Job ID = 10325498 sra ファイルのダウンロード中... Completed: 396465K bytes transferred in 23 seconds (141035K 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... Written 24145063 spots for /home/okishinya/chipatlas/results/rn6/SRX3398847/SRR6297868.sra Written 24145063 spots total 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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:52:05 24145063 reads; of these: 24145063 (100.00%) were unpaired; of these: 1980223 (8.20%) aligned 0 times 16091384 (66.64%) aligned exactly 1 time 6073456 (25.15%) aligned >1 times 91.80% overall alignment rate Time searching: 00:52:12 Overall time: 00:52:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 1653804 / 22164840 = 0.0746 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 @ Fri, 12 Jan 2018 03:48:58: # Command line: callpeak -t SRX3398847.bam -f BAM -g 2.15e9 -n SRX3398847.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3398847.10 # format = BAM # ChIP-seq file = ['SRX3398847.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 12 Jan 2018 03:48:58: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:48:58: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:48:58: # Command line: callpeak -t SRX3398847.bam -f BAM -g 2.15e9 -n SRX3398847.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3398847.20 # format = BAM # ChIP-seq file = ['SRX3398847.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 12 Jan 2018 03:48:58: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:48:58: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:48:58: # Command line: callpeak -t SRX3398847.bam -f BAM -g 2.15e9 -n SRX3398847.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3398847.05 # format = BAM # ChIP-seq file = ['SRX3398847.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 12 Jan 2018 03:48:58: #1 read tag files... INFO @ Fri, 12 Jan 2018 03:48:58: #1 read treatment tags... INFO @ Fri, 12 Jan 2018 03:49:13: 1000000 INFO @ Fri, 12 Jan 2018 03:49:14: 1000000 INFO @ Fri, 12 Jan 2018 03:49:14: 1000000 INFO @ Fri, 12 Jan 2018 03:49:29: 2000000 INFO @ Fri, 12 Jan 2018 03:49:29: 2000000 INFO @ Fri, 12 Jan 2018 03:49:30: 2000000 INFO @ Fri, 12 Jan 2018 03:49:44: 3000000 INFO @ Fri, 12 Jan 2018 03:49:44: 3000000 INFO @ Fri, 12 Jan 2018 03:49:46: 3000000 INFO @ Fri, 12 Jan 2018 03:50:00: 4000000 INFO @ Fri, 12 Jan 2018 03:50:00: 4000000 INFO @ Fri, 12 Jan 2018 03:50:01: 4000000 INFO @ Fri, 12 Jan 2018 03:50:15: 5000000 INFO @ Fri, 12 Jan 2018 03:50:16: 5000000 INFO @ Fri, 12 Jan 2018 03:50:17: 5000000 INFO @ Fri, 12 Jan 2018 03:50:31: 6000000 INFO @ Fri, 12 Jan 2018 03:50:32: 6000000 INFO @ Fri, 12 Jan 2018 03:50:33: 6000000 INFO @ Fri, 12 Jan 2018 03:50:48: 7000000 INFO @ Fri, 12 Jan 2018 03:50:48: 7000000 INFO @ Fri, 12 Jan 2018 03:50:50: 7000000 INFO @ Fri, 12 Jan 2018 03:51:03: 8000000 INFO @ Fri, 12 Jan 2018 03:51:04: 8000000 INFO @ Fri, 12 Jan 2018 03:51:05: 8000000 INFO @ Fri, 12 Jan 2018 03:51:18: 9000000 INFO @ Fri, 12 Jan 2018 03:51:20: 9000000 INFO @ Fri, 12 Jan 2018 03:51:21: 9000000 INFO @ Fri, 12 Jan 2018 03:51:34: 10000000 INFO @ Fri, 12 Jan 2018 03:51:35: 10000000 INFO @ Fri, 12 Jan 2018 03:51:36: 10000000 INFO @ Fri, 12 Jan 2018 03:51:50: 11000000 INFO @ Fri, 12 Jan 2018 03:51:51: 11000000 INFO @ Fri, 12 Jan 2018 03:51:52: 11000000 INFO @ Fri, 12 Jan 2018 03:52:06: 12000000 INFO @ Fri, 12 Jan 2018 03:52:07: 12000000 INFO @ Fri, 12 Jan 2018 03:52:09: 12000000 INFO @ Fri, 12 Jan 2018 03:52:22: 13000000 INFO @ Fri, 12 Jan 2018 03:52:23: 13000000 INFO @ Fri, 12 Jan 2018 03:52:25: 13000000 INFO @ Fri, 12 Jan 2018 03:52:37: 14000000 INFO @ Fri, 12 Jan 2018 03:52:39: 14000000 INFO @ Fri, 12 Jan 2018 03:52:41: 14000000 INFO @ Fri, 12 Jan 2018 03:52:52: 15000000 INFO @ Fri, 12 Jan 2018 03:52:55: 15000000 INFO @ Fri, 12 Jan 2018 03:52:56: 15000000 INFO @ Fri, 12 Jan 2018 03:53:08: 16000000 INFO @ Fri, 12 Jan 2018 03:53:11: 16000000 INFO @ Fri, 12 Jan 2018 03:53:12: 16000000 INFO @ Fri, 12 Jan 2018 03:53:24: 17000000 INFO @ Fri, 12 Jan 2018 03:53:27: 17000000 INFO @ Fri, 12 Jan 2018 03:53:29: 17000000 INFO @ Fri, 12 Jan 2018 03:53:40: 18000000 INFO @ Fri, 12 Jan 2018 03:53:43: 18000000 INFO @ Fri, 12 Jan 2018 03:53:45: 18000000 INFO @ Fri, 12 Jan 2018 03:53:56: 19000000 INFO @ Fri, 12 Jan 2018 03:53:59: 19000000 INFO @ Fri, 12 Jan 2018 03:54:00: 19000000 INFO @ Fri, 12 Jan 2018 03:54:11: 20000000 INFO @ Fri, 12 Jan 2018 03:54:15: 20000000 INFO @ Fri, 12 Jan 2018 03:54:17: 20000000 INFO @ Fri, 12 Jan 2018 03:54:20: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 03:54:20: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 03:54:20: #1 total tags in treatment: 20511036 INFO @ Fri, 12 Jan 2018 03:54:20: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 03:54:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 03:54:21: #1 tags after filtering in treatment: 20510908 INFO @ Fri, 12 Jan 2018 03:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 03:54:21: #1 finished! INFO @ Fri, 12 Jan 2018 03:54:21: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 03:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 03:54:23: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 03:54:23: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 03:54:23: #1 total tags in treatment: 20511036 INFO @ Fri, 12 Jan 2018 03:54:23: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 03:54:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 03:54:25: #1 tags after filtering in treatment: 20510908 INFO @ Fri, 12 Jan 2018 03:54:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 03:54:25: #1 finished! INFO @ Fri, 12 Jan 2018 03:54:25: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 03:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 03:54:25: #1 tag size is determined as 51 bps INFO @ Fri, 12 Jan 2018 03:54:25: #1 tag size = 51 INFO @ Fri, 12 Jan 2018 03:54:25: #1 total tags in treatment: 20511036 INFO @ Fri, 12 Jan 2018 03:54:25: #1 user defined the maximum tags... INFO @ Fri, 12 Jan 2018 03:54:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 12 Jan 2018 03:54:25: #2 number of paired peaks: 4415 INFO @ Fri, 12 Jan 2018 03:54:25: start model_add_line... INFO @ Fri, 12 Jan 2018 03:54:26: start X-correlation... INFO @ Fri, 12 Jan 2018 03:54:26: end of X-cor INFO @ Fri, 12 Jan 2018 03:54:26: #2 finished! INFO @ Fri, 12 Jan 2018 03:54:26: #2 predicted fragment length is 63 bps INFO @ Fri, 12 Jan 2018 03:54:26: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 12 Jan 2018 03:54:26: #2.2 Generate R script for model : SRX3398847.10_model.r WARNING @ Fri, 12 Jan 2018 03:54:26: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 03:54:26: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 12 Jan 2018 03:54:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 03:54:26: #3 Call peaks... INFO @ Fri, 12 Jan 2018 03:54:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 03:54:26: #1 tags after filtering in treatment: 20510908 INFO @ Fri, 12 Jan 2018 03:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 12 Jan 2018 03:54:26: #1 finished! INFO @ Fri, 12 Jan 2018 03:54:26: #2 Build Peak Model... INFO @ Fri, 12 Jan 2018 03:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 12 Jan 2018 03:54:29: #2 number of paired peaks: 4415 INFO @ Fri, 12 Jan 2018 03:54:29: start model_add_line... INFO @ Fri, 12 Jan 2018 03:54:29: start X-correlation... INFO @ Fri, 12 Jan 2018 03:54:29: end of X-cor INFO @ Fri, 12 Jan 2018 03:54:29: #2 finished! INFO @ Fri, 12 Jan 2018 03:54:29: #2 predicted fragment length is 63 bps INFO @ Fri, 12 Jan 2018 03:54:29: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 12 Jan 2018 03:54:29: #2.2 Generate R script for model : SRX3398847.20_model.r WARNING @ Fri, 12 Jan 2018 03:54:29: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 03:54:29: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 12 Jan 2018 03:54:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 03:54:29: #3 Call peaks... INFO @ Fri, 12 Jan 2018 03:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 03:54:30: #2 number of paired peaks: 4415 INFO @ Fri, 12 Jan 2018 03:54:30: start model_add_line... INFO @ Fri, 12 Jan 2018 03:54:31: start X-correlation... INFO @ Fri, 12 Jan 2018 03:54:31: end of X-cor INFO @ Fri, 12 Jan 2018 03:54:31: #2 finished! INFO @ Fri, 12 Jan 2018 03:54:31: #2 predicted fragment length is 63 bps INFO @ Fri, 12 Jan 2018 03:54:31: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 12 Jan 2018 03:54:31: #2.2 Generate R script for model : SRX3398847.05_model.r WARNING @ Fri, 12 Jan 2018 03:54:31: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 12 Jan 2018 03:54:31: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 12 Jan 2018 03:54:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 12 Jan 2018 03:54:31: #3 Call peaks... INFO @ Fri, 12 Jan 2018 03:54:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 12 Jan 2018 03:56:11: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 03:56:14: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 03:56:19: #3 Call peaks for each chromosome... INFO @ Fri, 12 Jan 2018 03:57:09: #4 Write output xls file... SRX3398847.05_peaks.xls INFO @ Fri, 12 Jan 2018 03:57:09: #4 Write peak in narrowPeak format file... SRX3398847.05_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 03:57:09: #4 Write summits bed file... SRX3398847.05_summits.bed INFO @ Fri, 12 Jan 2018 03:57:09: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (904 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 03:57:14: #4 Write output xls file... SRX3398847.20_peaks.xls INFO @ Fri, 12 Jan 2018 03:57:14: #4 Write peak in narrowPeak format file... SRX3398847.20_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 03:57:14: #4 Write summits bed file... SRX3398847.20_summits.bed INFO @ Fri, 12 Jan 2018 03:57:14: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (104 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 12 Jan 2018 03:57:15: #4 Write output xls file... SRX3398847.10_peaks.xls INFO @ Fri, 12 Jan 2018 03:57:15: #4 Write peak in narrowPeak format file... SRX3398847.10_peaks.narrowPeak INFO @ Fri, 12 Jan 2018 03:57:15: #4 Write summits bed file... SRX3398847.10_summits.bed INFO @ Fri, 12 Jan 2018 03:57:15: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。