Job ID = 10194887 sra ファイルのダウンロード中... Completed: 169997K bytes transferred in 7 seconds (183907K bits/sec), in 1 file. Completed: 168176K bytes transferred in 6 seconds (197939K bits/sec), in 1 file. Completed: 145430K bytes transferred in 6 seconds (179904K bits/sec), in 1 file. Completed: 147366K bytes transferred in 7 seconds (171496K bits/sec), in 1 file. Completed: 155136K bytes transferred in 5 seconds (222573K bits/sec), in 1 file. Completed: 154665K bytes transferred in 7 seconds (174699K 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 3290121 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319839.sra Written 3290121 spots total Written 3325905 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319838.sra Written 3325905 spots total Written 3476879 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319836.sra Written 3476879 spots total Written 3475529 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319837.sra Written 3475529 spots total Written 3694585 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319840.sra Written 3694585 spots total Written 3722041 spots for /home/okishinya/chipatlas/results/rn6/SRX2202882/SRR4319841.sra Written 3722041 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: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:15:06 20985060 reads; of these: 20985060 (100.00%) were unpaired; of these: 2358094 (11.24%) aligned 0 times 13896158 (66.22%) aligned exactly 1 time 4730808 (22.54%) aligned >1 times 88.76% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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] 1863273 / 18626966 = 0.1000 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 18:10:28: # Command line: callpeak -t SRX2202882.bam -f BAM -g 2.15e9 -n SRX2202882.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202882.05 # format = BAM # ChIP-seq file = ['SRX2202882.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 18:10:28: # Command line: callpeak -t SRX2202882.bam -f BAM -g 2.15e9 -n SRX2202882.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202882.10 # format = BAM # ChIP-seq file = ['SRX2202882.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 18:10:28: # Command line: callpeak -t SRX2202882.bam -f BAM -g 2.15e9 -n SRX2202882.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202882.20 # format = BAM # ChIP-seq file = ['SRX2202882.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 18:10:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:36: 1000000 INFO @ Fri, 10 Nov 2017 18:10:37: 1000000 INFO @ Fri, 10 Nov 2017 18:10:37: 1000000 INFO @ Fri, 10 Nov 2017 18:10:43: 2000000 INFO @ Fri, 10 Nov 2017 18:10:46: 2000000 INFO @ Fri, 10 Nov 2017 18:10:46: 2000000 INFO @ Fri, 10 Nov 2017 18:10:51: 3000000 INFO @ Fri, 10 Nov 2017 18:10:55: 3000000 INFO @ Fri, 10 Nov 2017 18:10:55: 3000000 INFO @ Fri, 10 Nov 2017 18:10:58: 4000000 INFO @ Fri, 10 Nov 2017 18:11:04: 4000000 INFO @ Fri, 10 Nov 2017 18:11:04: 4000000 INFO @ Fri, 10 Nov 2017 18:11:06: 5000000 INFO @ Fri, 10 Nov 2017 18:11:13: 5000000 INFO @ Fri, 10 Nov 2017 18:11:13: 5000000 INFO @ Fri, 10 Nov 2017 18:11:13: 6000000 INFO @ Fri, 10 Nov 2017 18:11:21: 7000000 INFO @ Fri, 10 Nov 2017 18:11:22: 6000000 INFO @ Fri, 10 Nov 2017 18:11:22: 6000000 INFO @ Fri, 10 Nov 2017 18:11:28: 8000000 INFO @ Fri, 10 Nov 2017 18:11:31: 7000000 INFO @ Fri, 10 Nov 2017 18:11:31: 7000000 INFO @ Fri, 10 Nov 2017 18:11:36: 9000000 INFO @ Fri, 10 Nov 2017 18:11:40: 8000000 INFO @ Fri, 10 Nov 2017 18:11:40: 8000000 INFO @ Fri, 10 Nov 2017 18:11:43: 10000000 INFO @ Fri, 10 Nov 2017 18:11:49: 9000000 INFO @ Fri, 10 Nov 2017 18:11:49: 9000000 INFO @ Fri, 10 Nov 2017 18:11:51: 11000000 INFO @ Fri, 10 Nov 2017 18:11:57: 10000000 INFO @ Fri, 10 Nov 2017 18:11:57: 10000000 INFO @ Fri, 10 Nov 2017 18:11:58: 12000000 INFO @ Fri, 10 Nov 2017 18:12:06: 13000000 INFO @ Fri, 10 Nov 2017 18:12:06: 11000000 INFO @ Fri, 10 Nov 2017 18:12:06: 11000000 INFO @ Fri, 10 Nov 2017 18:12:14: 14000000 INFO @ Fri, 10 Nov 2017 18:12:15: 12000000 INFO @ Fri, 10 Nov 2017 18:12:15: 12000000 INFO @ Fri, 10 Nov 2017 18:12:21: 15000000 INFO @ Fri, 10 Nov 2017 18:12:23: 13000000 INFO @ Fri, 10 Nov 2017 18:12:23: 13000000 INFO @ Fri, 10 Nov 2017 18:12:29: 16000000 INFO @ Fri, 10 Nov 2017 18:12:32: 14000000 INFO @ Fri, 10 Nov 2017 18:12:32: 14000000 INFO @ Fri, 10 Nov 2017 18:12:35: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:35: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:35: #1 total tags in treatment: 16763693 INFO @ Fri, 10 Nov 2017 18:12:35: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:35: #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 18:12:35: #1 tags after filtering in treatment: 16763535 INFO @ Fri, 10 Nov 2017 18:12:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:35: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:35: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:12:38: #2 number of paired peaks: 22473 INFO @ Fri, 10 Nov 2017 18:12:38: start model_add_line... INFO @ Fri, 10 Nov 2017 18:12:38: start X-correlation... INFO @ Fri, 10 Nov 2017 18:12:38: end of X-cor INFO @ Fri, 10 Nov 2017 18:12:38: #2 finished! INFO @ Fri, 10 Nov 2017 18:12:38: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Nov 2017 18:12:38: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Nov 2017 18:12:38: #2.2 Generate R script for model : SRX2202882.05_model.r INFO @ Fri, 10 Nov 2017 18:12:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:12:41: 15000000 INFO @ Fri, 10 Nov 2017 18:12:41: 15000000 INFO @ Fri, 10 Nov 2017 18:12:51: 16000000 INFO @ Fri, 10 Nov 2017 18:12:51: 16000000 INFO @ Fri, 10 Nov 2017 18:12:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:58: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:58: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:58: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:58: #1 total tags in treatment: 16763693 INFO @ Fri, 10 Nov 2017 18:12:58: #1 total tags in treatment: 16763693 INFO @ Fri, 10 Nov 2017 18:12:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:58: #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 18:12:58: #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 18:12:58: #1 tags after filtering in treatment: 16763535 INFO @ Fri, 10 Nov 2017 18:12:58: #1 tags after filtering in treatment: 16763535 INFO @ Fri, 10 Nov 2017 18:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:58: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:58: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:58: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:12:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:13:00: #2 number of paired peaks: 22473 INFO @ Fri, 10 Nov 2017 18:13:00: start model_add_line... INFO @ Fri, 10 Nov 2017 18:13:01: #2 number of paired peaks: 22473 INFO @ Fri, 10 Nov 2017 18:13:01: start model_add_line... INFO @ Fri, 10 Nov 2017 18:13:01: start X-correlation... INFO @ Fri, 10 Nov 2017 18:13:01: end of X-cor INFO @ Fri, 10 Nov 2017 18:13:01: #2 finished! INFO @ Fri, 10 Nov 2017 18:13:01: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Nov 2017 18:13:01: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Nov 2017 18:13:01: #2.2 Generate R script for model : SRX2202882.20_model.r INFO @ Fri, 10 Nov 2017 18:13:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:13:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:13:01: start X-correlation... INFO @ Fri, 10 Nov 2017 18:13:01: end of X-cor INFO @ Fri, 10 Nov 2017 18:13:01: #2 finished! INFO @ Fri, 10 Nov 2017 18:13:01: #2 predicted fragment length is 129 bps INFO @ Fri, 10 Nov 2017 18:13:01: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 10 Nov 2017 18:13:01: #2.2 Generate R script for model : SRX2202882.10_model.r INFO @ Fri, 10 Nov 2017 18:13:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:13:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:13:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:13:45: #4 Write output xls file... SRX2202882.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:13:45: #4 Write peak in narrowPeak format file... SRX2202882.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:13:45: #4 Write summits bed file... SRX2202882.05_summits.bed INFO @ Fri, 10 Nov 2017 18:13:45: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (3820 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:13:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:14:06: #4 Write output xls file... SRX2202882.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:14:06: #4 Write peak in narrowPeak format file... SRX2202882.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:14:06: #4 Write summits bed file... SRX2202882.20_summits.bed INFO @ Fri, 10 Nov 2017 18:14:06: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:14:11: #4 Write output xls file... SRX2202882.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:14:11: #4 Write peak in narrowPeak format file... SRX2202882.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:14:11: #4 Write summits bed file... SRX2202882.10_summits.bed INFO @ Fri, 10 Nov 2017 18:14:11: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。