Job ID = 10194900 sra ファイルのダウンロード中... Completed: 148151K bytes transferred in 15 seconds (80742K bits/sec), in 1 file. Completed: 144871K bytes transferred in 16 seconds (70368K bits/sec), in 1 file. Completed: 244090K bytes transferred in 19 seconds (104605K bits/sec), in 1 file. Completed: 239540K bytes transferred in 21 seconds (91463K bits/sec), in 1 file. Completed: 240657K bytes transferred in 17 seconds (114364K bits/sec), in 1 file. Completed: 237050K bytes transferred in 15 seconds (126904K 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 3493169 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319914.sra Written 3493169 spots total Written 3401921 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319915.sra Written 3401921 spots total Written 5269697 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319918.sra Written 5269697 spots total Written 5197695 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319919.sra Written 5197695 spots total Written 5207399 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319917.sra Written 5207399 spots total Written 5344043 spots for /home/okishinya/chipatlas/results/rn6/SRX2202895/SRR4319916.sra Written 5344043 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 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:49:07 27913924 reads; of these: 27913924 (100.00%) were unpaired; of these: 864593 (3.10%) aligned 0 times 18220726 (65.27%) aligned exactly 1 time 8828605 (31.63%) aligned >1 times 96.90% overall alignment rate Time searching: 00:49:10 Overall time: 00:49:10 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] 3271207 / 27049331 = 0.1209 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, 10 Nov 2017 22:57:46: # Command line: callpeak -t SRX2202895.bam -f BAM -g 2.15e9 -n SRX2202895.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202895.20 # format = BAM # ChIP-seq file = ['SRX2202895.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, 10 Nov 2017 22:57:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:57:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:57:46: # Command line: callpeak -t SRX2202895.bam -f BAM -g 2.15e9 -n SRX2202895.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202895.05 # format = BAM # ChIP-seq file = ['SRX2202895.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, 10 Nov 2017 22:57:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:57:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:57:46: # Command line: callpeak -t SRX2202895.bam -f BAM -g 2.15e9 -n SRX2202895.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202895.10 # format = BAM # ChIP-seq file = ['SRX2202895.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, 10 Nov 2017 22:57:46: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:57:46: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:58:00: 1000000 INFO @ Fri, 10 Nov 2017 22:58:00: 1000000 INFO @ Fri, 10 Nov 2017 22:58:02: 1000000 INFO @ Fri, 10 Nov 2017 22:58:13: 2000000 INFO @ Fri, 10 Nov 2017 22:58:16: 2000000 INFO @ Fri, 10 Nov 2017 22:58:17: 2000000 INFO @ Fri, 10 Nov 2017 22:58:27: 3000000 INFO @ Fri, 10 Nov 2017 22:58:27: 3000000 INFO @ Fri, 10 Nov 2017 22:58:28: 3000000 INFO @ Fri, 10 Nov 2017 22:58:38: 4000000 INFO @ Fri, 10 Nov 2017 22:58:43: 4000000 INFO @ Fri, 10 Nov 2017 22:58:43: 4000000 INFO @ Fri, 10 Nov 2017 22:58:49: 5000000 INFO @ Fri, 10 Nov 2017 22:58:57: 5000000 INFO @ Fri, 10 Nov 2017 22:58:58: 5000000 INFO @ Fri, 10 Nov 2017 22:58:59: 6000000 INFO @ Fri, 10 Nov 2017 22:59:10: 7000000 INFO @ Fri, 10 Nov 2017 22:59:11: 6000000 INFO @ Fri, 10 Nov 2017 22:59:12: 6000000 INFO @ Fri, 10 Nov 2017 22:59:21: 8000000 INFO @ Fri, 10 Nov 2017 22:59:25: 7000000 INFO @ Fri, 10 Nov 2017 22:59:26: 7000000 INFO @ Fri, 10 Nov 2017 22:59:32: 9000000 INFO @ Fri, 10 Nov 2017 22:59:39: 8000000 INFO @ Fri, 10 Nov 2017 22:59:40: 8000000 INFO @ Fri, 10 Nov 2017 22:59:42: 10000000 INFO @ Fri, 10 Nov 2017 22:59:52: 9000000 INFO @ Fri, 10 Nov 2017 22:59:53: 11000000 INFO @ Fri, 10 Nov 2017 22:59:54: 9000000 INFO @ Fri, 10 Nov 2017 23:00:04: 12000000 INFO @ Fri, 10 Nov 2017 23:00:05: 10000000 INFO @ Fri, 10 Nov 2017 23:00:08: 10000000 INFO @ Fri, 10 Nov 2017 23:00:15: 13000000 INFO @ Fri, 10 Nov 2017 23:00:18: 11000000 INFO @ Fri, 10 Nov 2017 23:00:22: 11000000 INFO @ Fri, 10 Nov 2017 23:00:25: 14000000 INFO @ Fri, 10 Nov 2017 23:00:33: 12000000 INFO @ Fri, 10 Nov 2017 23:00:38: 15000000 INFO @ Fri, 10 Nov 2017 23:00:38: 12000000 INFO @ Fri, 10 Nov 2017 23:00:48: 13000000 INFO @ Fri, 10 Nov 2017 23:00:51: 16000000 INFO @ Fri, 10 Nov 2017 23:00:55: 13000000 INFO @ Fri, 10 Nov 2017 23:01:03: 14000000 INFO @ Fri, 10 Nov 2017 23:01:04: 17000000 INFO @ Fri, 10 Nov 2017 23:01:13: 14000000 INFO @ Fri, 10 Nov 2017 23:01:17: 18000000 INFO @ Fri, 10 Nov 2017 23:01:17: 15000000 INFO @ Fri, 10 Nov 2017 23:01:30: 15000000 INFO @ Fri, 10 Nov 2017 23:01:30: 19000000 INFO @ Fri, 10 Nov 2017 23:01:33: 16000000 INFO @ Fri, 10 Nov 2017 23:01:43: 20000000 INFO @ Fri, 10 Nov 2017 23:01:47: 16000000 INFO @ Fri, 10 Nov 2017 23:01:49: 17000000 INFO @ Fri, 10 Nov 2017 23:01:57: 21000000 INFO @ Fri, 10 Nov 2017 23:02:04: 17000000 INFO @ Fri, 10 Nov 2017 23:02:05: 18000000 INFO @ Fri, 10 Nov 2017 23:02:10: 22000000 INFO @ Fri, 10 Nov 2017 23:02:21: 19000000 INFO @ Fri, 10 Nov 2017 23:02:21: 18000000 INFO @ Fri, 10 Nov 2017 23:02:23: 23000000 INFO @ Fri, 10 Nov 2017 23:02:33: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:02:33: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:02:33: #1 total tags in treatment: 23778124 INFO @ Fri, 10 Nov 2017 23:02:33: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:02:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:02:34: #1 tags after filtering in treatment: 23778010 INFO @ Fri, 10 Nov 2017 23:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:02:34: #1 finished! INFO @ Fri, 10 Nov 2017 23:02:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:02:36: 19000000 INFO @ Fri, 10 Nov 2017 23:02:37: 20000000 INFO @ Fri, 10 Nov 2017 23:02:37: #2 number of paired peaks: 11927 INFO @ Fri, 10 Nov 2017 23:02:37: start model_add_line... INFO @ Fri, 10 Nov 2017 23:02:38: start X-correlation... INFO @ Fri, 10 Nov 2017 23:02:38: end of X-cor INFO @ Fri, 10 Nov 2017 23:02:38: #2 finished! INFO @ Fri, 10 Nov 2017 23:02:38: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 23:02:38: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 23:02:38: #2.2 Generate R script for model : SRX2202895.10_model.r WARNING @ Fri, 10 Nov 2017 23:02:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:02:38: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 23:02:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:02:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:02:48: 20000000 INFO @ Fri, 10 Nov 2017 23:02:54: 21000000 INFO @ Fri, 10 Nov 2017 23:02:59: 21000000 INFO @ Fri, 10 Nov 2017 23:03:10: 22000000 INFO @ Fri, 10 Nov 2017 23:03:12: 22000000 INFO @ Fri, 10 Nov 2017 23:03:26: 23000000 INFO @ Fri, 10 Nov 2017 23:03:26: 23000000 INFO @ Fri, 10 Nov 2017 23:03:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:03:37: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:03:37: #1 total tags in treatment: 23778124 INFO @ Fri, 10 Nov 2017 23:03:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:03:38: #1 tags after filtering in treatment: 23778010 INFO @ Fri, 10 Nov 2017 23:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:03:38: #1 finished! INFO @ Fri, 10 Nov 2017 23:03:38: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:03:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:03:39: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:03:39: #1 total tags in treatment: 23778124 INFO @ Fri, 10 Nov 2017 23:03:39: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:03:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:03:40: #1 tags after filtering in treatment: 23778010 INFO @ Fri, 10 Nov 2017 23:03:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:03:40: #1 finished! INFO @ Fri, 10 Nov 2017 23:03:40: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:03:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:03:41: #2 number of paired peaks: 11927 INFO @ Fri, 10 Nov 2017 23:03:41: start model_add_line... INFO @ Fri, 10 Nov 2017 23:03:42: start X-correlation... INFO @ Fri, 10 Nov 2017 23:03:42: end of X-cor INFO @ Fri, 10 Nov 2017 23:03:42: #2 finished! INFO @ Fri, 10 Nov 2017 23:03:42: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 23:03:42: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 23:03:42: #2.2 Generate R script for model : SRX2202895.05_model.r WARNING @ Fri, 10 Nov 2017 23:03:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:03:42: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 23:03:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:03:42: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:03:43: #2 number of paired peaks: 11927 INFO @ Fri, 10 Nov 2017 23:03:43: start model_add_line... INFO @ Fri, 10 Nov 2017 23:03:44: start X-correlation... INFO @ Fri, 10 Nov 2017 23:03:44: end of X-cor INFO @ Fri, 10 Nov 2017 23:03:44: #2 finished! INFO @ Fri, 10 Nov 2017 23:03:44: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Nov 2017 23:03:44: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Nov 2017 23:03:44: #2.2 Generate R script for model : SRX2202895.20_model.r WARNING @ Fri, 10 Nov 2017 23:03:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:03:44: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Nov 2017 23:03:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:03:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:03:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:04:41: #4 Write output xls file... SRX2202895.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:04:41: #4 Write peak in narrowPeak format file... SRX2202895.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:04:41: #4 Write summits bed file... SRX2202895.10_summits.bed INFO @ Fri, 10 Nov 2017 23:04:41: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1258 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:04:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:05:02: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:05:38: #4 Write output xls file... SRX2202895.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:05:38: #4 Write peak in narrowPeak format file... SRX2202895.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:05:38: #4 Write summits bed file... SRX2202895.20_summits.bed INFO @ Fri, 10 Nov 2017 23:05:38: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:05:50: #4 Write output xls file... SRX2202895.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:05:50: #4 Write peak in narrowPeak format file... SRX2202895.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:05:50: #4 Write summits bed file... SRX2202895.05_summits.bed INFO @ Fri, 10 Nov 2017 23:05:50: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (2136 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。