Job ID = 10194881 sra ファイルのダウンロード中... Completed: 206177K bytes transferred in 8 seconds (204964K bits/sec), in 1 file. Completed: 206508K bytes transferred in 7 seconds (234952K bits/sec), in 1 file. Completed: 228252K bytes transferred in 10 seconds (170557K bits/sec), in 1 file. Completed: 226201K bytes transferred in 8 seconds (216117K bits/sec), in 1 file. Completed: 194730K bytes transferred in 8 seconds (189845K bits/sec), in 1 file. Completed: 197389K bytes transferred in 10 seconds (149512K 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 4373049 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319803.sra Written 4373049 spots total Written 4422062 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319802.sra Written 4422062 spots total Written 4598548 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319801.sra Written 4598548 spots total Written 4606993 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319800.sra Written 4606993 spots total Written 4969213 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319805.sra Written 4969213 spots total Written 4942040 spots for /home/okishinya/chipatlas/results/rn6/SRX2202876/SRR4319804.sra Written 4942040 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:19:15 27911905 reads; of these: 27911905 (100.00%) were unpaired; of these: 1441953 (5.17%) aligned 0 times 20872165 (74.78%) aligned exactly 1 time 5597787 (20.06%) aligned >1 times 94.83% overall alignment rate Time searching: 00:19:17 Overall time: 00:19:17 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] 8303469 / 26469952 = 0.3137 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 18:00:47: # Command line: callpeak -t SRX2202876.bam -f BAM -g 2.15e9 -n SRX2202876.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202876.20 # format = BAM # ChIP-seq file = ['SRX2202876.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 18:00:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:00:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:00:47: # Command line: callpeak -t SRX2202876.bam -f BAM -g 2.15e9 -n SRX2202876.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202876.10 # format = BAM # ChIP-seq file = ['SRX2202876.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 18:00:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:00:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:00:47: # Command line: callpeak -t SRX2202876.bam -f BAM -g 2.15e9 -n SRX2202876.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202876.05 # format = BAM # ChIP-seq file = ['SRX2202876.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 18:00:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:00:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:00:54: 1000000 INFO @ Fri, 10 Nov 2017 18:00:54: 1000000 INFO @ Fri, 10 Nov 2017 18:00:54: 1000000 INFO @ Fri, 10 Nov 2017 18:01:00: 2000000 INFO @ Fri, 10 Nov 2017 18:01:00: 2000000 INFO @ Fri, 10 Nov 2017 18:01:00: 2000000 INFO @ Fri, 10 Nov 2017 18:01:07: 3000000 INFO @ Fri, 10 Nov 2017 18:01:07: 3000000 INFO @ Fri, 10 Nov 2017 18:01:07: 3000000 INFO @ Fri, 10 Nov 2017 18:01:14: 4000000 INFO @ Fri, 10 Nov 2017 18:01:14: 4000000 INFO @ Fri, 10 Nov 2017 18:01:14: 4000000 INFO @ Fri, 10 Nov 2017 18:01:20: 5000000 INFO @ Fri, 10 Nov 2017 18:01:20: 5000000 INFO @ Fri, 10 Nov 2017 18:01:20: 5000000 INFO @ Fri, 10 Nov 2017 18:01:27: 6000000 INFO @ Fri, 10 Nov 2017 18:01:27: 6000000 INFO @ Fri, 10 Nov 2017 18:01:27: 6000000 INFO @ Fri, 10 Nov 2017 18:01:34: 7000000 INFO @ Fri, 10 Nov 2017 18:01:34: 7000000 INFO @ Fri, 10 Nov 2017 18:01:34: 7000000 INFO @ Fri, 10 Nov 2017 18:01:41: 8000000 INFO @ Fri, 10 Nov 2017 18:01:41: 8000000 INFO @ Fri, 10 Nov 2017 18:01:41: 8000000 INFO @ Fri, 10 Nov 2017 18:01:47: 9000000 INFO @ Fri, 10 Nov 2017 18:01:47: 9000000 INFO @ Fri, 10 Nov 2017 18:01:48: 9000000 INFO @ Fri, 10 Nov 2017 18:01:54: 10000000 INFO @ Fri, 10 Nov 2017 18:01:54: 10000000 INFO @ Fri, 10 Nov 2017 18:01:55: 10000000 INFO @ Fri, 10 Nov 2017 18:02:01: 11000000 INFO @ Fri, 10 Nov 2017 18:02:01: 11000000 INFO @ Fri, 10 Nov 2017 18:02:01: 11000000 INFO @ Fri, 10 Nov 2017 18:02:07: 12000000 INFO @ Fri, 10 Nov 2017 18:02:08: 12000000 INFO @ Fri, 10 Nov 2017 18:02:08: 12000000 INFO @ Fri, 10 Nov 2017 18:02:14: 13000000 INFO @ Fri, 10 Nov 2017 18:02:14: 13000000 INFO @ Fri, 10 Nov 2017 18:02:15: 13000000 INFO @ Fri, 10 Nov 2017 18:02:20: 14000000 INFO @ Fri, 10 Nov 2017 18:02:21: 14000000 INFO @ Fri, 10 Nov 2017 18:02:21: 14000000 INFO @ Fri, 10 Nov 2017 18:02:27: 15000000 INFO @ Fri, 10 Nov 2017 18:02:28: 15000000 INFO @ Fri, 10 Nov 2017 18:02:28: 15000000 INFO @ Fri, 10 Nov 2017 18:02:33: 16000000 INFO @ Fri, 10 Nov 2017 18:02:35: 16000000 INFO @ Fri, 10 Nov 2017 18:02:35: 16000000 INFO @ Fri, 10 Nov 2017 18:02:40: 17000000 INFO @ Fri, 10 Nov 2017 18:02:41: 17000000 INFO @ Fri, 10 Nov 2017 18:02:42: 17000000 INFO @ Fri, 10 Nov 2017 18:02:47: 18000000 INFO @ Fri, 10 Nov 2017 18:02:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:02:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:02:48: #1 total tags in treatment: 18166483 INFO @ Fri, 10 Nov 2017 18:02:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:02:48: #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 18:02:48: #1 tags after filtering in treatment: 18166332 INFO @ Fri, 10 Nov 2017 18:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:02:48: #1 finished! INFO @ Fri, 10 Nov 2017 18:02:48: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:02:49: 18000000 INFO @ Fri, 10 Nov 2017 18:02:49: 18000000 INFO @ Fri, 10 Nov 2017 18:02:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:02:50: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:02:50: #1 total tags in treatment: 18166483 INFO @ Fri, 10 Nov 2017 18:02:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:02:50: #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 18:02:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:02:50: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:02:50: #1 total tags in treatment: 18166483 INFO @ Fri, 10 Nov 2017 18:02:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:02:50: #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 18:02:50: #1 tags after filtering in treatment: 18166332 INFO @ Fri, 10 Nov 2017 18:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:02:50: #1 finished! INFO @ Fri, 10 Nov 2017 18:02:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:02:51: #1 tags after filtering in treatment: 18166332 INFO @ Fri, 10 Nov 2017 18:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:02:51: #1 finished! INFO @ Fri, 10 Nov 2017 18:02:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:02:52: #2 number of paired peaks: 52668 INFO @ Fri, 10 Nov 2017 18:02:52: start model_add_line... INFO @ Fri, 10 Nov 2017 18:02:52: start X-correlation... INFO @ Fri, 10 Nov 2017 18:02:52: end of X-cor INFO @ Fri, 10 Nov 2017 18:02:52: #2 finished! INFO @ Fri, 10 Nov 2017 18:02:52: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Nov 2017 18:02:52: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Nov 2017 18:02:52: #2.2 Generate R script for model : SRX2202876.10_model.r INFO @ Fri, 10 Nov 2017 18:02:52: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:02:54: #2 number of paired peaks: 52668 INFO @ Fri, 10 Nov 2017 18:02:54: start model_add_line... INFO @ Fri, 10 Nov 2017 18:02:54: start X-correlation... INFO @ Fri, 10 Nov 2017 18:02:54: end of X-cor INFO @ Fri, 10 Nov 2017 18:02:54: #2 finished! INFO @ Fri, 10 Nov 2017 18:02:54: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Nov 2017 18:02:54: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Nov 2017 18:02:54: #2.2 Generate R script for model : SRX2202876.05_model.r INFO @ Fri, 10 Nov 2017 18:02:54: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:02:54: #2 number of paired peaks: 52668 INFO @ Fri, 10 Nov 2017 18:02:54: start model_add_line... INFO @ Fri, 10 Nov 2017 18:02:55: start X-correlation... INFO @ Fri, 10 Nov 2017 18:02:55: end of X-cor INFO @ Fri, 10 Nov 2017 18:02:55: #2 finished! INFO @ Fri, 10 Nov 2017 18:02:55: #2 predicted fragment length is 161 bps INFO @ Fri, 10 Nov 2017 18:02:55: #2 alternative fragment length(s) may be 161 bps INFO @ Fri, 10 Nov 2017 18:02:55: #2.2 Generate R script for model : SRX2202876.20_model.r INFO @ Fri, 10 Nov 2017 18:02:55: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:02:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:03:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:03:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:03:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:04:05: #4 Write output xls file... SRX2202876.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:04:05: #4 Write peak in narrowPeak format file... SRX2202876.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:04:06: #4 Write summits bed file... SRX2202876.10_summits.bed INFO @ Fri, 10 Nov 2017 18:04:06: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (9639 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:04:06: #4 Write output xls file... SRX2202876.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:04:07: #4 Write peak in narrowPeak format file... SRX2202876.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:04:07: #4 Write summits bed file... SRX2202876.05_summits.bed INFO @ Fri, 10 Nov 2017 18:04:07: Done! pass1 - making usageList (90 chroms): 4 millis pass2 - checking and writing primary data (18574 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:04:10: #4 Write output xls file... SRX2202876.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:04:10: #4 Write peak in narrowPeak format file... SRX2202876.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:04:10: #4 Write summits bed file... SRX2202876.20_summits.bed INFO @ Fri, 10 Nov 2017 18:04:10: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (2439 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。