Job ID = 2236697 sra ファイルのダウンロード中... Completed: 431580K bytes transferred in 6 seconds (548730K 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 --:--:-- --:--:-- --:--:-- 0 100 13456 0 13456 0 0 21402 0 --:--:-- --:--:-- --:--:-- 30721 100 35019 0 35019 0 0 42792 0 --:--:-- --:--:-- --:--:-- 55762 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 21006018 spots for /home/okishinya/chipatlas/results/ce10/SRX027210/SRR066593.sra Written 21006018 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: 00:03:06 21006018 reads; of these: 21006018 (100.00%) were unpaired; of these: 7277935 (34.65%) aligned 0 times 12187042 (58.02%) aligned exactly 1 time 1541041 (7.34%) aligned >1 times 65.35% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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_rmdupse_core] 3460056 / 13728083 = 0.2520 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 @ Thu, 30 Apr 2015 11:02:22: # Command line: callpeak -t SRX027210.bam -f BAM -g ce -n SRX027210.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX027210.20 # format = BAM # ChIP-seq file = ['SRX027210.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 @ Thu, 30 Apr 2015 11:02:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:02:22: # Command line: callpeak -t SRX027210.bam -f BAM -g ce -n SRX027210.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX027210.05 # format = BAM # ChIP-seq file = ['SRX027210.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 @ Thu, 30 Apr 2015 11:02:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:02:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:02:22: # Command line: callpeak -t SRX027210.bam -f BAM -g ce -n SRX027210.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX027210.10 # format = BAM # ChIP-seq file = ['SRX027210.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 @ Thu, 30 Apr 2015 11:02:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:02:22: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:02:22: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:02:27: 1000000 INFO @ Thu, 30 Apr 2015 11:02:27: 1000000 INFO @ Thu, 30 Apr 2015 11:02:27: 1000000 INFO @ Thu, 30 Apr 2015 11:02:33: 2000000 INFO @ Thu, 30 Apr 2015 11:02:33: 2000000 INFO @ Thu, 30 Apr 2015 11:02:33: 2000000 INFO @ Thu, 30 Apr 2015 11:02:39: 3000000 INFO @ Thu, 30 Apr 2015 11:02:39: 3000000 INFO @ Thu, 30 Apr 2015 11:02:40: 3000000 INFO @ Thu, 30 Apr 2015 11:02:45: 4000000 INFO @ Thu, 30 Apr 2015 11:02:46: 4000000 INFO @ Thu, 30 Apr 2015 11:02:46: 4000000 INFO @ Thu, 30 Apr 2015 11:02:52: 5000000 INFO @ Thu, 30 Apr 2015 11:02:52: 5000000 INFO @ Thu, 30 Apr 2015 11:02:53: 5000000 INFO @ Thu, 30 Apr 2015 11:02:57: 6000000 INFO @ Thu, 30 Apr 2015 11:02:58: 6000000 INFO @ Thu, 30 Apr 2015 11:02:59: 6000000 INFO @ Thu, 30 Apr 2015 11:03:03: 7000000 INFO @ Thu, 30 Apr 2015 11:03:04: 7000000 INFO @ Thu, 30 Apr 2015 11:03:05: 7000000 INFO @ Thu, 30 Apr 2015 11:03:09: 8000000 INFO @ Thu, 30 Apr 2015 11:03:10: 8000000 INFO @ Thu, 30 Apr 2015 11:03:11: 8000000 INFO @ Thu, 30 Apr 2015 11:03:15: 9000000 INFO @ Thu, 30 Apr 2015 11:03:16: 9000000 INFO @ Thu, 30 Apr 2015 11:03:17: 9000000 INFO @ Thu, 30 Apr 2015 11:03:20: 10000000 INFO @ Thu, 30 Apr 2015 11:03:22: 10000000 INFO @ Thu, 30 Apr 2015 11:03:22: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:03:22: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:03:22: #1 total tags in treatment: 10268027 INFO @ Thu, 30 Apr 2015 11:03:22: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:03:23: 10000000 INFO @ Thu, 30 Apr 2015 11:03:24: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:03:24: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:03:24: #1 total tags in treatment: 10268027 INFO @ Thu, 30 Apr 2015 11:03:24: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:03:24: #1 tags after filtering in treatment: 10267262 INFO @ Thu, 30 Apr 2015 11:03:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:03:24: #1 finished! INFO @ Thu, 30 Apr 2015 11:03:24: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:03:24: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:03:24: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:03:24: #1 total tags in treatment: 10268027 INFO @ Thu, 30 Apr 2015 11:03:24: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:03:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:03:25: #1 tags after filtering in treatment: 10267262 INFO @ Thu, 30 Apr 2015 11:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:03:25: #1 finished! INFO @ Thu, 30 Apr 2015 11:03:25: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:03:26: #2 number of paired peaks: 3991 INFO @ Thu, 30 Apr 2015 11:03:26: start model_add_line... INFO @ Thu, 30 Apr 2015 11:03:26: #1 tags after filtering in treatment: 10267262 INFO @ Thu, 30 Apr 2015 11:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:03:26: #1 finished! INFO @ Thu, 30 Apr 2015 11:03:26: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:03:28: #2 number of paired peaks: 3991 INFO @ Thu, 30 Apr 2015 11:03:28: start model_add_line... INFO @ Thu, 30 Apr 2015 11:03:29: #2 number of paired peaks: 3991 INFO @ Thu, 30 Apr 2015 11:03:29: start model_add_line... INFO @ Thu, 30 Apr 2015 11:04:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:04:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:04:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:04:03: #2 predicted fragment length is 234 bps INFO @ Thu, 30 Apr 2015 11:04:03: #2 alternative fragment length(s) may be 234 bps INFO @ Thu, 30 Apr 2015 11:04:03: #2.2 Generate R script for model : SRX027210.20_model.r INFO @ Thu, 30 Apr 2015 11:04:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:04:03: start X-correlation... INFO @ Thu, 30 Apr 2015 11:04:03: end of X-cor INFO @ Thu, 30 Apr 2015 11:04:03: #2 finished! INFO @ Thu, 30 Apr 2015 11:04:03: #2 predicted fragment length is 234 bps INFO @ Thu, 30 Apr 2015 11:04:03: #2 alternative fragment length(s) may be 234 bps INFO @ Thu, 30 Apr 2015 11:04:03: #2.2 Generate R script for model : SRX027210.05_model.r INFO @ Thu, 30 Apr 2015 11:04:03: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:04:04: start X-correlation... INFO @ Thu, 30 Apr 2015 11:04:04: end of X-cor INFO @ Thu, 30 Apr 2015 11:04:04: #2 finished! INFO @ Thu, 30 Apr 2015 11:04:04: #2 predicted fragment length is 234 bps INFO @ Thu, 30 Apr 2015 11:04:04: #2 alternative fragment length(s) may be 234 bps INFO @ Thu, 30 Apr 2015 11:04:04: #2.2 Generate R script for model : SRX027210.10_model.r INFO @ Thu, 30 Apr 2015 11:04:04: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:05:08: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:05:09: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:05:11: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:05:59: #4 Write output xls file... SRX027210.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:06:00: #4 Write peak in narrowPeak format file... SRX027210.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:06:00: #4 Write summits bed file... SRX027210.20_summits.bed INFO @ Thu, 30 Apr 2015 11:06:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3511 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:06:01: #4 Write output xls file... SRX027210.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:06:01: #4 Write peak in narrowPeak format file... SRX027210.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:06:01: #4 Write summits bed file... SRX027210.10_summits.bed INFO @ Thu, 30 Apr 2015 11:06:01: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4294 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:06:02: #4 Write output xls file... SRX027210.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:06:02: #4 Write peak in narrowPeak format file... SRX027210.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:06:02: #4 Write summits bed file... SRX027210.05_summits.bed INFO @ Thu, 30 Apr 2015 11:06:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5240 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。