Job ID = 10487575 sra ファイルのダウンロード中... Completed: 4597732K bytes transferred in 166 seconds (226627K 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 67782524 spots for /home/okishinya/chipatlas/results/rn6/SRX2611105/SRR5311149.sra Written 67782524 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: 03:53:23 67782524 reads; of these: 67782524 (100.00%) were unpaired; of these: 18073516 (26.66%) aligned 0 times 42702541 (63.00%) aligned exactly 1 time 7006467 (10.34%) aligned >1 times 73.34% overall alignment rate Time searching: 03:53:25 Overall time: 03:53:25 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 40 files... [bam_rmdupse_core] 12440088 / 49709008 = 0.2503 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 @ Sun, 18 Mar 2018 13:57:57: # Command line: callpeak -t SRX2611105.bam -f BAM -g 2.15e9 -n SRX2611105.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611105.05 # format = BAM # ChIP-seq file = ['SRX2611105.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 @ Sun, 18 Mar 2018 13:57:57: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:57:57: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:57:57: # Command line: callpeak -t SRX2611105.bam -f BAM -g 2.15e9 -n SRX2611105.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611105.10 # format = BAM # ChIP-seq file = ['SRX2611105.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 @ Sun, 18 Mar 2018 13:57:57: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:57:57: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:57:57: # Command line: callpeak -t SRX2611105.bam -f BAM -g 2.15e9 -n SRX2611105.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611105.20 # format = BAM # ChIP-seq file = ['SRX2611105.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 @ Sun, 18 Mar 2018 13:57:57: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:57:57: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:58:08: 1000000 INFO @ Sun, 18 Mar 2018 13:58:08: 1000000 INFO @ Sun, 18 Mar 2018 13:58:08: 1000000 INFO @ Sun, 18 Mar 2018 13:58:18: 2000000 INFO @ Sun, 18 Mar 2018 13:58:18: 2000000 INFO @ Sun, 18 Mar 2018 13:58:18: 2000000 INFO @ Sun, 18 Mar 2018 13:58:28: 3000000 INFO @ Sun, 18 Mar 2018 13:58:28: 3000000 INFO @ Sun, 18 Mar 2018 13:58:28: 3000000 INFO @ Sun, 18 Mar 2018 13:58:38: 4000000 INFO @ Sun, 18 Mar 2018 13:58:38: 4000000 INFO @ Sun, 18 Mar 2018 13:58:38: 4000000 INFO @ Sun, 18 Mar 2018 13:58:48: 5000000 INFO @ Sun, 18 Mar 2018 13:58:48: 5000000 INFO @ Sun, 18 Mar 2018 13:58:48: 5000000 INFO @ Sun, 18 Mar 2018 13:58:58: 6000000 INFO @ Sun, 18 Mar 2018 13:58:58: 6000000 INFO @ Sun, 18 Mar 2018 13:58:58: 6000000 INFO @ Sun, 18 Mar 2018 13:59:08: 7000000 INFO @ Sun, 18 Mar 2018 13:59:08: 7000000 INFO @ Sun, 18 Mar 2018 13:59:08: 7000000 INFO @ Sun, 18 Mar 2018 13:59:18: 8000000 INFO @ Sun, 18 Mar 2018 13:59:18: 8000000 INFO @ Sun, 18 Mar 2018 13:59:18: 8000000 INFO @ Sun, 18 Mar 2018 13:59:28: 9000000 INFO @ Sun, 18 Mar 2018 13:59:28: 9000000 INFO @ Sun, 18 Mar 2018 13:59:28: 9000000 INFO @ Sun, 18 Mar 2018 13:59:38: 10000000 INFO @ Sun, 18 Mar 2018 13:59:38: 10000000 INFO @ Sun, 18 Mar 2018 13:59:38: 10000000 INFO @ Sun, 18 Mar 2018 13:59:48: 11000000 INFO @ Sun, 18 Mar 2018 13:59:48: 11000000 INFO @ Sun, 18 Mar 2018 13:59:48: 11000000 INFO @ Sun, 18 Mar 2018 13:59:58: 12000000 INFO @ Sun, 18 Mar 2018 13:59:58: 12000000 INFO @ Sun, 18 Mar 2018 13:59:58: 12000000 INFO @ Sun, 18 Mar 2018 14:00:08: 13000000 INFO @ Sun, 18 Mar 2018 14:00:08: 13000000 INFO @ Sun, 18 Mar 2018 14:00:08: 13000000 INFO @ Sun, 18 Mar 2018 14:00:17: 14000000 INFO @ Sun, 18 Mar 2018 14:00:18: 14000000 INFO @ Sun, 18 Mar 2018 14:00:18: 14000000 INFO @ Sun, 18 Mar 2018 14:00:28: 15000000 INFO @ Sun, 18 Mar 2018 14:00:28: 15000000 INFO @ Sun, 18 Mar 2018 14:00:28: 15000000 INFO @ Sun, 18 Mar 2018 14:00:38: 16000000 INFO @ Sun, 18 Mar 2018 14:00:38: 16000000 INFO @ Sun, 18 Mar 2018 14:00:38: 16000000 INFO @ Sun, 18 Mar 2018 14:00:47: 17000000 INFO @ Sun, 18 Mar 2018 14:00:48: 17000000 INFO @ Sun, 18 Mar 2018 14:00:48: 17000000 INFO @ Sun, 18 Mar 2018 14:00:57: 18000000 INFO @ Sun, 18 Mar 2018 14:00:57: 18000000 INFO @ Sun, 18 Mar 2018 14:00:58: 18000000 INFO @ Sun, 18 Mar 2018 14:01:07: 19000000 INFO @ Sun, 18 Mar 2018 14:01:07: 19000000 INFO @ Sun, 18 Mar 2018 14:01:07: 19000000 INFO @ Sun, 18 Mar 2018 14:01:17: 20000000 INFO @ Sun, 18 Mar 2018 14:01:17: 20000000 INFO @ Sun, 18 Mar 2018 14:01:17: 20000000 INFO @ Sun, 18 Mar 2018 14:01:27: 21000000 INFO @ Sun, 18 Mar 2018 14:01:27: 21000000 INFO @ Sun, 18 Mar 2018 14:01:27: 21000000 INFO @ Sun, 18 Mar 2018 14:01:37: 22000000 INFO @ Sun, 18 Mar 2018 14:01:37: 22000000 INFO @ Sun, 18 Mar 2018 14:01:37: 22000000 INFO @ Sun, 18 Mar 2018 14:01:47: 23000000 INFO @ Sun, 18 Mar 2018 14:01:47: 23000000 INFO @ Sun, 18 Mar 2018 14:01:47: 23000000 INFO @ Sun, 18 Mar 2018 14:01:57: 24000000 INFO @ Sun, 18 Mar 2018 14:01:57: 24000000 INFO @ Sun, 18 Mar 2018 14:01:57: 24000000 INFO @ Sun, 18 Mar 2018 14:02:07: 25000000 INFO @ Sun, 18 Mar 2018 14:02:07: 25000000 INFO @ Sun, 18 Mar 2018 14:02:08: 25000000 INFO @ Sun, 18 Mar 2018 14:02:17: 26000000 INFO @ Sun, 18 Mar 2018 14:02:17: 26000000 INFO @ Sun, 18 Mar 2018 14:02:18: 26000000 INFO @ Sun, 18 Mar 2018 14:02:27: 27000000 INFO @ Sun, 18 Mar 2018 14:02:28: 27000000 INFO @ Sun, 18 Mar 2018 14:02:28: 27000000 INFO @ Sun, 18 Mar 2018 14:02:37: 28000000 INFO @ Sun, 18 Mar 2018 14:02:38: 28000000 INFO @ Sun, 18 Mar 2018 14:02:38: 28000000 INFO @ Sun, 18 Mar 2018 14:02:47: 29000000 INFO @ Sun, 18 Mar 2018 14:02:48: 29000000 INFO @ Sun, 18 Mar 2018 14:02:48: 29000000 INFO @ Sun, 18 Mar 2018 14:02:57: 30000000 INFO @ Sun, 18 Mar 2018 14:02:58: 30000000 INFO @ Sun, 18 Mar 2018 14:02:58: 30000000 INFO @ Sun, 18 Mar 2018 14:03:07: 31000000 INFO @ Sun, 18 Mar 2018 14:03:08: 31000000 INFO @ Sun, 18 Mar 2018 14:03:09: 31000000 INFO @ Sun, 18 Mar 2018 14:03:17: 32000000 INFO @ Sun, 18 Mar 2018 14:03:18: 32000000 INFO @ Sun, 18 Mar 2018 14:03:19: 32000000 INFO @ Sun, 18 Mar 2018 14:03:27: 33000000 INFO @ Sun, 18 Mar 2018 14:03:29: 33000000 INFO @ Sun, 18 Mar 2018 14:03:29: 33000000 INFO @ Sun, 18 Mar 2018 14:03:37: 34000000 INFO @ Sun, 18 Mar 2018 14:03:39: 34000000 INFO @ Sun, 18 Mar 2018 14:03:39: 34000000 INFO @ Sun, 18 Mar 2018 14:03:47: 35000000 INFO @ Sun, 18 Mar 2018 14:03:48: 35000000 INFO @ Sun, 18 Mar 2018 14:03:50: 35000000 INFO @ Sun, 18 Mar 2018 14:03:58: 36000000 INFO @ Sun, 18 Mar 2018 14:03:58: 36000000 INFO @ Sun, 18 Mar 2018 14:04:00: 36000000 INFO @ Sun, 18 Mar 2018 14:04:08: 37000000 INFO @ Sun, 18 Mar 2018 14:04:09: 37000000 INFO @ Sun, 18 Mar 2018 14:04:11: 37000000 INFO @ Sun, 18 Mar 2018 14:04:11: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:04:11: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:04:11: #1 total tags in treatment: 37268920 INFO @ Sun, 18 Mar 2018 14:04:11: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:04:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:04:12: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:04:12: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:04:12: #1 total tags in treatment: 37268920 INFO @ Sun, 18 Mar 2018 14:04:12: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:04:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:04:12: #1 tags after filtering in treatment: 37268820 INFO @ Sun, 18 Mar 2018 14:04:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:04:12: #1 finished! INFO @ Sun, 18 Mar 2018 14:04:12: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:04:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:04:13: #1 tags after filtering in treatment: 37268820 INFO @ Sun, 18 Mar 2018 14:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:04:13: #1 finished! INFO @ Sun, 18 Mar 2018 14:04:13: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:04:14: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:04:14: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:04:14: #1 total tags in treatment: 37268920 INFO @ Sun, 18 Mar 2018 14:04:14: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:04:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:04:15: #1 tags after filtering in treatment: 37268820 INFO @ Sun, 18 Mar 2018 14:04:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:04:15: #1 finished! INFO @ Sun, 18 Mar 2018 14:04:15: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:04:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:04:16: #2 number of paired peaks: 7996 INFO @ Sun, 18 Mar 2018 14:04:16: start model_add_line... INFO @ Sun, 18 Mar 2018 14:04:16: #2 number of paired peaks: 7996 INFO @ Sun, 18 Mar 2018 14:04:16: start model_add_line... INFO @ Sun, 18 Mar 2018 14:04:17: start X-correlation... INFO @ Sun, 18 Mar 2018 14:04:17: end of X-cor INFO @ Sun, 18 Mar 2018 14:04:17: #2 finished! INFO @ Sun, 18 Mar 2018 14:04:17: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:04:17: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:04:17: #2.2 Generate R script for model : SRX2611105.05_model.r WARNING @ Sun, 18 Mar 2018 14:04:17: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:04:17: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:04:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:04:17: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:04:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:04:17: start X-correlation... INFO @ Sun, 18 Mar 2018 14:04:17: end of X-cor INFO @ Sun, 18 Mar 2018 14:04:17: #2 finished! INFO @ Sun, 18 Mar 2018 14:04:17: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:04:17: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:04:17: #2.2 Generate R script for model : SRX2611105.20_model.r WARNING @ Sun, 18 Mar 2018 14:04:17: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:04:17: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:04:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:04:17: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:04:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:04:19: #2 number of paired peaks: 7996 INFO @ Sun, 18 Mar 2018 14:04:19: start model_add_line... INFO @ Sun, 18 Mar 2018 14:04:19: start X-correlation... INFO @ Sun, 18 Mar 2018 14:04:19: end of X-cor INFO @ Sun, 18 Mar 2018 14:04:19: #2 finished! INFO @ Sun, 18 Mar 2018 14:04:19: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:04:20: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:04:20: #2.2 Generate R script for model : SRX2611105.10_model.r WARNING @ Sun, 18 Mar 2018 14:04:20: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:04:20: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:04:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:04:20: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:04:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:05:41: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:05:49: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:05:58: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:06:32: #4 Write output xls file... SRX2611105.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:06:32: #4 Write peak in narrowPeak format file... SRX2611105.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:06:32: #4 Write summits bed file... SRX2611105.20_summits.bed INFO @ Sun, 18 Mar 2018 14:06:32: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:06:41: #4 Write output xls file... SRX2611105.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:06:41: #4 Write peak in narrowPeak format file... SRX2611105.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:06:41: #4 Write summits bed file... SRX2611105.05_summits.bed INFO @ Sun, 18 Mar 2018 14:06:41: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (4600 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:06:49: #4 Write output xls file... SRX2611105.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:06:49: #4 Write peak in narrowPeak format file... SRX2611105.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:06:49: #4 Write summits bed file... SRX2611105.10_summits.bed INFO @ Sun, 18 Mar 2018 14:06:49: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (1184 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。