Job ID = 10714383 sra ファイルのダウンロード中... Completed: 411662K bytes transferred in 11 seconds (304818K 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 19830957 spots for /home/okishinya/chipatlas/results/ce10/SRX4082343/SRR7164161.sra Written 19830957 spots for /home/okishinya/chipatlas/results/ce10/SRX4082343/SRR7164161.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:25 19830957 reads; of these: 19830957 (100.00%) were unpaired; of these: 3093249 (15.60%) aligned 0 times 15367462 (77.49%) aligned exactly 1 time 1370246 (6.91%) aligned >1 times 84.40% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6907546 / 16737708 = 0.4127 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 @ Sun, 03 Jun 2018 12:37:05: # Command line: callpeak -t SRX4082343.bam -f BAM -g ce -n SRX4082343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4082343.05 # format = BAM # ChIP-seq file = ['SRX4082343.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:37:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:05: # Command line: callpeak -t SRX4082343.bam -f BAM -g ce -n SRX4082343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4082343.20 # format = BAM # ChIP-seq file = ['SRX4082343.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:37:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:05: # Command line: callpeak -t SRX4082343.bam -f BAM -g ce -n SRX4082343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4082343.10 # format = BAM # ChIP-seq file = ['SRX4082343.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 03 Jun 2018 12:37:05: #1 read tag files... INFO @ Sun, 03 Jun 2018 12:37:05: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 12:37:12: 1000000 INFO @ Sun, 03 Jun 2018 12:37:12: 1000000 INFO @ Sun, 03 Jun 2018 12:37:12: 1000000 INFO @ Sun, 03 Jun 2018 12:37:18: 2000000 INFO @ Sun, 03 Jun 2018 12:37:19: 2000000 INFO @ Sun, 03 Jun 2018 12:37:19: 2000000 INFO @ Sun, 03 Jun 2018 12:37:25: 3000000 INFO @ Sun, 03 Jun 2018 12:37:25: 3000000 INFO @ Sun, 03 Jun 2018 12:37:25: 3000000 INFO @ Sun, 03 Jun 2018 12:37:31: 4000000 INFO @ Sun, 03 Jun 2018 12:37:32: 4000000 INFO @ Sun, 03 Jun 2018 12:37:32: 4000000 INFO @ Sun, 03 Jun 2018 12:37:38: 5000000 INFO @ Sun, 03 Jun 2018 12:37:38: 5000000 INFO @ Sun, 03 Jun 2018 12:37:38: 5000000 INFO @ Sun, 03 Jun 2018 12:37:44: 6000000 INFO @ Sun, 03 Jun 2018 12:37:45: 6000000 INFO @ Sun, 03 Jun 2018 12:37:45: 6000000 INFO @ Sun, 03 Jun 2018 12:37:51: 7000000 INFO @ Sun, 03 Jun 2018 12:37:51: 7000000 INFO @ Sun, 03 Jun 2018 12:37:52: 7000000 INFO @ Sun, 03 Jun 2018 12:37:57: 8000000 INFO @ Sun, 03 Jun 2018 12:37:58: 8000000 INFO @ Sun, 03 Jun 2018 12:37:58: 8000000 INFO @ Sun, 03 Jun 2018 12:38:04: 9000000 INFO @ Sun, 03 Jun 2018 12:38:05: 9000000 INFO @ Sun, 03 Jun 2018 12:38:05: 9000000 INFO @ Sun, 03 Jun 2018 12:38:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:38:09: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:38:09: #1 total tags in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:09: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:09: #1 tags after filtering in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:09: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:09: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:10: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:38:10: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:38:10: #1 total tags in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:10: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:10: #1 tags after filtering in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:10: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:10: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:11: #2 number of paired peaks: 5746 INFO @ Sun, 03 Jun 2018 12:38:11: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:11: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:11: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:11: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:11: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Jun 2018 12:38:11: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 03 Jun 2018 12:38:11: #2.2 Generate R script for model : SRX4082343.05_model.r INFO @ Sun, 03 Jun 2018 12:38:11: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:11: #1 tag size is determined as 51 bps INFO @ Sun, 03 Jun 2018 12:38:11: #1 tag size = 51 INFO @ Sun, 03 Jun 2018 12:38:11: #1 total tags in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:11: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 12:38:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 12:38:11: #1 tags after filtering in treatment: 9830162 INFO @ Sun, 03 Jun 2018 12:38:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 12:38:11: #1 finished! INFO @ Sun, 03 Jun 2018 12:38:11: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 12:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 12:38:12: #2 number of paired peaks: 5746 INFO @ Sun, 03 Jun 2018 12:38:12: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:12: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:12: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:12: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:12: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Jun 2018 12:38:12: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 03 Jun 2018 12:38:12: #2.2 Generate R script for model : SRX4082343.10_model.r INFO @ Sun, 03 Jun 2018 12:38:12: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:12: #2 number of paired peaks: 5746 INFO @ Sun, 03 Jun 2018 12:38:12: start model_add_line... INFO @ Sun, 03 Jun 2018 12:38:12: start X-correlation... INFO @ Sun, 03 Jun 2018 12:38:12: end of X-cor INFO @ Sun, 03 Jun 2018 12:38:12: #2 finished! INFO @ Sun, 03 Jun 2018 12:38:12: #2 predicted fragment length is 178 bps INFO @ Sun, 03 Jun 2018 12:38:12: #2 alternative fragment length(s) may be 178 bps INFO @ Sun, 03 Jun 2018 12:38:12: #2.2 Generate R script for model : SRX4082343.20_model.r INFO @ Sun, 03 Jun 2018 12:38:12: #3 Call peaks... INFO @ Sun, 03 Jun 2018 12:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 12:38:41: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:45: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 12:38:53: #4 Write output xls file... SRX4082343.05_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:53: #4 Write peak in narrowPeak format file... SRX4082343.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:53: #4 Write summits bed file... SRX4082343.05_summits.bed INFO @ Sun, 03 Jun 2018 12:38:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6653 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:56: #4 Write output xls file... SRX4082343.10_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:56: #4 Write peak in narrowPeak format file... SRX4082343.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:56: #4 Write summits bed file... SRX4082343.10_summits.bed INFO @ Sun, 03 Jun 2018 12:38:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5216 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 12:38:57: #4 Write output xls file... SRX4082343.20_peaks.xls INFO @ Sun, 03 Jun 2018 12:38:57: #4 Write peak in narrowPeak format file... SRX4082343.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 12:38:57: #4 Write summits bed file... SRX4082343.20_summits.bed INFO @ Sun, 03 Jun 2018 12:38:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3972 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。