Job ID = 10194908 sra ファイルのダウンロード中... Completed: 100885K bytes transferred in 6 seconds (119272K bits/sec), in 1 file. Completed: 98611K bytes transferred in 8 seconds (94612K bits/sec), in 1 file. Completed: 166309K bytes transferred in 8 seconds (153910K bits/sec), in 1 file. Completed: 163056K bytes transferred in 10 seconds (129993K bits/sec), in 1 file. Completed: 164210K bytes transferred in 8 seconds (158855K bits/sec), in 1 file. Completed: 161562K bytes transferred in 10 seconds (130753K 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 2314697 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319963.sra Written 2314697 spots total Written 2377657 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319962.sra Written 2377657 spots total Written 3530978 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319967.sra Written 3530978 spots total Written 3533853 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319965.sra Written 3533853 spots total Written 3628139 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319964.sra Written 3628139 spots total Written 3582014 spots for /home/okishinya/chipatlas/results/rn6/SRX2202903/SRR4319966.sra Written 3582014 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:38:02 18967338 reads; of these: 18967338 (100.00%) were unpaired; of these: 755542 (3.98%) aligned 0 times 12478699 (65.79%) aligned exactly 1 time 5733097 (30.23%) aligned >1 times 96.02% overall alignment rate Time searching: 00:38:05 Overall time: 00:38:05 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] 8083265 / 18211796 = 0.4438 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 22:55:11: # Command line: callpeak -t SRX2202903.bam -f BAM -g 2.15e9 -n SRX2202903.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202903.05 # format = BAM # ChIP-seq file = ['SRX2202903.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 22:55:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:55:11: # Command line: callpeak -t SRX2202903.bam -f BAM -g 2.15e9 -n SRX2202903.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202903.20 # format = BAM # ChIP-seq file = ['SRX2202903.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 22:55:11: # Command line: callpeak -t SRX2202903.bam -f BAM -g 2.15e9 -n SRX2202903.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202903.10 # format = BAM # ChIP-seq file = ['SRX2202903.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 22:55:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:11: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:55:11: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:55:23: 1000000 INFO @ Fri, 10 Nov 2017 22:55:34: 1000000 INFO @ Fri, 10 Nov 2017 22:55:35: 2000000 INFO @ Fri, 10 Nov 2017 22:55:36: 1000000 INFO @ Fri, 10 Nov 2017 22:55:47: 3000000 INFO @ Fri, 10 Nov 2017 22:55:57: 2000000 INFO @ Fri, 10 Nov 2017 22:56:00: 4000000 INFO @ Fri, 10 Nov 2017 22:56:00: 2000000 INFO @ Fri, 10 Nov 2017 22:56:12: 5000000 INFO @ Fri, 10 Nov 2017 22:56:20: 3000000 INFO @ Fri, 10 Nov 2017 22:56:24: 3000000 INFO @ Fri, 10 Nov 2017 22:56:24: 6000000 INFO @ Fri, 10 Nov 2017 22:56:36: 7000000 INFO @ Fri, 10 Nov 2017 22:56:42: 4000000 INFO @ Fri, 10 Nov 2017 22:56:46: 4000000 INFO @ Fri, 10 Nov 2017 22:56:49: 8000000 INFO @ Fri, 10 Nov 2017 22:57:01: 9000000 INFO @ Fri, 10 Nov 2017 22:57:05: 5000000 INFO @ Fri, 10 Nov 2017 22:57:09: 5000000 INFO @ Fri, 10 Nov 2017 22:57:14: 10000000 INFO @ Fri, 10 Nov 2017 22:57:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:57:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:57:16: #1 total tags in treatment: 10128531 INFO @ Fri, 10 Nov 2017 22:57:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:57:16: #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 22:57:16: #1 tags after filtering in treatment: 10128337 INFO @ Fri, 10 Nov 2017 22:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:57:16: #1 finished! INFO @ Fri, 10 Nov 2017 22:57:16: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:57:19: #2 number of paired peaks: 29910 INFO @ Fri, 10 Nov 2017 22:57:19: start model_add_line... INFO @ Fri, 10 Nov 2017 22:57:20: start X-correlation... INFO @ Fri, 10 Nov 2017 22:57:20: end of X-cor INFO @ Fri, 10 Nov 2017 22:57:20: #2 finished! INFO @ Fri, 10 Nov 2017 22:57:20: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Nov 2017 22:57:20: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Nov 2017 22:57:20: #2.2 Generate R script for model : SRX2202903.10_model.r INFO @ Fri, 10 Nov 2017 22:57:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:57:27: 6000000 INFO @ Fri, 10 Nov 2017 22:57:32: 6000000 INFO @ Fri, 10 Nov 2017 22:57:51: 7000000 INFO @ Fri, 10 Nov 2017 22:57:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:57:54: 7000000 INFO @ Fri, 10 Nov 2017 22:58:11: 8000000 INFO @ Fri, 10 Nov 2017 22:58:12: #4 Write output xls file... SRX2202903.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:58:12: #4 Write peak in narrowPeak format file... SRX2202903.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:58:12: #4 Write summits bed file... SRX2202903.10_summits.bed INFO @ Fri, 10 Nov 2017 22:58:12: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (798 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:58:15: 8000000 INFO @ Fri, 10 Nov 2017 22:58:28: 9000000 INFO @ Fri, 10 Nov 2017 22:58:40: 9000000 INFO @ Fri, 10 Nov 2017 22:58:46: 10000000 INFO @ Fri, 10 Nov 2017 22:58:48: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:58:48: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:58:48: #1 total tags in treatment: 10128531 INFO @ Fri, 10 Nov 2017 22:58:48: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:58:48: #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 22:58:48: #1 tags after filtering in treatment: 10128337 INFO @ Fri, 10 Nov 2017 22:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:58:48: #1 finished! INFO @ Fri, 10 Nov 2017 22:58:48: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:58:51: #2 number of paired peaks: 29910 INFO @ Fri, 10 Nov 2017 22:58:51: start model_add_line... INFO @ Fri, 10 Nov 2017 22:58:51: start X-correlation... INFO @ Fri, 10 Nov 2017 22:58:51: end of X-cor INFO @ Fri, 10 Nov 2017 22:58:51: #2 finished! INFO @ Fri, 10 Nov 2017 22:58:51: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Nov 2017 22:58:51: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Nov 2017 22:58:51: #2.2 Generate R script for model : SRX2202903.20_model.r INFO @ Fri, 10 Nov 2017 22:58:51: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:59:04: 10000000 INFO @ Fri, 10 Nov 2017 22:59:07: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 22:59:07: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 22:59:07: #1 total tags in treatment: 10128531 INFO @ Fri, 10 Nov 2017 22:59:07: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:59:07: #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 22:59:07: #1 tags after filtering in treatment: 10128337 INFO @ Fri, 10 Nov 2017 22:59:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:59:07: #1 finished! INFO @ Fri, 10 Nov 2017 22:59:07: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:59:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:59:10: #2 number of paired peaks: 29910 INFO @ Fri, 10 Nov 2017 22:59:10: start model_add_line... INFO @ Fri, 10 Nov 2017 22:59:10: start X-correlation... INFO @ Fri, 10 Nov 2017 22:59:11: end of X-cor INFO @ Fri, 10 Nov 2017 22:59:11: #2 finished! INFO @ Fri, 10 Nov 2017 22:59:11: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Nov 2017 22:59:11: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Nov 2017 22:59:11: #2.2 Generate R script for model : SRX2202903.05_model.r INFO @ Fri, 10 Nov 2017 22:59:11: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:59:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:59:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:59:44: #4 Write output xls file... SRX2202903.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:59:44: #4 Write peak in narrowPeak format file... SRX2202903.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:59:44: #4 Write summits bed file... SRX2202903.20_summits.bed INFO @ Fri, 10 Nov 2017 22:59:44: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (396 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:00:04: #4 Write output xls file... SRX2202903.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:00:04: #4 Write peak in narrowPeak format file... SRX2202903.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:00:04: #4 Write summits bed file... SRX2202903.05_summits.bed INFO @ Fri, 10 Nov 2017 23:00:04: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (3209 records, 4 fields): 48 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。