Job ID = 10194847 sra ファイルのダウンロード中... Completed: 1436465K bytes transferred in 27 seconds (425156K 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 74754476 spots for /home/okishinya/chipatlas/results/rn6/SRX1977136/SRR3952268.sra Written 74754476 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:40:25 74754476 reads; of these: 74754476 (100.00%) were unpaired; of these: 62674959 (83.84%) aligned 0 times 7350748 (9.83%) aligned exactly 1 time 4728769 (6.33%) aligned >1 times 16.16% overall alignment rate Time searching: 00:40:28 Overall time: 00:40:28 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 8 files... [bam_rmdupse_core] 2494679 / 12079517 = 0.2065 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 02:35:17: # Command line: callpeak -t SRX1977136.bam -f BAM -g 2.15e9 -n SRX1977136.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977136.10 # format = BAM # ChIP-seq file = ['SRX1977136.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 02:35:17: # Command line: callpeak -t SRX1977136.bam -f BAM -g 2.15e9 -n SRX1977136.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977136.05 # format = BAM # ChIP-seq file = ['SRX1977136.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 02:35:17: # Command line: callpeak -t SRX1977136.bam -f BAM -g 2.15e9 -n SRX1977136.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977136.20 # format = BAM # ChIP-seq file = ['SRX1977136.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 02:35:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:35:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:35:17: #1 read tag files... INFO @ Sat, 11 Nov 2017 02:35:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:35:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:35:17: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 02:35:23: 1000000 INFO @ Sat, 11 Nov 2017 02:35:24: 1000000 INFO @ Sat, 11 Nov 2017 02:35:24: 1000000 INFO @ Sat, 11 Nov 2017 02:35:30: 2000000 INFO @ Sat, 11 Nov 2017 02:35:30: 2000000 INFO @ Sat, 11 Nov 2017 02:35:31: 2000000 INFO @ Sat, 11 Nov 2017 02:35:36: 3000000 INFO @ Sat, 11 Nov 2017 02:35:37: 3000000 INFO @ Sat, 11 Nov 2017 02:35:38: 3000000 INFO @ Sat, 11 Nov 2017 02:35:43: 4000000 INFO @ Sat, 11 Nov 2017 02:35:44: 4000000 INFO @ Sat, 11 Nov 2017 02:35:45: 4000000 INFO @ Sat, 11 Nov 2017 02:35:49: 5000000 INFO @ Sat, 11 Nov 2017 02:35:51: 5000000 INFO @ Sat, 11 Nov 2017 02:35:52: 5000000 INFO @ Sat, 11 Nov 2017 02:35:55: 6000000 INFO @ Sat, 11 Nov 2017 02:35:58: 6000000 INFO @ Sat, 11 Nov 2017 02:35:59: 6000000 INFO @ Sat, 11 Nov 2017 02:36:02: 7000000 INFO @ Sat, 11 Nov 2017 02:36:04: 7000000 INFO @ Sat, 11 Nov 2017 02:36:06: 7000000 INFO @ Sat, 11 Nov 2017 02:36:08: 8000000 INFO @ Sat, 11 Nov 2017 02:36:11: 8000000 INFO @ Sat, 11 Nov 2017 02:36:13: 8000000 INFO @ Sat, 11 Nov 2017 02:36:14: 9000000 INFO @ Sat, 11 Nov 2017 02:36:18: 9000000 INFO @ Sat, 11 Nov 2017 02:36:18: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:36:18: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:36:18: #1 total tags in treatment: 9584838 INFO @ Sat, 11 Nov 2017 02:36:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:36:18: #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 02:36:19: #1 tags after filtering in treatment: 9584651 INFO @ Sat, 11 Nov 2017 02:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:36:19: #1 finished! INFO @ Sat, 11 Nov 2017 02:36:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:36:20: 9000000 INFO @ Sat, 11 Nov 2017 02:36:22: #2 number of paired peaks: 59976 INFO @ Sat, 11 Nov 2017 02:36:22: start model_add_line... INFO @ Sat, 11 Nov 2017 02:36:22: start X-correlation... INFO @ Sat, 11 Nov 2017 02:36:22: end of X-cor INFO @ Sat, 11 Nov 2017 02:36:22: #2 finished! INFO @ Sat, 11 Nov 2017 02:36:22: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:36:22: #2 alternative fragment length(s) may be 52,139 bps INFO @ Sat, 11 Nov 2017 02:36:22: #2.2 Generate R script for model : SRX1977136.05_model.r WARNING @ Sat, 11 Nov 2017 02:36:22: #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 02:36:22: #2 You may need to consider one of the other alternative d(s): 52,139 WARNING @ Sat, 11 Nov 2017 02:36:22: #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 02:36:22: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:36:22: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:36:22: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:36:22: #1 total tags in treatment: 9584838 INFO @ Sat, 11 Nov 2017 02:36:22: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:36:22: #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 02:36:23: #1 tags after filtering in treatment: 9584651 INFO @ Sat, 11 Nov 2017 02:36:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:36:23: #1 finished! INFO @ Sat, 11 Nov 2017 02:36:23: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:36:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:36:24: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 02:36:24: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 02:36:24: #1 total tags in treatment: 9584838 INFO @ Sat, 11 Nov 2017 02:36:24: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 02:36:24: #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 02:36:25: #1 tags after filtering in treatment: 9584651 INFO @ Sat, 11 Nov 2017 02:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 02:36:25: #1 finished! INFO @ Sat, 11 Nov 2017 02:36:25: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 02:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 02:36:26: #2 number of paired peaks: 59976 INFO @ Sat, 11 Nov 2017 02:36:26: start model_add_line... INFO @ Sat, 11 Nov 2017 02:36:26: start X-correlation... INFO @ Sat, 11 Nov 2017 02:36:26: end of X-cor INFO @ Sat, 11 Nov 2017 02:36:26: #2 finished! INFO @ Sat, 11 Nov 2017 02:36:26: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:36:26: #2 alternative fragment length(s) may be 52,139 bps INFO @ Sat, 11 Nov 2017 02:36:26: #2.2 Generate R script for model : SRX1977136.10_model.r WARNING @ Sat, 11 Nov 2017 02:36:26: #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 02:36:26: #2 You may need to consider one of the other alternative d(s): 52,139 WARNING @ Sat, 11 Nov 2017 02:36:26: #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 02:36:26: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:36:28: #2 number of paired peaks: 59976 INFO @ Sat, 11 Nov 2017 02:36:28: start model_add_line... INFO @ Sat, 11 Nov 2017 02:36:28: start X-correlation... INFO @ Sat, 11 Nov 2017 02:36:28: end of X-cor INFO @ Sat, 11 Nov 2017 02:36:28: #2 finished! INFO @ Sat, 11 Nov 2017 02:36:28: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Nov 2017 02:36:28: #2 alternative fragment length(s) may be 52,139 bps INFO @ Sat, 11 Nov 2017 02:36:28: #2.2 Generate R script for model : SRX1977136.20_model.r WARNING @ Sat, 11 Nov 2017 02:36:28: #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 02:36:28: #2 You may need to consider one of the other alternative d(s): 52,139 WARNING @ Sat, 11 Nov 2017 02:36:28: #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 02:36:28: #3 Call peaks... INFO @ Sat, 11 Nov 2017 02:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 02:36:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:36:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:36:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 02:37:01: #4 Write output xls file... SRX1977136.05_peaks.xls INFO @ Sat, 11 Nov 2017 02:37:02: #4 Write peak in narrowPeak format file... SRX1977136.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:37:02: #4 Write summits bed file... SRX1977136.05_summits.bed INFO @ Sat, 11 Nov 2017 02:37:02: Done! pass1 - making usageList (130 chroms): 3 millis pass2 - checking and writing primary data (11132 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write output xls file... SRX1977136.10_peaks.xls INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write peak in narrowPeak format file... SRX1977136.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write summits bed file... SRX1977136.10_summits.bed INFO @ Sat, 11 Nov 2017 02:37:04: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (3716 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write output xls file... SRX1977136.20_peaks.xls INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write peak in narrowPeak format file... SRX1977136.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 02:37:04: #4 Write summits bed file... SRX1977136.20_summits.bed INFO @ Sat, 11 Nov 2017 02:37:04: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (935 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。