Job ID = 9025555 sra ファイルのダウンロード中... Completed: 901739K bytes transferred in 11 seconds (627493K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2862 0 --:--:-- 0:00:07 --:--:-- 15650 100 46318 0 46318 0 0 5267 0 --:--:-- 0:00:08 --:--:-- 19123 100 69957 0 69957 0 0 7665 0 --:--:-- 0:00:09 --:--:-- 25392 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 36972865 spots for /home/okishinya/chipatlas/results/ce10/SRX1674102/SRR3320148.sra Written 36972865 spots total 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: 00:10:22 36972865 reads; of these: 36972865 (100.00%) were unpaired; of these: 5433523 (14.70%) aligned 0 times 20609832 (55.74%) aligned exactly 1 time 10929510 (29.56%) aligned >1 times 85.30% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12318561 / 31539342 = 0.3906 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 @ Sat, 03 Jun 2017 04:37:43: # Command line: callpeak -t SRX1674102.bam -f BAM -g ce -n SRX1674102.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674102.20 # format = BAM # ChIP-seq file = ['SRX1674102.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 INFO @ Sat, 03 Jun 2017 04:37:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:43: # Command line: callpeak -t SRX1674102.bam -f BAM -g ce -n SRX1674102.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674102.10 # format = BAM # ChIP-seq file = ['SRX1674102.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 INFO @ Sat, 03 Jun 2017 04:37:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:43: # Command line: callpeak -t SRX1674102.bam -f BAM -g ce -n SRX1674102.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674102.05 # format = BAM # ChIP-seq file = ['SRX1674102.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 INFO @ Sat, 03 Jun 2017 04:37:43: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:37:43: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:37:50: 1000000 INFO @ Sat, 03 Jun 2017 04:37:50: 1000000 INFO @ Sat, 03 Jun 2017 04:37:50: 1000000 INFO @ Sat, 03 Jun 2017 04:37:57: 2000000 INFO @ Sat, 03 Jun 2017 04:37:57: 2000000 INFO @ Sat, 03 Jun 2017 04:37:57: 2000000 INFO @ Sat, 03 Jun 2017 04:38:03: 3000000 INFO @ Sat, 03 Jun 2017 04:38:03: 3000000 INFO @ Sat, 03 Jun 2017 04:38:03: 3000000 INFO @ Sat, 03 Jun 2017 04:38:10: 4000000 INFO @ Sat, 03 Jun 2017 04:38:10: 4000000 INFO @ Sat, 03 Jun 2017 04:38:10: 4000000 INFO @ Sat, 03 Jun 2017 04:38:16: 5000000 INFO @ Sat, 03 Jun 2017 04:38:16: 5000000 INFO @ Sat, 03 Jun 2017 04:38:16: 5000000 INFO @ Sat, 03 Jun 2017 04:38:23: 6000000 INFO @ Sat, 03 Jun 2017 04:38:23: 6000000 INFO @ Sat, 03 Jun 2017 04:38:23: 6000000 INFO @ Sat, 03 Jun 2017 04:38:30: 7000000 INFO @ Sat, 03 Jun 2017 04:38:30: 7000000 INFO @ Sat, 03 Jun 2017 04:38:30: 7000000 INFO @ Sat, 03 Jun 2017 04:38:37: 8000000 INFO @ Sat, 03 Jun 2017 04:38:37: 8000000 INFO @ Sat, 03 Jun 2017 04:38:37: 8000000 INFO @ Sat, 03 Jun 2017 04:38:44: 9000000 INFO @ Sat, 03 Jun 2017 04:38:44: 9000000 INFO @ Sat, 03 Jun 2017 04:38:44: 9000000 INFO @ Sat, 03 Jun 2017 04:38:51: 10000000 INFO @ Sat, 03 Jun 2017 04:38:51: 10000000 INFO @ Sat, 03 Jun 2017 04:38:51: 10000000 INFO @ Sat, 03 Jun 2017 04:38:58: 11000000 INFO @ Sat, 03 Jun 2017 04:38:58: 11000000 INFO @ Sat, 03 Jun 2017 04:38:58: 11000000 INFO @ Sat, 03 Jun 2017 04:39:05: 12000000 INFO @ Sat, 03 Jun 2017 04:39:05: 12000000 INFO @ Sat, 03 Jun 2017 04:39:05: 12000000 INFO @ Sat, 03 Jun 2017 04:39:12: 13000000 INFO @ Sat, 03 Jun 2017 04:39:12: 13000000 INFO @ Sat, 03 Jun 2017 04:39:12: 13000000 INFO @ Sat, 03 Jun 2017 04:39:19: 14000000 INFO @ Sat, 03 Jun 2017 04:39:19: 14000000 INFO @ Sat, 03 Jun 2017 04:39:19: 14000000 INFO @ Sat, 03 Jun 2017 04:39:26: 15000000 INFO @ Sat, 03 Jun 2017 04:39:26: 15000000 INFO @ Sat, 03 Jun 2017 04:39:26: 15000000 INFO @ Sat, 03 Jun 2017 04:39:33: 16000000 INFO @ Sat, 03 Jun 2017 04:39:33: 16000000 INFO @ Sat, 03 Jun 2017 04:39:33: 16000000 INFO @ Sat, 03 Jun 2017 04:39:40: 17000000 INFO @ Sat, 03 Jun 2017 04:39:40: 17000000 INFO @ Sat, 03 Jun 2017 04:39:40: 17000000 INFO @ Sat, 03 Jun 2017 04:39:46: 18000000 INFO @ Sat, 03 Jun 2017 04:39:46: 18000000 INFO @ Sat, 03 Jun 2017 04:39:47: 18000000 INFO @ Sat, 03 Jun 2017 04:39:54: 19000000 INFO @ Sat, 03 Jun 2017 04:39:54: 19000000 INFO @ Sat, 03 Jun 2017 04:39:54: 19000000 INFO @ Sat, 03 Jun 2017 04:39:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:39:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:39:55: #1 total tags in treatment: 19220781 INFO @ Sat, 03 Jun 2017 04:39:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:39:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:39:55: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:39:55: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:39:55: #1 total tags in treatment: 19220781 INFO @ Sat, 03 Jun 2017 04:39:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:39:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:39:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:39:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:39:56: #1 total tags in treatment: 19220781 INFO @ Sat, 03 Jun 2017 04:39:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:39:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 04:39:59: #1 tags after filtering in treatment: 19205242 INFO @ Sat, 03 Jun 2017 04:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:39:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:39:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:39:59: #1 tags after filtering in treatment: 19205242 INFO @ Sat, 03 Jun 2017 04:39:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:39:59: #1 finished! INFO @ Sat, 03 Jun 2017 04:39:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:40:00: #1 tags after filtering in treatment: 19205242 INFO @ Sat, 03 Jun 2017 04:40:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:40:00: #1 finished! INFO @ Sat, 03 Jun 2017 04:40:00: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:40:03: #2 number of paired peaks: 4484 INFO @ Sat, 03 Jun 2017 04:40:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:40:03: #2 number of paired peaks: 4484 INFO @ Sat, 03 Jun 2017 04:40:03: start model_add_line... INFO @ Sat, 03 Jun 2017 04:40:04: #2 number of paired peaks: 4484 INFO @ Sat, 03 Jun 2017 04:40:04: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:16: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:16: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:16: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:16: #2 predicted fragment length is 233 bps INFO @ Sat, 03 Jun 2017 04:41:16: #2 alternative fragment length(s) may be 1,207,233 bps INFO @ Sat, 03 Jun 2017 04:41:16: #2.2 Generate R script for model : SRX1674102.05_model.r INFO @ Sat, 03 Jun 2017 04:41:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:17: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:17: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:17: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:17: #2 predicted fragment length is 233 bps INFO @ Sat, 03 Jun 2017 04:41:17: #2 alternative fragment length(s) may be 1,207,233 bps INFO @ Sat, 03 Jun 2017 04:41:17: #2.2 Generate R script for model : SRX1674102.10_model.r INFO @ Sat, 03 Jun 2017 04:41:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:18: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:18: #2 predicted fragment length is 233 bps INFO @ Sat, 03 Jun 2017 04:41:18: #2 alternative fragment length(s) may be 1,207,233 bps INFO @ Sat, 03 Jun 2017 04:41:18: #2.2 Generate R script for model : SRX1674102.20_model.r INFO @ Sat, 03 Jun 2017 04:41:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:33: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write output xls file... SRX1674102.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write peak in narrowPeak format file... SRX1674102.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:34: #4 Write summits bed file... SRX1674102.20_summits.bed INFO @ Sat, 03 Jun 2017 04:44:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1433 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:42: #4 Write output xls file... SRX1674102.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:42: #4 Write peak in narrowPeak format file... SRX1674102.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:42: #4 Write summits bed file... SRX1674102.05_summits.bed INFO @ Sat, 03 Jun 2017 04:44:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5311 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:44: #4 Write output xls file... SRX1674102.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:44: #4 Write peak in narrowPeak format file... SRX1674102.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:44: #4 Write summits bed file... SRX1674102.10_summits.bed INFO @ Sat, 03 Jun 2017 04:44:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3133 records, 4 fields): 5 millis CompletedMACS2peakCalling