Job ID = 11632730 sra ファイルのダウンロード中... Completed: 455397K bytes transferred in 7 seconds (503069K 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... Read 24379502 spots for /home/okishinya/chipatlas/results/rn6/SRX4497200/SRR7633470.sra Written 24379502 spots for /home/okishinya/chipatlas/results/rn6/SRX4497200/SRR7633470.sra 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 rm: cannot remove `[DSE]RR*.fastq': 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: 00:19:20 24379502 reads; of these: 24379502 (100.00%) were unpaired; of these: 750060 (3.08%) aligned 0 times 17049212 (69.93%) aligned exactly 1 time 6580230 (26.99%) aligned >1 times 96.92% overall alignment rate Time searching: 00:19:22 Overall time: 00:19:22 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] 2343208 / 23629442 = 0.0992 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, 15 Feb 2019 07:08:03: # Command line: callpeak -t SRX4497200.bam -f BAM -g 2.15e9 -n SRX4497200.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497200.20 # format = BAM # ChIP-seq file = ['SRX4497200.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, 15 Feb 2019 07:08:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:03: # Command line: callpeak -t SRX4497200.bam -f BAM -g 2.15e9 -n SRX4497200.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497200.05 # format = BAM # ChIP-seq file = ['SRX4497200.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, 15 Feb 2019 07:08:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:03: # Command line: callpeak -t SRX4497200.bam -f BAM -g 2.15e9 -n SRX4497200.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497200.10 # format = BAM # ChIP-seq file = ['SRX4497200.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, 15 Feb 2019 07:08:03: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:08:03: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:08:09: 1000000 INFO @ Fri, 15 Feb 2019 07:08:10: 1000000 INFO @ Fri, 15 Feb 2019 07:08:10: 1000000 INFO @ Fri, 15 Feb 2019 07:08:16: 2000000 INFO @ Fri, 15 Feb 2019 07:08:16: 2000000 INFO @ Fri, 15 Feb 2019 07:08:16: 2000000 INFO @ Fri, 15 Feb 2019 07:08:23: 3000000 INFO @ Fri, 15 Feb 2019 07:08:23: 3000000 INFO @ Fri, 15 Feb 2019 07:08:23: 3000000 INFO @ Fri, 15 Feb 2019 07:08:29: 4000000 INFO @ Fri, 15 Feb 2019 07:08:30: 4000000 INFO @ Fri, 15 Feb 2019 07:08:30: 4000000 INFO @ Fri, 15 Feb 2019 07:08:36: 5000000 INFO @ Fri, 15 Feb 2019 07:08:37: 5000000 INFO @ Fri, 15 Feb 2019 07:08:37: 5000000 INFO @ Fri, 15 Feb 2019 07:08:43: 6000000 INFO @ Fri, 15 Feb 2019 07:08:44: 6000000 INFO @ Fri, 15 Feb 2019 07:08:44: 6000000 INFO @ Fri, 15 Feb 2019 07:08:49: 7000000 INFO @ Fri, 15 Feb 2019 07:08:51: 7000000 INFO @ Fri, 15 Feb 2019 07:08:51: 7000000 INFO @ Fri, 15 Feb 2019 07:08:56: 8000000 INFO @ Fri, 15 Feb 2019 07:08:58: 8000000 INFO @ Fri, 15 Feb 2019 07:08:58: 8000000 INFO @ Fri, 15 Feb 2019 07:09:02: 9000000 INFO @ Fri, 15 Feb 2019 07:09:05: 9000000 INFO @ Fri, 15 Feb 2019 07:09:05: 9000000 INFO @ Fri, 15 Feb 2019 07:09:09: 10000000 INFO @ Fri, 15 Feb 2019 07:09:12: 10000000 INFO @ Fri, 15 Feb 2019 07:09:13: 10000000 INFO @ Fri, 15 Feb 2019 07:09:17: 11000000 INFO @ Fri, 15 Feb 2019 07:09:19: 11000000 INFO @ Fri, 15 Feb 2019 07:09:20: 11000000 INFO @ Fri, 15 Feb 2019 07:09:24: 12000000 INFO @ Fri, 15 Feb 2019 07:09:26: 12000000 INFO @ Fri, 15 Feb 2019 07:09:27: 12000000 INFO @ Fri, 15 Feb 2019 07:09:32: 13000000 INFO @ Fri, 15 Feb 2019 07:09:33: 13000000 INFO @ Fri, 15 Feb 2019 07:09:35: 13000000 INFO @ Fri, 15 Feb 2019 07:09:39: 14000000 INFO @ Fri, 15 Feb 2019 07:09:40: 14000000 INFO @ Fri, 15 Feb 2019 07:09:42: 14000000 INFO @ Fri, 15 Feb 2019 07:09:46: 15000000 INFO @ Fri, 15 Feb 2019 07:09:47: 15000000 INFO @ Fri, 15 Feb 2019 07:09:49: 15000000 INFO @ Fri, 15 Feb 2019 07:09:52: 16000000 INFO @ Fri, 15 Feb 2019 07:09:54: 16000000 INFO @ Fri, 15 Feb 2019 07:09:56: 16000000 INFO @ Fri, 15 Feb 2019 07:09:59: 17000000 INFO @ Fri, 15 Feb 2019 07:10:02: 17000000 INFO @ Fri, 15 Feb 2019 07:10:04: 17000000 INFO @ Fri, 15 Feb 2019 07:10:06: 18000000 INFO @ Fri, 15 Feb 2019 07:10:09: 18000000 INFO @ Fri, 15 Feb 2019 07:10:11: 18000000 INFO @ Fri, 15 Feb 2019 07:10:12: 19000000 INFO @ Fri, 15 Feb 2019 07:10:16: 19000000 INFO @ Fri, 15 Feb 2019 07:10:18: 19000000 INFO @ Fri, 15 Feb 2019 07:10:19: 20000000 INFO @ Fri, 15 Feb 2019 07:10:23: 20000000 INFO @ Fri, 15 Feb 2019 07:10:25: 20000000 INFO @ Fri, 15 Feb 2019 07:10:26: 21000000 INFO @ Fri, 15 Feb 2019 07:10:28: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:10:28: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:10:28: #1 total tags in treatment: 21286234 INFO @ Fri, 15 Feb 2019 07:10:28: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:10:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:10:29: #1 tags after filtering in treatment: 21286086 INFO @ Fri, 15 Feb 2019 07:10:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:10:29: #1 finished! INFO @ Fri, 15 Feb 2019 07:10:29: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:10:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:10:30: 21000000 INFO @ Fri, 15 Feb 2019 07:10:32: #2 number of paired peaks: 18556 INFO @ Fri, 15 Feb 2019 07:10:32: start model_add_line... INFO @ Fri, 15 Feb 2019 07:10:32: start X-correlation... INFO @ Fri, 15 Feb 2019 07:10:32: end of X-cor INFO @ Fri, 15 Feb 2019 07:10:32: #2 finished! INFO @ Fri, 15 Feb 2019 07:10:32: #2 predicted fragment length is 221 bps INFO @ Fri, 15 Feb 2019 07:10:32: #2 alternative fragment length(s) may be 55,221 bps INFO @ Fri, 15 Feb 2019 07:10:32: #2.2 Generate R script for model : SRX4497200.20_model.r INFO @ Fri, 15 Feb 2019 07:10:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:10:32: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:10:32: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:10:32: #1 total tags in treatment: 21286234 INFO @ Fri, 15 Feb 2019 07:10:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:10:32: 21000000 INFO @ Fri, 15 Feb 2019 07:10:33: #1 tags after filtering in treatment: 21286086 INFO @ Fri, 15 Feb 2019 07:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:10:33: #1 finished! INFO @ Fri, 15 Feb 2019 07:10:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:10:35: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:10:35: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:10:35: #1 total tags in treatment: 21286234 INFO @ Fri, 15 Feb 2019 07:10:35: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:10:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:10:35: #1 tags after filtering in treatment: 21286086 INFO @ Fri, 15 Feb 2019 07:10:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:10:35: #1 finished! INFO @ Fri, 15 Feb 2019 07:10:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:10:36: #2 number of paired peaks: 18556 INFO @ Fri, 15 Feb 2019 07:10:36: start model_add_line... INFO @ Fri, 15 Feb 2019 07:10:36: start X-correlation... INFO @ Fri, 15 Feb 2019 07:10:36: end of X-cor INFO @ Fri, 15 Feb 2019 07:10:36: #2 finished! INFO @ Fri, 15 Feb 2019 07:10:36: #2 predicted fragment length is 221 bps INFO @ Fri, 15 Feb 2019 07:10:36: #2 alternative fragment length(s) may be 55,221 bps INFO @ Fri, 15 Feb 2019 07:10:36: #2.2 Generate R script for model : SRX4497200.10_model.r INFO @ Fri, 15 Feb 2019 07:10:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:10:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:10:38: #2 number of paired peaks: 18556 INFO @ Fri, 15 Feb 2019 07:10:38: start model_add_line... INFO @ Fri, 15 Feb 2019 07:10:39: start X-correlation... INFO @ Fri, 15 Feb 2019 07:10:39: end of X-cor INFO @ Fri, 15 Feb 2019 07:10:39: #2 finished! INFO @ Fri, 15 Feb 2019 07:10:39: #2 predicted fragment length is 221 bps INFO @ Fri, 15 Feb 2019 07:10:39: #2 alternative fragment length(s) may be 55,221 bps INFO @ Fri, 15 Feb 2019 07:10:39: #2.2 Generate R script for model : SRX4497200.05_model.r INFO @ Fri, 15 Feb 2019 07:10:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:11:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:11:30: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:11:35: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:11:56: #4 Write output xls file... SRX4497200.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:11:56: #4 Write peak in narrowPeak format file... SRX4497200.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:11:56: #4 Write summits bed file... SRX4497200.20_summits.bed INFO @ Fri, 15 Feb 2019 07:11:56: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:12:00: #4 Write output xls file... SRX4497200.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:12:00: #4 Write peak in narrowPeak format file... SRX4497200.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:12:00: #4 Write summits bed file... SRX4497200.10_summits.bed INFO @ Fri, 15 Feb 2019 07:12:00: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:12:07: #4 Write output xls file... SRX4497200.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:12:07: #4 Write peak in narrowPeak format file... SRX4497200.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:12:07: #4 Write summits bed file... SRX4497200.05_summits.bed INFO @ Fri, 15 Feb 2019 07:12:07: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (907 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。