 08 Sep 2018 11:43:33: 11000000 INFO @ Sat, 08 Sep 2018 11:43:36: 11000000 INFO @ Sat, 08 Sep 2018 11:43:37: 11000000 INFO @ Sat, 08 Sep 2018 11:43:40: 12000000 INFO @ Sat, 08 Sep 2018 11:43:44: 12000000 INFO @ Sat, 08 Sep 2018 11:43:44: 12000000 INFO @ Sat, 08 Sep 2018 11:43:47: 13000000 INFO @ Sat, 08 Sep 2018 11:43:51: 13000000 INFO @ Sat, 08 Sep 2018 11:43:51: 13000000 INFO @ Sat, 08 Sep 2018 11:43:53: 14000000 INFO @ Sat, 08 Sep 2018 11:43:58: 14000000 INFO @ Sat, 08 Sep 2018 11:43:59: 14000000 INFO @ Sat, 08 Sep 2018 11:44:00: 15000000 INFO @ Sat, 08 Sep 2018 11:44:05: 15000000 INFO @ Sat, 08 Sep 2018 11:44:06: 15000000 INFO @ Sat, 08 Sep 2018 11:44:07: 16000000 INFO @ Sat, 08 Sep 2018 11:44:13: 16000000 INFO @ Sat, 08 Sep 2018 11:44:13: 16000000 INFO @ Sat, 08 Sep 2018 11:44:14: 17000000 INFO @ Sat, 08 Sep 2018 11:44:20: 18000000 INFO @ Sat, 08 Sep 2018 11:44:20: 17000000 INFO @ Sat, 08 Sep 2018 11:44:21: 17000000 INFO @ Sat, 08 Sep 2018 11:44:26: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:44:26: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:44:26: #1 total tags in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:26: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:26: #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 11:44:26: #1 tags after filtering in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:26: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:26: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:28: #2 number of paired peaks: 3047 INFO @ Sat, 08 Sep 2018 11:44:28: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:28: 18000000 INFO @ Sat, 08 Sep 2018 11:44:28: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:28: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:28: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:28: #2 predicted fragment length is 95 bps INFO @ Sat, 08 Sep 2018 11:44:28: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 08 Sep 2018 11:44:28: #2.2 Generate R script for model : SRX3043418.05_model.r WARNING @ Sat, 08 Sep 2018 11:44:28: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:44:28: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sat, 08 Sep 2018 11:44:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:44:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:44:29: 18000000 INFO @ Sat, 08 Sep 2018 11:44:34: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:44:34: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:44:34: #1 total tags in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:34: #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 11:44:34: #1 tags after filtering in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:34: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:34: #1 tag size is determined as 76 bps INFO @ Sat, 08 Sep 2018 11:44:34: #1 tag size = 76 INFO @ Sat, 08 Sep 2018 11:44:34: #1 total tags in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:34: #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 11:44:35: #1 tags after filtering in treatment: 18761958 INFO @ Sat, 08 Sep 2018 11:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:35: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:35: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:36: #2 number of paired peaks: 3047 INFO @ Sat, 08 Sep 2018 11:44:36: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:36: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:36: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:36: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:36: #2 predicted fragment length is 95 bps INFO @ Sat, 08 Sep 2018 11:44:36: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 08 Sep 2018 11:44:36: #2.2 Generate R script for model : SRX3043418.10_model.r WARNING @ Sat, 08 Sep 2018 11:44:36: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:44:36: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sat, 08 Sep 2018 11:44:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:44:36: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:44:36: #2 number of paired peaks: 3047 INFO @ Sat, 08 Sep 2018 11:44:36: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:37: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:37: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:37: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:37: #2 predicted fragment length is 95 bps INFO @ Sat, 08 Sep 2018 11:44:37: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 08 Sep 2018 11:44:37: #2.2 Generate R script for model : SRX3043418.20_model.r WARNING @ Sat, 08 Sep 2018 11:44:37: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 11:44:37: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Sat, 08 Sep 2018 11:44:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 11:44:37: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:45:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:18: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:35: #4 Write output xls file... SRX3043418.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:35: #4 Write peak in narrowPeak format file... SRX3043418.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:45:35: #4 Write summits bed file... SRX3043418.05_summits.bed INFO @ Sat, 08 Sep 2018 11:45:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6564 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write output xls file... SRX3043418.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write peak in narrowPeak format file... SRX3043418.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write summits bed file... SRX3043418.10_summits.bed INFO @ Sat, 08 Sep 2018 11:45:39: Done! pass1 - making usageList (6 chroms): 79 millis pass2 - checking and writing primary data (4805 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write output xls file... SRX3043418.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write peak in narrowPeak format file... SRX3043418.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:45:39: #4 Write summits bed file... SRX3043418.20_summits.bed INFO @ Sat, 08 Sep 2018 11:45:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3567 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。