Job ID = 10487582 sra ファイルのダウンロード中... Completed: 3588591K bytes transferred in 137 seconds (213637K 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 53381402 spots for /home/okishinya/chipatlas/results/rn6/SRX2611109/SRR5311153.sra Written 53381402 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: 02:39:07 53381402 reads; of these: 53381402 (100.00%) were unpaired; of these: 25439514 (47.66%) aligned 0 times 24104066 (45.15%) aligned exactly 1 time 3837822 (7.19%) aligned >1 times 52.34% overall alignment rate Time searching: 02:39:09 Overall time: 02:39:09 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 24 files... [bam_rmdupse_core] 6324212 / 27941888 = 0.2263 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 12:32:48: # Command line: callpeak -t SRX2611109.bam -f BAM -g 2.15e9 -n SRX2611109.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611109.20 # format = BAM # ChIP-seq file = ['SRX2611109.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 12:32:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:32:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:32:48: # Command line: callpeak -t SRX2611109.bam -f BAM -g 2.15e9 -n SRX2611109.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611109.05 # format = BAM # ChIP-seq file = ['SRX2611109.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 12:32:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:32:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:32:48: # Command line: callpeak -t SRX2611109.bam -f BAM -g 2.15e9 -n SRX2611109.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611109.10 # format = BAM # ChIP-seq file = ['SRX2611109.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 12:32:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:32:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:32:58: 1000000 INFO @ Sun, 18 Mar 2018 12:32:58: 1000000 INFO @ Sun, 18 Mar 2018 12:32:58: 1000000 INFO @ Sun, 18 Mar 2018 12:33:07: 2000000 INFO @ Sun, 18 Mar 2018 12:33:08: 2000000 INFO @ Sun, 18 Mar 2018 12:33:09: 2000000 INFO @ Sun, 18 Mar 2018 12:33:17: 3000000 INFO @ Sun, 18 Mar 2018 12:33:18: 3000000 INFO @ Sun, 18 Mar 2018 12:33:19: 3000000 INFO @ Sun, 18 Mar 2018 12:33:27: 4000000 INFO @ Sun, 18 Mar 2018 12:33:29: 4000000 INFO @ Sun, 18 Mar 2018 12:33:30: 4000000 INFO @ Sun, 18 Mar 2018 12:33:36: 5000000 INFO @ Sun, 18 Mar 2018 12:33:39: 5000000 INFO @ Sun, 18 Mar 2018 12:33:41: 5000000 INFO @ Sun, 18 Mar 2018 12:33:46: 6000000 INFO @ Sun, 18 Mar 2018 12:33:50: 6000000 INFO @ Sun, 18 Mar 2018 12:33:52: 6000000 INFO @ Sun, 18 Mar 2018 12:33:55: 7000000 INFO @ Sun, 18 Mar 2018 12:34:00: 7000000 INFO @ Sun, 18 Mar 2018 12:34:03: 7000000 INFO @ Sun, 18 Mar 2018 12:34:05: 8000000 INFO @ Sun, 18 Mar 2018 12:34:10: 8000000 INFO @ Sun, 18 Mar 2018 12:34:13: 8000000 INFO @ Sun, 18 Mar 2018 12:34:15: 9000000 INFO @ Sun, 18 Mar 2018 12:34:21: 9000000 INFO @ Sun, 18 Mar 2018 12:34:24: 10000000 INFO @ Sun, 18 Mar 2018 12:34:24: 9000000 INFO @ Sun, 18 Mar 2018 12:34:31: 10000000 INFO @ Sun, 18 Mar 2018 12:34:34: 11000000 INFO @ Sun, 18 Mar 2018 12:34:35: 10000000 INFO @ Sun, 18 Mar 2018 12:34:42: 11000000 INFO @ Sun, 18 Mar 2018 12:34:43: 12000000 INFO @ Sun, 18 Mar 2018 12:34:46: 11000000 INFO @ Sun, 18 Mar 2018 12:34:52: 12000000 INFO @ Sun, 18 Mar 2018 12:34:53: 13000000 INFO @ Sun, 18 Mar 2018 12:34:57: 12000000 INFO @ Sun, 18 Mar 2018 12:35:02: 13000000 INFO @ Sun, 18 Mar 2018 12:35:03: 14000000 INFO @ Sun, 18 Mar 2018 12:35:07: 13000000 INFO @ Sun, 18 Mar 2018 12:35:12: 15000000 INFO @ Sun, 18 Mar 2018 12:35:13: 14000000 INFO @ Sun, 18 Mar 2018 12:35:18: 14000000 INFO @ Sun, 18 Mar 2018 12:35:22: 16000000 INFO @ Sun, 18 Mar 2018 12:35:23: 15000000 INFO @ Sun, 18 Mar 2018 12:35:29: 15000000 INFO @ Sun, 18 Mar 2018 12:35:32: 17000000 INFO @ Sun, 18 Mar 2018 12:35:33: 16000000 INFO @ Sun, 18 Mar 2018 12:35:40: 16000000 INFO @ Sun, 18 Mar 2018 12:35:41: 18000000 INFO @ Sun, 18 Mar 2018 12:35:44: 17000000 INFO @ Sun, 18 Mar 2018 12:35:50: 17000000 INFO @ Sun, 18 Mar 2018 12:35:51: 19000000 INFO @ Sun, 18 Mar 2018 12:35:54: 18000000 INFO @ Sun, 18 Mar 2018 12:36:00: 20000000 INFO @ Sun, 18 Mar 2018 12:36:01: 18000000 INFO @ Sun, 18 Mar 2018 12:36:04: 19000000 INFO @ Sun, 18 Mar 2018 12:36:10: 21000000 INFO @ Sun, 18 Mar 2018 12:36:12: 19000000 INFO @ Sun, 18 Mar 2018 12:36:15: 20000000 INFO @ Sun, 18 Mar 2018 12:36:16: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 12:36:16: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 12:36:16: #1 total tags in treatment: 21617676 INFO @ Sun, 18 Mar 2018 12:36:16: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:36:16: #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 12:36:17: #1 tags after filtering in treatment: 21617536 INFO @ Sun, 18 Mar 2018 12:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:36:17: #1 finished! INFO @ Sun, 18 Mar 2018 12:36:17: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:36:20: #2 number of paired peaks: 12713 INFO @ Sun, 18 Mar 2018 12:36:20: start model_add_line... INFO @ Sun, 18 Mar 2018 12:36:20: start X-correlation... INFO @ Sun, 18 Mar 2018 12:36:20: end of X-cor INFO @ Sun, 18 Mar 2018 12:36:20: #2 finished! INFO @ Sun, 18 Mar 2018 12:36:20: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 12:36:20: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 12:36:20: #2.2 Generate R script for model : SRX2611109.10_model.r WARNING @ Sun, 18 Mar 2018 12:36:20: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 12:36:20: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 12:36:20: #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 12:36:20: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:36:23: 20000000 INFO @ Sun, 18 Mar 2018 12:36:25: 21000000 INFO @ Sun, 18 Mar 2018 12:36:32: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 12:36:32: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 12:36:32: #1 total tags in treatment: 21617676 INFO @ Sun, 18 Mar 2018 12:36:32: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:36:32: #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 12:36:33: #1 tags after filtering in treatment: 21617536 INFO @ Sun, 18 Mar 2018 12:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:36:33: #1 finished! INFO @ Sun, 18 Mar 2018 12:36:33: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:36:34: 21000000 INFO @ Sun, 18 Mar 2018 12:36:35: #2 number of paired peaks: 12713 INFO @ Sun, 18 Mar 2018 12:36:35: start model_add_line... INFO @ Sun, 18 Mar 2018 12:36:36: start X-correlation... INFO @ Sun, 18 Mar 2018 12:36:36: end of X-cor INFO @ Sun, 18 Mar 2018 12:36:36: #2 finished! INFO @ Sun, 18 Mar 2018 12:36:36: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 12:36:36: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 12:36:36: #2.2 Generate R script for model : SRX2611109.05_model.r WARNING @ Sun, 18 Mar 2018 12:36:36: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 12:36:36: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 12:36:36: #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 12:36:36: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:36:40: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 12:36:40: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 12:36:40: #1 total tags in treatment: 21617676 INFO @ Sun, 18 Mar 2018 12:36:40: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:36:40: #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 12:36:40: #1 tags after filtering in treatment: 21617536 INFO @ Sun, 18 Mar 2018 12:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:36:40: #1 finished! INFO @ Sun, 18 Mar 2018 12:36:40: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:36:43: #2 number of paired peaks: 12713 INFO @ Sun, 18 Mar 2018 12:36:43: start model_add_line... INFO @ Sun, 18 Mar 2018 12:36:43: start X-correlation... INFO @ Sun, 18 Mar 2018 12:36:43: end of X-cor INFO @ Sun, 18 Mar 2018 12:36:43: #2 finished! INFO @ Sun, 18 Mar 2018 12:36:43: #2 predicted fragment length is 156 bps INFO @ Sun, 18 Mar 2018 12:36:43: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 18 Mar 2018 12:36:43: #2.2 Generate R script for model : SRX2611109.20_model.r WARNING @ Sun, 18 Mar 2018 12:36:43: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 12:36:43: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sun, 18 Mar 2018 12:36:43: #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 12:36:43: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:37:11: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:37:32: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:37:34: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:37:39: #4 Write output xls file... SRX2611109.10_peaks.xls INFO @ Sun, 18 Mar 2018 12:37:39: #4 Write peak in narrowPeak format file... SRX2611109.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:37:39: #4 Write summits bed file... SRX2611109.10_summits.bed INFO @ Sun, 18 Mar 2018 12:37:39: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (638 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 12:38:01: #4 Write output xls file... SRX2611109.05_peaks.xls INFO @ Sun, 18 Mar 2018 12:38:01: #4 Write peak in narrowPeak format file... SRX2611109.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:38:01: #4 Write summits bed file... SRX2611109.05_summits.bed INFO @ Sun, 18 Mar 2018 12:38:01: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (2022 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 12:38:04: #4 Write output xls file... SRX2611109.20_peaks.xls INFO @ Sun, 18 Mar 2018 12:38:04: #4 Write peak in narrowPeak format file... SRX2611109.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:38:04: #4 Write summits bed file... SRX2611109.20_summits.bed INFO @ Sun, 18 Mar 2018 12:38:04: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。