Job ID = 10194909 sra ファイルのダウンロード中... Completed: 108529K bytes transferred in 10 seconds (88195K bits/sec), in 1 file. Completed: 106272K bytes transferred in 7 seconds (116431K bits/sec), in 1 file. Completed: 179107K bytes transferred in 9 seconds (150004K bits/sec), in 1 file. Completed: 176174K bytes transferred in 10 seconds (131888K bits/sec), in 1 file. Completed: 176546K bytes transferred in 9 seconds (150020K bits/sec), in 1 file. Completed: 174102K bytes transferred in 22 seconds (63632K 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 2487455 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319969.sra Written 2487455 spots total Written 2551072 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319968.sra Written 2551072 spots total Written 3795244 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319973.sra Written 3795244 spots total Written 3809438 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319971.sra Written 3809438 spots total Written 3842020 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319972.sra Written 3842020 spots total Written 3897945 spots for /home/okishinya/chipatlas/results/rn6/SRX2202904/SRR4319970.sra Written 3897945 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:35:55 20383174 reads; of these: 20383174 (100.00%) were unpaired; of these: 601918 (2.95%) aligned 0 times 13421355 (65.85%) aligned exactly 1 time 6359901 (31.20%) aligned >1 times 97.05% overall alignment rate Time searching: 00:36:00 Overall time: 00:36:00 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] 1133937 / 19781256 = 0.0573 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 23:00:21: # Command line: callpeak -t SRX2202904.bam -f BAM -g 2.15e9 -n SRX2202904.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202904.10 # format = BAM # ChIP-seq file = ['SRX2202904.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 23:00:21: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:00:21: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:00:21: # Command line: callpeak -t SRX2202904.bam -f BAM -g 2.15e9 -n SRX2202904.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202904.05 # format = BAM # ChIP-seq file = ['SRX2202904.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 23:00:21: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:00:21: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:00:21: # Command line: callpeak -t SRX2202904.bam -f BAM -g 2.15e9 -n SRX2202904.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202904.20 # format = BAM # ChIP-seq file = ['SRX2202904.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 23:00:21: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:00:21: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:00:41: 1000000 INFO @ Fri, 10 Nov 2017 23:00:41: 1000000 INFO @ Fri, 10 Nov 2017 23:00:46: 1000000 INFO @ Fri, 10 Nov 2017 23:01:05: 2000000 INFO @ Fri, 10 Nov 2017 23:01:07: 2000000 INFO @ Fri, 10 Nov 2017 23:01:12: 2000000 INFO @ Fri, 10 Nov 2017 23:01:27: 3000000 INFO @ Fri, 10 Nov 2017 23:01:36: 3000000 INFO @ Fri, 10 Nov 2017 23:01:37: 3000000 INFO @ Fri, 10 Nov 2017 23:01:45: 4000000 INFO @ Fri, 10 Nov 2017 23:02:01: 4000000 INFO @ Fri, 10 Nov 2017 23:02:03: 5000000 INFO @ Fri, 10 Nov 2017 23:02:05: 4000000 INFO @ Fri, 10 Nov 2017 23:02:21: 6000000 INFO @ Fri, 10 Nov 2017 23:02:24: 5000000 INFO @ Fri, 10 Nov 2017 23:02:33: 5000000 INFO @ Fri, 10 Nov 2017 23:02:38: 7000000 INFO @ Fri, 10 Nov 2017 23:02:46: 6000000 INFO @ Fri, 10 Nov 2017 23:02:56: 8000000 INFO @ Fri, 10 Nov 2017 23:03:03: 6000000 INFO @ Fri, 10 Nov 2017 23:03:04: 7000000 INFO @ Fri, 10 Nov 2017 23:03:14: 9000000 INFO @ Fri, 10 Nov 2017 23:03:23: 8000000 INFO @ Fri, 10 Nov 2017 23:03:30: 7000000 INFO @ Fri, 10 Nov 2017 23:03:32: 10000000 INFO @ Fri, 10 Nov 2017 23:03:48: 9000000 INFO @ Fri, 10 Nov 2017 23:03:52: 11000000 INFO @ Fri, 10 Nov 2017 23:03:53: 8000000 INFO @ Fri, 10 Nov 2017 23:04:03: 10000000 INFO @ Fri, 10 Nov 2017 23:04:13: 12000000 INFO @ Fri, 10 Nov 2017 23:04:18: 9000000 INFO @ Fri, 10 Nov 2017 23:04:24: 11000000 INFO @ Fri, 10 Nov 2017 23:04:33: 13000000 INFO @ Fri, 10 Nov 2017 23:04:42: 10000000 INFO @ Fri, 10 Nov 2017 23:04:46: 12000000 INFO @ Fri, 10 Nov 2017 23:04:53: 14000000 INFO @ Fri, 10 Nov 2017 23:05:06: 11000000 INFO @ Fri, 10 Nov 2017 23:05:10: 13000000 INFO @ Fri, 10 Nov 2017 23:05:12: 15000000 INFO @ Fri, 10 Nov 2017 23:05:31: 12000000 INFO @ Fri, 10 Nov 2017 23:05:31: 16000000 INFO @ Fri, 10 Nov 2017 23:05:35: 14000000 INFO @ Fri, 10 Nov 2017 23:05:50: 17000000 INFO @ Fri, 10 Nov 2017 23:05:56: 13000000 INFO @ Fri, 10 Nov 2017 23:05:59: 15000000 INFO @ Fri, 10 Nov 2017 23:06:10: 18000000 INFO @ Fri, 10 Nov 2017 23:06:20: 14000000 INFO @ Fri, 10 Nov 2017 23:06:21: 16000000 INFO @ Fri, 10 Nov 2017 23:06:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:06:22: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:06:22: #1 total tags in treatment: 18647319 INFO @ Fri, 10 Nov 2017 23:06:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:06:22: #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 23:06:23: #1 tags after filtering in treatment: 18647188 INFO @ Fri, 10 Nov 2017 23:06:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:06:23: #1 finished! INFO @ Fri, 10 Nov 2017 23:06:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:06:26: #2 number of paired peaks: 19706 INFO @ Fri, 10 Nov 2017 23:06:26: start model_add_line... INFO @ Fri, 10 Nov 2017 23:06:26: start X-correlation... INFO @ Fri, 10 Nov 2017 23:06:26: end of X-cor INFO @ Fri, 10 Nov 2017 23:06:26: #2 finished! INFO @ Fri, 10 Nov 2017 23:06:26: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Nov 2017 23:06:26: #2 alternative fragment length(s) may be 55,110 bps INFO @ Fri, 10 Nov 2017 23:06:26: #2.2 Generate R script for model : SRX2202904.05_model.r WARNING @ Fri, 10 Nov 2017 23:06:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:06:26: #2 You may need to consider one of the other alternative d(s): 55,110 WARNING @ Fri, 10 Nov 2017 23:06:26: #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 23:06:26: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:06:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:06:40: 17000000 INFO @ Fri, 10 Nov 2017 23:06:45: 15000000 INFO @ Fri, 10 Nov 2017 23:06:59: 18000000 INFO @ Fri, 10 Nov 2017 23:07:09: 16000000 INFO @ Fri, 10 Nov 2017 23:07:11: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:07:11: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:07:11: #1 total tags in treatment: 18647319 INFO @ Fri, 10 Nov 2017 23:07:11: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:07:11: #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 23:07:11: #1 tags after filtering in treatment: 18647188 INFO @ Fri, 10 Nov 2017 23:07:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:07:11: #1 finished! INFO @ Fri, 10 Nov 2017 23:07:11: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:07:15: #2 number of paired peaks: 19706 INFO @ Fri, 10 Nov 2017 23:07:15: start model_add_line... INFO @ Fri, 10 Nov 2017 23:07:15: start X-correlation... INFO @ Fri, 10 Nov 2017 23:07:15: end of X-cor INFO @ Fri, 10 Nov 2017 23:07:15: #2 finished! INFO @ Fri, 10 Nov 2017 23:07:15: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Nov 2017 23:07:15: #2 alternative fragment length(s) may be 55,110 bps INFO @ Fri, 10 Nov 2017 23:07:15: #2.2 Generate R script for model : SRX2202904.10_model.r WARNING @ Fri, 10 Nov 2017 23:07:15: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:07:15: #2 You may need to consider one of the other alternative d(s): 55,110 WARNING @ Fri, 10 Nov 2017 23:07:15: #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 23:07:15: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:07:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:07:33: 17000000 INFO @ Fri, 10 Nov 2017 23:07:57: 18000000 INFO @ Fri, 10 Nov 2017 23:08:09: #4 Write output xls file... SRX2202904.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:08:09: #4 Write peak in narrowPeak format file... SRX2202904.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:08:09: #4 Write summits bed file... SRX2202904.05_summits.bed INFO @ Fri, 10 Nov 2017 23:08:09: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (2086 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:08:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 23:08:12: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 23:08:12: #1 total tags in treatment: 18647319 INFO @ Fri, 10 Nov 2017 23:08:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:08:12: #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 23:08:13: #1 tags after filtering in treatment: 18647188 INFO @ Fri, 10 Nov 2017 23:08:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:08:13: #1 finished! INFO @ Fri, 10 Nov 2017 23:08:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:08:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:08:17: #2 number of paired peaks: 19706 INFO @ Fri, 10 Nov 2017 23:08:17: start model_add_line... INFO @ Fri, 10 Nov 2017 23:08:17: start X-correlation... INFO @ Fri, 10 Nov 2017 23:08:17: end of X-cor INFO @ Fri, 10 Nov 2017 23:08:17: #2 finished! INFO @ Fri, 10 Nov 2017 23:08:17: #2 predicted fragment length is 55 bps INFO @ Fri, 10 Nov 2017 23:08:17: #2 alternative fragment length(s) may be 55,110 bps INFO @ Fri, 10 Nov 2017 23:08:17: #2.2 Generate R script for model : SRX2202904.20_model.r WARNING @ Fri, 10 Nov 2017 23:08:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:08:17: #2 You may need to consider one of the other alternative d(s): 55,110 WARNING @ Fri, 10 Nov 2017 23:08:17: #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 23:08:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:08:52: #4 Write output xls file... SRX2202904.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:08:53: #4 Write peak in narrowPeak format file... SRX2202904.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:08:53: #4 Write summits bed file... SRX2202904.10_summits.bed INFO @ Fri, 10 Nov 2017 23:08:53: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (1074 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:09:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:09:51: #4 Write output xls file... SRX2202904.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:09:51: #4 Write peak in narrowPeak format file... SRX2202904.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:09:51: #4 Write summits bed file... SRX2202904.20_summits.bed INFO @ Fri, 10 Nov 2017 23:09:51: Done! pass1 - making usageList (36 chroms): 2 millis pass2 - checking and writing primary data (553 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。