Job ID = 10194848 sra ファイルのダウンロード中... Completed: 858117K bytes transferred in 11 seconds (586436K 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 42460734 spots for /home/okishinya/chipatlas/results/rn6/SRX1977137/SRR3952269.sra Written 42460734 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:35 42460734 reads; of these: 42460734 (100.00%) were unpaired; of these: 15053147 (35.45%) aligned 0 times 16198775 (38.15%) aligned exactly 1 time 11208812 (26.40%) aligned >1 times 64.55% overall alignment rate Time searching: 00:51:37 Overall time: 00:51:38 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] 1643266 / 27407587 = 0.0600 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, 11 Nov 2017 02:48:21: # Command line: callpeak -t SRX1977137.bam -f BAM -g 2.15e9 -n SRX1977137.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977137.10 # format = BAM # ChIP-seq file = ['SRX1977137.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 @ Sat, 11 Nov 2017 02:48:21: # Command line: callpeak -t SRX1977137.bam -f BAM -g 2.15e9 -n SRX1977137.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977137.05 # format = BAM # ChIP-seq file = ['SRX1977137.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 @ Sat, 11 Nov 2017 02:48:21: # Command line: callpeak -t SRX1977137.bam -f BAM -g 2.15e9 -n SRX1977137.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977137.20 # format = BAM # ChIP-seq file = ['SRX1977137.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 @ Sat, 11 Nov 2017 02:48:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:48:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:48:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:48:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:48:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:48:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:48:28: 1000000 INFO @ Sat, 11 Nov 2017 02:48:28: 1000000 INFO @ Sat, 11 Nov 2017 02:48:28: 1000000 INFO @ Sat, 11 Nov 2017 02:48:35: 2000000 INFO @ Sat, 11 Nov 2017 02:48:36: 2000000 INFO @ Sat, 11 Nov 2017 02:48:36: 2000000 INFO @ Sat, 11 Nov 2017 02:48:43: 3000000 INFO @ Sat, 11 Nov 2017 02:48:43: 3000000 INFO @ Sat, 11 Nov 2017 02:48:43: 3000000 INFO @ Sat, 11 Nov 2017 02:48:50: 4000000 INFO @ Sat, 11 Nov 2017 02:48:50: 4000000 INFO @ Sat, 11 Nov 2017 02:48:50: 4000000 INFO @ Sat, 11 Nov 2017 02:48:57: 5000000 INFO @ Sat, 11 Nov 2017 02:48:57: 5000000 INFO @ Sat, 11 Nov 2017 02:48:57: 5000000 INFO @ Sat, 11 Nov 2017 02:49:04: 6000000 INFO @ Sat, 11 Nov 2017 02:49:04: 6000000 INFO @ Sat, 11 Nov 2017 02:49:05: 6000000 INFO @ Sat, 11 Nov 2017 02:49:12: 7000000 INFO @ Sat, 11 Nov 2017 02:49:12: 7000000 INFO @ Sat, 11 Nov 2017 02:49:12: 7000000 INFO @ Sat, 11 Nov 2017 02:49:19: 8000000 INFO @ Sat, 11 Nov 2017 02:49:19: 8000000 INFO @ Sat, 11 Nov 2017 02:49:19: 8000000 INFO @ Sat, 11 Nov 2017 02:49:26: 9000000 INFO @ Sat, 11 Nov 2017 02:49:26: 9000000 INFO @ Sat, 11 Nov 2017 02:49:27: 9000000 INFO @ Sat, 11 Nov 2017 02:49:33: 10000000 INFO @ Sat, 11 Nov 2017 02:49:33: 10000000 INFO @ Sat, 11 Nov 2017 02:49:34: 10000000 INFO @ Sat, 11 Nov 2017 02:49:41: 11000000 INFO @ Sat, 11 Nov 2017 02:49:41: 11000000 INFO @ Sat, 11 Nov 2017 02:49:41: 11000000 INFO @ Sat, 11 Nov 2017 02:49:48: 12000000 INFO @ Sat, 11 Nov 2017 02:49:48: 12000000 INFO @ Sat, 11 Nov 2017 02:49:49: 12000000 INFO @ Sat, 11 Nov 2017 02:49:55: 13000000 INFO @ Sat, 11 Nov 2017 02:49:56: 13000000 INFO @ Sat, 11 Nov 2017 02:49:56: 13000000 INFO @ Sat, 11 Nov 2017 02:50:03: 14000000 INFO @ Sat, 11 Nov 2017 02:50:03: 14000000 INFO @ Sat, 11 Nov 2017 02:50:04: 14000000 INFO @ Sat, 11 Nov 2017 02:50:10: 15000000 INFO @ Sat, 11 Nov 2017 02:50:11: 15000000 INFO @ Sat, 11 Nov 2017 02:50:12: 15000000 INFO @ Sat, 11 Nov 2017 02:50:17: 16000000 INFO @ Sat, 11 Nov 2017 02:50:18: 16000000 INFO @ Sat, 11 Nov 2017 02:50:19: 16000000 INFO @ Sat, 11 Nov 2017 02:50:24: 17000000 INFO @ Sat, 11 Nov 2017 02:50:26: 17000000 INFO @ Sat, 11 Nov 2017 02:50:27: 17000000 INFO @ Sat, 11 Nov 2017 02:50:31: 18000000 INFO @ Sat, 11 Nov 2017 02:50:34: 18000000 INFO @ Sat, 11 Nov 2017 02:50:35: 18000000 INFO @ Sat, 11 Nov 2017 02:50:39: 19000000 INFO @ Sat, 11 Nov 2017 02:50:42: 19000000 INFO @ Sat, 11 Nov 2017 02:50:43: 19000000 INFO @ Sat, 11 Nov 2017 02:50:46: 20000000 INFO @ Sat, 11 Nov 2017 02:50:50: 20000000 INFO @ Sat, 11 Nov 2017 02:50:51: 20000000 INFO @ Sat, 11 Nov 2017 02:50:53: 21000000 INFO @ Sat, 11 Nov 2017 02:50:58: 21000000 INFO @ Sat, 11 Nov 2017 02:50:59: 21000000 INFO @ Sat, 11 Nov 2017 02:51:00: 22000000 INFO @ Sat, 11 Nov 2017 02:51:05: 22000000 INFO @ Sat, 11 Nov 2017 02:51:07: 22000000 INFO @ Sat, 11 Nov 2017 02:51:08: 23000000 INFO @ Sat, 11 Nov 2017 02:51:13: 23000000 INFO @ Sat, 11 Nov 2017 02:51:15: 23000000 INFO @ Sat, 11 Nov 2017 02:51:15: 24000000 INFO @ Sat, 11 Nov 2017 02:51:21: 24000000 INFO @ Sat, 11 Nov 2017 02:51:22: 25000000 INFO @ Sat, 11 Nov 2017 02:51:22: 24000000 INFO @ Sat, 11 Nov 2017 02:51:28: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:51:28: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:51:28: #1 total tags in treatment: 25764321 INFO @ Sat, 11 Nov 2017 02:51:28: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:51:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:51:29: 25000000 INFO @ Sat, 11 Nov 2017 02:51:29: #1 tags after filtering in treatment: 25764238 INFO @ Sat, 11 Nov 2017 02:51:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:51:29: #1 finished! INFO @ Sat, 11 Nov 2017 02:51:29: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:51:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:51:30: 25000000 INFO @ Sat, 11 Nov 2017 02:51:32: #2 number of paired peaks: 8585 INFO @ Sat, 11 Nov 2017 02:51:32: start model_add_line... INFO @ Sat, 11 Nov 2017 02:51:32: start X-correlation... INFO @ Sat, 11 Nov 2017 02:51:32: end of X-cor INFO @ Sat, 11 Nov 2017 02:51:32: #2 finished! INFO @ Sat, 11 Nov 2017 02:51:32: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:51:32: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 02:51:32: #2.2 Generate R script for model : SRX1977137.05_model.r WARNING @ Sat, 11 Nov 2017 02:51:32: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:51:32: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 02:51:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:51:32: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:51:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:51:35: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:51:35: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:51:35: #1 total tags in treatment: 25764321 INFO @ Sat, 11 Nov 2017 02:51:35: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:51:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:51:35: #1 tags after filtering in treatment: 25764238 INFO @ Sat, 11 Nov 2017 02:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:51:35: #1 finished! INFO @ Sat, 11 Nov 2017 02:51:35: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:51:36: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:51:36: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:51:36: #1 total tags in treatment: 25764321 INFO @ Sat, 11 Nov 2017 02:51:36: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 02:51:37: #1 tags after filtering in treatment: 25764238 INFO @ Sat, 11 Nov 2017 02:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:51:37: #1 finished! INFO @ Sat, 11 Nov 2017 02:51:37: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:51:38: #2 number of paired peaks: 8585 INFO @ Sat, 11 Nov 2017 02:51:38: start model_add_line... INFO @ Sat, 11 Nov 2017 02:51:39: start X-correlation... INFO @ Sat, 11 Nov 2017 02:51:39: end of X-cor INFO @ Sat, 11 Nov 2017 02:51:39: #2 finished! INFO @ Sat, 11 Nov 2017 02:51:39: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:51:39: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 02:51:39: #2.2 Generate R script for model : SRX1977137.20_model.r WARNING @ Sat, 11 Nov 2017 02:51:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:51:39: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 02:51:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:51:39: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:51:40: #2 number of paired peaks: 8585 INFO @ Sat, 11 Nov 2017 02:51:40: start model_add_line... INFO @ Sat, 11 Nov 2017 02:51:40: start X-correlation... INFO @ Sat, 11 Nov 2017 02:51:40: end of X-cor INFO @ Sat, 11 Nov 2017 02:51:40: #2 finished! INFO @ Sat, 11 Nov 2017 02:51:40: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:51:40: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Nov 2017 02:51:40: #2.2 Generate R script for model : SRX1977137.10_model.r WARNING @ Sat, 11 Nov 2017 02:51:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 02:51:40: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Nov 2017 02:51:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 02:51:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:52:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:52:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:52:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:53:09: #4 Write output xls file... SRX1977137.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:53:09: #4 Write peak in narrowPeak format file... SRX1977137.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:53:09: #4 Write summits bed file... SRX1977137.05_summits.bed INFO @ Sat, 11 Nov 2017 02:53:09: Done! pass1 - making usageList (108 chroms): 1 millis pass2 - checking and writing primary data (4849 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:53:14: #4 Write output xls file... SRX1977137.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:53:14: #4 Write peak in narrowPeak format file... SRX1977137.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:53:14: #4 Write summits bed file... SRX1977137.20_summits.bed INFO @ Sat, 11 Nov 2017 02:53:14: Done! pass1 - making usageList (53 chroms): 0 millis pass2 - checking and writing primary data (696 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:53:21: #4 Write output xls file... SRX1977137.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:53:21: #4 Write peak in narrowPeak format file... SRX1977137.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:53:21: #4 Write summits bed file... SRX1977137.10_summits.bed INFO @ Sat, 11 Nov 2017 02:53:21: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (1785 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。