Job ID = 10194928 sra ファイルのダウンロード中... Completed: 87458K bytes transferred in 6 seconds (114237K bits/sec), in 1 file. Completed: 85445K bytes transferred in 6 seconds (101613K bits/sec), in 1 file. Completed: 145099K bytes transferred in 9 seconds (126408K bits/sec), in 1 file. Completed: 143397K bytes transferred in 11 seconds (105927K bits/sec), in 1 file. Completed: 140842K bytes transferred in 11 seconds (98631K bits/sec), in 1 file. Completed: 142135K bytes transferred in 11 seconds (101917K 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 2012700 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320083.sra Written 2012700 spots total Written 2069891 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320082.sra Written 2069891 spots total Written 3089648 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320087.sra Written 3089648 spots total Written 3092309 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320085.sra Written 3092309 spots total Written 3140874 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320086.sra Written 3140874 spots total Written 3179013 spots for /home/okishinya/chipatlas/results/rn6/SRX2202923/SRR4320084.sra Written 3179013 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: 00:00:00 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:30:23 16584435 reads; of these: 16584435 (100.00%) were unpaired; of these: 413508 (2.49%) aligned 0 times 11493969 (69.31%) aligned exactly 1 time 4676958 (28.20%) aligned >1 times 97.51% overall alignment rate Time searching: 00:30:27 Overall time: 00:30:27 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] 501733 / 16170927 = 0.0310 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 00:04:50: # Command line: callpeak -t SRX2202923.bam -f BAM -g 2.15e9 -n SRX2202923.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202923.05 # format = BAM # ChIP-seq file = ['SRX2202923.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 00:04:50: # Command line: callpeak -t SRX2202923.bam -f BAM -g 2.15e9 -n SRX2202923.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202923.20 # format = BAM # ChIP-seq file = ['SRX2202923.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 00:04:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:50: # Command line: callpeak -t SRX2202923.bam -f BAM -g 2.15e9 -n SRX2202923.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202923.10 # format = BAM # ChIP-seq file = ['SRX2202923.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 00:04:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:04:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:04:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:05:04: 1000000 INFO @ Sat, 11 Nov 2017 00:05:10: 1000000 INFO @ Sat, 11 Nov 2017 00:05:11: 1000000 INFO @ Sat, 11 Nov 2017 00:05:18: 2000000 INFO @ Sat, 11 Nov 2017 00:05:29: 2000000 INFO @ Sat, 11 Nov 2017 00:05:30: 2000000 INFO @ Sat, 11 Nov 2017 00:05:33: 3000000 INFO @ Sat, 11 Nov 2017 00:05:46: 3000000 INFO @ Sat, 11 Nov 2017 00:05:48: 4000000 INFO @ Sat, 11 Nov 2017 00:05:50: 3000000 INFO @ Sat, 11 Nov 2017 00:06:01: 5000000 INFO @ Sat, 11 Nov 2017 00:06:02: 4000000 INFO @ Sat, 11 Nov 2017 00:06:09: 4000000 INFO @ Sat, 11 Nov 2017 00:06:14: 6000000 INFO @ Sat, 11 Nov 2017 00:06:21: 5000000 INFO @ Sat, 11 Nov 2017 00:06:28: 7000000 INFO @ Sat, 11 Nov 2017 00:06:29: 5000000 INFO @ Sat, 11 Nov 2017 00:06:36: 6000000 INFO @ Sat, 11 Nov 2017 00:06:38: 8000000 INFO @ Sat, 11 Nov 2017 00:06:48: 9000000 INFO @ Sat, 11 Nov 2017 00:06:48: 6000000 INFO @ Sat, 11 Nov 2017 00:06:52: 7000000 INFO @ Sat, 11 Nov 2017 00:07:00: 10000000 INFO @ Sat, 11 Nov 2017 00:07:08: 7000000 INFO @ Sat, 11 Nov 2017 00:07:09: 8000000 INFO @ Sat, 11 Nov 2017 00:07:11: 11000000 INFO @ Sat, 11 Nov 2017 00:07:22: 12000000 INFO @ Sat, 11 Nov 2017 00:07:24: 9000000 INFO @ Sat, 11 Nov 2017 00:07:28: 8000000 INFO @ Sat, 11 Nov 2017 00:07:34: 13000000 INFO @ Sat, 11 Nov 2017 00:07:43: 10000000 INFO @ Sat, 11 Nov 2017 00:07:45: 14000000 INFO @ Sat, 11 Nov 2017 00:07:49: 9000000 INFO @ Sat, 11 Nov 2017 00:07:58: 15000000 INFO @ Sat, 11 Nov 2017 00:07:59: 11000000 INFO @ Sat, 11 Nov 2017 00:08:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:08:07: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:08:07: #1 total tags in treatment: 15669194 INFO @ Sat, 11 Nov 2017 00:08:07: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:08:07: #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 00:08:08: #1 tags after filtering in treatment: 15669038 INFO @ Sat, 11 Nov 2017 00:08:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:08:08: #1 finished! INFO @ Sat, 11 Nov 2017 00:08:08: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:08:09: 10000000 INFO @ Sat, 11 Nov 2017 00:08:10: #2 number of paired peaks: 5436 INFO @ Sat, 11 Nov 2017 00:08:10: start model_add_line... INFO @ Sat, 11 Nov 2017 00:08:10: start X-correlation... INFO @ Sat, 11 Nov 2017 00:08:10: end of X-cor INFO @ Sat, 11 Nov 2017 00:08:10: #2 finished! INFO @ Sat, 11 Nov 2017 00:08:10: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:08:10: #2 alternative fragment length(s) may be 50,225,403 bps INFO @ Sat, 11 Nov 2017 00:08:10: #2.2 Generate R script for model : SRX2202923.20_model.r WARNING @ Sat, 11 Nov 2017 00:08:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:08:10: #2 You may need to consider one of the other alternative d(s): 50,225,403 WARNING @ Sat, 11 Nov 2017 00:08:10: #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 00:08:10: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:08:15: 12000000 INFO @ Sat, 11 Nov 2017 00:08:28: 11000000 INFO @ Sat, 11 Nov 2017 00:08:35: 13000000 INFO @ Sat, 11 Nov 2017 00:08:46: 12000000 INFO @ Sat, 11 Nov 2017 00:08:50: 14000000 INFO @ Sat, 11 Nov 2017 00:09:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:09:05: 13000000 INFO @ Sat, 11 Nov 2017 00:09:08: 15000000 INFO @ Sat, 11 Nov 2017 00:09:18: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:09:18: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:09:18: #1 total tags in treatment: 15669194 INFO @ Sat, 11 Nov 2017 00:09:18: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:09:18: #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 00:09:19: #1 tags after filtering in treatment: 15669038 INFO @ Sat, 11 Nov 2017 00:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:09:19: #1 finished! INFO @ Sat, 11 Nov 2017 00:09:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:09:21: #2 number of paired peaks: 5436 INFO @ Sat, 11 Nov 2017 00:09:21: start model_add_line... INFO @ Sat, 11 Nov 2017 00:09:22: start X-correlation... INFO @ Sat, 11 Nov 2017 00:09:22: end of X-cor INFO @ Sat, 11 Nov 2017 00:09:22: #2 finished! INFO @ Sat, 11 Nov 2017 00:09:22: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:09:22: #2 alternative fragment length(s) may be 50,225,403 bps INFO @ Sat, 11 Nov 2017 00:09:22: #2.2 Generate R script for model : SRX2202923.05_model.r WARNING @ Sat, 11 Nov 2017 00:09:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:09:22: #2 You may need to consider one of the other alternative d(s): 50,225,403 WARNING @ Sat, 11 Nov 2017 00:09:22: #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 00:09:22: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:09:23: 14000000 INFO @ Sat, 11 Nov 2017 00:09:28: #4 Write output xls file... SRX2202923.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:09:28: #4 Write peak in narrowPeak format file... SRX2202923.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:09:28: #4 Write summits bed file... SRX2202923.20_summits.bed INFO @ Sat, 11 Nov 2017 00:09:28: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (401 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:09:41: 15000000 INFO @ Sat, 11 Nov 2017 00:09:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 00:09:54: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 00:09:54: #1 total tags in treatment: 15669194 INFO @ Sat, 11 Nov 2017 00:09:54: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:09:54: #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 00:09:55: #1 tags after filtering in treatment: 15669038 INFO @ Sat, 11 Nov 2017 00:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:09:55: #1 finished! INFO @ Sat, 11 Nov 2017 00:09:55: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:09:57: #2 number of paired peaks: 5436 INFO @ Sat, 11 Nov 2017 00:09:57: start model_add_line... INFO @ Sat, 11 Nov 2017 00:09:58: start X-correlation... INFO @ Sat, 11 Nov 2017 00:09:58: end of X-cor INFO @ Sat, 11 Nov 2017 00:09:58: #2 finished! INFO @ Sat, 11 Nov 2017 00:09:58: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:09:58: #2 alternative fragment length(s) may be 50,225,403 bps INFO @ Sat, 11 Nov 2017 00:09:58: #2.2 Generate R script for model : SRX2202923.10_model.r WARNING @ Sat, 11 Nov 2017 00:09:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:09:58: #2 You may need to consider one of the other alternative d(s): 50,225,403 WARNING @ Sat, 11 Nov 2017 00:09:58: #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 00:09:58: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:09:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:10:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:10:41: #4 Write output xls file... SRX2202923.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:10:41: #4 Write peak in narrowPeak format file... SRX2202923.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:10:41: #4 Write summits bed file... SRX2202923.05_summits.bed INFO @ Sat, 11 Nov 2017 00:10:41: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (1290 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:10:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:11:13: #4 Write output xls file... SRX2202923.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:11:13: #4 Write peak in narrowPeak format file... SRX2202923.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:11:13: #4 Write summits bed file... SRX2202923.10_summits.bed INFO @ Sat, 11 Nov 2017 00:11:13: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (802 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。