Job ID = 10194911 sra ファイルのダウンロード中... Completed: 117384K bytes transferred in 8 seconds (112840K bits/sec), in 1 file. Completed: 114324K bytes transferred in 8 seconds (105845K bits/sec), in 1 file. Completed: 198389K bytes transferred in 14 seconds (113483K bits/sec), in 1 file. Completed: 194793K bytes transferred in 12 seconds (130380K bits/sec), in 1 file. Completed: 194988K bytes transferred in 11 seconds (137111K bits/sec), in 1 file. Completed: 192006K bytes transferred in 13 seconds (120081K 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 2676642 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319981.sra Written 2676642 spots total Written 2761291 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319980.sra Written 2761291 spots total Written 4198221 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319985.sra Written 4198221 spots total Written 4255665 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319984.sra Written 4255665 spots total Written 4327217 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319982.sra Written 4327217 spots total Written 4221602 spots for /home/okishinya/chipatlas/results/rn6/SRX2202906/SRR4319983.sra Written 4221602 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:54:09 22440638 reads; of these: 22440638 (100.00%) were unpaired; of these: 596677 (2.66%) aligned 0 times 14903770 (66.41%) aligned exactly 1 time 6940191 (30.93%) aligned >1 times 97.34% overall alignment rate Time searching: 00:54:13 Overall time: 00:54:13 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] 759505 / 21843961 = 0.0348 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 23:26:50: # Command line: callpeak -t SRX2202906.bam -f BAM -g 2.15e9 -n SRX2202906.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202906.10 # format = BAM # ChIP-seq file = ['SRX2202906.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 23:26:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:26:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:26:50: # Command line: callpeak -t SRX2202906.bam -f BAM -g 2.15e9 -n SRX2202906.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202906.05 # format = BAM # ChIP-seq file = ['SRX2202906.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 23:26:50: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:26:50: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:26:51: # Command line: callpeak -t SRX2202906.bam -f BAM -g 2.15e9 -n SRX2202906.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202906.20 # format = BAM # ChIP-seq file = ['SRX2202906.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 23:26:51: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:26:51: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:27:09: 1000000 INFO @ Fri, 10 Nov 2017 23:27:11: 1000000 INFO @ Fri, 10 Nov 2017 23:27:13: 1000000 INFO @ Fri, 10 Nov 2017 23:27:27: 2000000 INFO @ Fri, 10 Nov 2017 23:27:31: 2000000 INFO @ Fri, 10 Nov 2017 23:27:35: 2000000 INFO @ Fri, 10 Nov 2017 23:27:39: 3000000 INFO @ Fri, 10 Nov 2017 23:27:49: 3000000 INFO @ Fri, 10 Nov 2017 23:27:52: 4000000 INFO @ Fri, 10 Nov 2017 23:27:58: 3000000 INFO @ Fri, 10 Nov 2017 23:28:06: 5000000 INFO @ Fri, 10 Nov 2017 23:28:07: 4000000 INFO @ Fri, 10 Nov 2017 23:28:19: 6000000 INFO @ Fri, 10 Nov 2017 23:28:21: 4000000 INFO @ Fri, 10 Nov 2017 23:28:25: 5000000 INFO @ Fri, 10 Nov 2017 23:28:32: 7000000 INFO @ Fri, 10 Nov 2017 23:28:36: 5000000 INFO @ Fri, 10 Nov 2017 23:28:43: 6000000 INFO @ Fri, 10 Nov 2017 23:28:45: 8000000 INFO @ Fri, 10 Nov 2017 23:28:52: 6000000 INFO @ Fri, 10 Nov 2017 23:28:58: 9000000 INFO @ Fri, 10 Nov 2017 23:29:02: 7000000 INFO @ Fri, 10 Nov 2017 23:29:08: 7000000 INFO @ Fri, 10 Nov 2017 23:29:14: 10000000 INFO @ Fri, 10 Nov 2017 23:29:19: 8000000 INFO @ Fri, 10 Nov 2017 23:29:23: 8000000 INFO @ Fri, 10 Nov 2017 23:29:29: 11000000 INFO @ Fri, 10 Nov 2017 23:29:37: 9000000 INFO @ Fri, 10 Nov 2017 23:29:38: 9000000 INFO @ Fri, 10 Nov 2017 23:29:42: 12000000 INFO @ Fri, 10 Nov 2017 23:29:55: 10000000 INFO @ Fri, 10 Nov 2017 23:29:57: 13000000 INFO @ Fri, 10 Nov 2017 23:29:58: 10000000 INFO @ Fri, 10 Nov 2017 23:30:14: 14000000 INFO @ Fri, 10 Nov 2017 23:30:14: 11000000 INFO @ Fri, 10 Nov 2017 23:30:20: 11000000 INFO @ Fri, 10 Nov 2017 23:30:32: 12000000 INFO @ Fri, 10 Nov 2017 23:30:36: 15000000 INFO @ Fri, 10 Nov 2017 23:30:44: 12000000 INFO @ Fri, 10 Nov 2017 23:30:50: 13000000 INFO @ Fri, 10 Nov 2017 23:30:58: 16000000 INFO @ Fri, 10 Nov 2017 23:31:06: 13000000 INFO @ Fri, 10 Nov 2017 23:31:08: 14000000 INFO @ Fri, 10 Nov 2017 23:31:21: 17000000 INFO @ Fri, 10 Nov 2017 23:31:26: 15000000 INFO @ Fri, 10 Nov 2017 23:31:30: 14000000 INFO @ Fri, 10 Nov 2017 23:31:43: 18000000 INFO @ Fri, 10 Nov 2017 23:31:45: 16000000 INFO @ Fri, 10 Nov 2017 23:31:53: 15000000 INFO @ Fri, 10 Nov 2017 23:32:03: 17000000 INFO @ Fri, 10 Nov 2017 23:32:05: 19000000 INFO @ Fri, 10 Nov 2017 23:32:16: 16000000 INFO @ Fri, 10 Nov 2017 23:32:22: 18000000 INFO @ Fri, 10 Nov 2017 23:32:28: 20000000 INFO @ Fri, 10 Nov 2017 23:32:39: 17000000 INFO @ Fri, 10 Nov 2017 23:32:40: 19000000 INFO @ Fri, 10 Nov 2017 23:32:50: 21000000 INFO @ Fri, 10 Nov 2017 23:32:52: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:32:52: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:32:52: #1 total tags in treatment: 21084456 INFO @ Fri, 10 Nov 2017 23:32:52: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:32:52: #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 23:32:52: #1 tags after filtering in treatment: 21084334 INFO @ Fri, 10 Nov 2017 23:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:32:52: #1 finished! INFO @ Fri, 10 Nov 2017 23:32:52: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:32:55: #2 number of paired peaks: 6648 INFO @ Fri, 10 Nov 2017 23:32:55: start model_add_line... INFO @ Fri, 10 Nov 2017 23:32:56: start X-correlation... INFO @ Fri, 10 Nov 2017 23:32:56: end of X-cor INFO @ Fri, 10 Nov 2017 23:32:56: #2 finished! INFO @ Fri, 10 Nov 2017 23:32:56: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 23:32:56: #2 alternative fragment length(s) may be 50,229,392 bps INFO @ Fri, 10 Nov 2017 23:32:56: #2.2 Generate R script for model : SRX2202906.05_model.r WARNING @ Fri, 10 Nov 2017 23:32:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:32:56: #2 You may need to consider one of the other alternative d(s): 50,229,392 WARNING @ Fri, 10 Nov 2017 23:32:56: #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 23:32:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:32:58: 20000000 INFO @ Fri, 10 Nov 2017 23:33:02: 18000000 INFO @ Fri, 10 Nov 2017 23:33:17: 21000000 INFO @ Fri, 10 Nov 2017 23:33:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:33:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:33:18: #1 total tags in treatment: 21084456 INFO @ Fri, 10 Nov 2017 23:33:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:33:18: #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 23:33:19: #1 tags after filtering in treatment: 21084334 INFO @ Fri, 10 Nov 2017 23:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:33:19: #1 finished! INFO @ Fri, 10 Nov 2017 23:33:19: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:33:22: #2 number of paired peaks: 6648 INFO @ Fri, 10 Nov 2017 23:33:22: start model_add_line... INFO @ Fri, 10 Nov 2017 23:33:22: start X-correlation... INFO @ Fri, 10 Nov 2017 23:33:22: end of X-cor INFO @ Fri, 10 Nov 2017 23:33:22: #2 finished! INFO @ Fri, 10 Nov 2017 23:33:22: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 23:33:22: #2 alternative fragment length(s) may be 50,229,392 bps INFO @ Fri, 10 Nov 2017 23:33:22: #2.2 Generate R script for model : SRX2202906.10_model.r WARNING @ Fri, 10 Nov 2017 23:33:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:33:22: #2 You may need to consider one of the other alternative d(s): 50,229,392 WARNING @ Fri, 10 Nov 2017 23:33:22: #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 23:33:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:33:24: 19000000 INFO @ Fri, 10 Nov 2017 23:33:46: 20000000 INFO @ Fri, 10 Nov 2017 23:34:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:34:05: 21000000 INFO @ Fri, 10 Nov 2017 23:34:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:34:07: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:34:07: #1 total tags in treatment: 21084456 INFO @ Fri, 10 Nov 2017 23:34:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:34:07: #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 23:34:08: #1 tags after filtering in treatment: 21084334 INFO @ Fri, 10 Nov 2017 23:34:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:34:08: #1 finished! INFO @ Fri, 10 Nov 2017 23:34:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:34:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:34:11: #2 number of paired peaks: 6648 INFO @ Fri, 10 Nov 2017 23:34:11: start model_add_line... INFO @ Fri, 10 Nov 2017 23:34:11: start X-correlation... INFO @ Fri, 10 Nov 2017 23:34:11: end of X-cor INFO @ Fri, 10 Nov 2017 23:34:11: #2 finished! INFO @ Fri, 10 Nov 2017 23:34:11: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 23:34:11: #2 alternative fragment length(s) may be 50,229,392 bps INFO @ Fri, 10 Nov 2017 23:34:11: #2.2 Generate R script for model : SRX2202906.20_model.r WARNING @ Fri, 10 Nov 2017 23:34:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:34:11: #2 You may need to consider one of the other alternative d(s): 50,229,392 WARNING @ Fri, 10 Nov 2017 23:34:11: #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 23:34:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:34:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:34:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:34:38: #4 Write output xls file... SRX2202906.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:34:38: #4 Write peak in narrowPeak format file... SRX2202906.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:34:39: #4 Write summits bed file... SRX2202906.05_summits.bed INFO @ Fri, 10 Nov 2017 23:34:39: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (1805 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:35:07: #4 Write output xls file... SRX2202906.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:35:07: #4 Write peak in narrowPeak format file... SRX2202906.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:35:07: #4 Write summits bed file... SRX2202906.10_summits.bed INFO @ Fri, 10 Nov 2017 23:35:07: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (1041 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:35:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:35:54: #4 Write output xls file... SRX2202906.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:35:54: #4 Write peak in narrowPeak format file... SRX2202906.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:35:54: #4 Write summits bed file... SRX2202906.20_summits.bed INFO @ Fri, 10 Nov 2017 23:35:54: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (529 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。