Job ID = 9025550 sra ファイルのダウンロード中... Completed: 1729245K bytes transferred in 18 seconds (781839K 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 18661 0 18661 0 0 2452 0 --:--:-- 0:00:07 --:--:-- 15486 100 70789 0 70789 0 0 8226 0 --:--:-- 0:00:08 --:--:-- 32162 100 148k 0 148k 0 0 15848 0 --:--:-- 0:00:09 --:--:-- 47581 100 151k 0 151k 0 0 16135 0 --:--:-- 0:00:09 --:--:-- 48432 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 72777330 spots for /home/okishinya/chipatlas/results/ce10/SRX1674097/SRR3320143.sra Written 72777330 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: 00:11:56 72777330 reads; of these: 72777330 (100.00%) were unpaired; of these: 43840239 (60.24%) aligned 0 times 23190425 (31.86%) aligned exactly 1 time 5746666 (7.90%) aligned >1 times 39.76% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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 12 files... [bam_rmdupse_core] 14569218 / 28937091 = 0.5035 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 04:39:51: # Command line: callpeak -t SRX1674097.bam -f BAM -g ce -n SRX1674097.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1674097.05 # format = BAM # ChIP-seq file = ['SRX1674097.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 04:39:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:39:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:39:51: # Command line: callpeak -t SRX1674097.bam -f BAM -g ce -n SRX1674097.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1674097.20 # format = BAM # ChIP-seq file = ['SRX1674097.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 04:39:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:39:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:39:51: # Command line: callpeak -t SRX1674097.bam -f BAM -g ce -n SRX1674097.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1674097.10 # format = BAM # ChIP-seq file = ['SRX1674097.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 04:39:51: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:39:51: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:39:56: 1000000 INFO @ Sat, 03 Jun 2017 04:39:56: 1000000 INFO @ Sat, 03 Jun 2017 04:39:56: 1000000 INFO @ Sat, 03 Jun 2017 04:40:01: 2000000 INFO @ Sat, 03 Jun 2017 04:40:01: 2000000 INFO @ Sat, 03 Jun 2017 04:40:02: 2000000 INFO @ Sat, 03 Jun 2017 04:40:07: 3000000 INFO @ Sat, 03 Jun 2017 04:40:07: 3000000 INFO @ Sat, 03 Jun 2017 04:40:07: 3000000 INFO @ Sat, 03 Jun 2017 04:40:12: 4000000 INFO @ Sat, 03 Jun 2017 04:40:12: 4000000 INFO @ Sat, 03 Jun 2017 04:40:12: 4000000 INFO @ Sat, 03 Jun 2017 04:40:18: 5000000 INFO @ Sat, 03 Jun 2017 04:40:18: 5000000 INFO @ Sat, 03 Jun 2017 04:40:18: 5000000 INFO @ Sat, 03 Jun 2017 04:40:23: 6000000 INFO @ Sat, 03 Jun 2017 04:40:23: 6000000 INFO @ Sat, 03 Jun 2017 04:40:23: 6000000 INFO @ Sat, 03 Jun 2017 04:40:29: 7000000 INFO @ Sat, 03 Jun 2017 04:40:29: 7000000 INFO @ Sat, 03 Jun 2017 04:40:29: 7000000 INFO @ Sat, 03 Jun 2017 04:40:34: 8000000 INFO @ Sat, 03 Jun 2017 04:40:34: 8000000 INFO @ Sat, 03 Jun 2017 04:40:34: 8000000 INFO @ Sat, 03 Jun 2017 04:40:39: 9000000 INFO @ Sat, 03 Jun 2017 04:40:39: 9000000 INFO @ Sat, 03 Jun 2017 04:40:40: 9000000 INFO @ Sat, 03 Jun 2017 04:40:45: 10000000 INFO @ Sat, 03 Jun 2017 04:40:45: 10000000 INFO @ Sat, 03 Jun 2017 04:40:45: 10000000 INFO @ Sat, 03 Jun 2017 04:40:50: 11000000 INFO @ Sat, 03 Jun 2017 04:40:50: 11000000 INFO @ Sat, 03 Jun 2017 04:40:50: 11000000 INFO @ Sat, 03 Jun 2017 04:40:55: 12000000 INFO @ Sat, 03 Jun 2017 04:40:56: 12000000 INFO @ Sat, 03 Jun 2017 04:40:56: 12000000 INFO @ Sat, 03 Jun 2017 04:41:01: 13000000 INFO @ Sat, 03 Jun 2017 04:41:01: 13000000 INFO @ Sat, 03 Jun 2017 04:41:01: 13000000 INFO @ Sat, 03 Jun 2017 04:41:06: 14000000 INFO @ Sat, 03 Jun 2017 04:41:06: 14000000 INFO @ Sat, 03 Jun 2017 04:41:07: 14000000 INFO @ Sat, 03 Jun 2017 04:41:08: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:41:08: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:41:08: #1 total tags in treatment: 14367873 INFO @ Sat, 03 Jun 2017 04:41:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:08: #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 04:41:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:41:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:41:09: #1 total tags in treatment: 14367873 INFO @ Sat, 03 Jun 2017 04:41:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:09: #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 04:41:09: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:41:09: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:41:09: #1 total tags in treatment: 14367873 INFO @ Sat, 03 Jun 2017 04:41:09: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:41:09: #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 04:41:11: #1 tags after filtering in treatment: 14346866 INFO @ Sat, 03 Jun 2017 04:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:11: #1 tags after filtering in treatment: 14346866 INFO @ Sat, 03 Jun 2017 04:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:11: #1 tags after filtering in treatment: 14346866 INFO @ Sat, 03 Jun 2017 04:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:41:11: #1 finished! INFO @ Sat, 03 Jun 2017 04:41:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:41:13: #2 number of paired peaks: 2350 INFO @ Sat, 03 Jun 2017 04:41:13: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:14: #2 number of paired peaks: 2350 INFO @ Sat, 03 Jun 2017 04:41:14: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:14: #2 number of paired peaks: 2350 INFO @ Sat, 03 Jun 2017 04:41:14: start model_add_line... INFO @ Sat, 03 Jun 2017 04:41:41: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:41: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:41: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:41: #2 predicted fragment length is 261 bps INFO @ Sat, 03 Jun 2017 04:41:41: #2 alternative fragment length(s) may be 261 bps INFO @ Sat, 03 Jun 2017 04:41:41: #2.2 Generate R script for model : SRX1674097.05_model.r INFO @ Sat, 03 Jun 2017 04:41:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:43: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:43: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:43: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:43: #2 predicted fragment length is 261 bps INFO @ Sat, 03 Jun 2017 04:41:43: #2 alternative fragment length(s) may be 261 bps INFO @ Sat, 03 Jun 2017 04:41:43: #2.2 Generate R script for model : SRX1674097.10_model.r INFO @ Sat, 03 Jun 2017 04:41:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:41:43: start X-correlation... INFO @ Sat, 03 Jun 2017 04:41:43: end of X-cor INFO @ Sat, 03 Jun 2017 04:41:43: #2 finished! INFO @ Sat, 03 Jun 2017 04:41:43: #2 predicted fragment length is 261 bps INFO @ Sat, 03 Jun 2017 04:41:43: #2 alternative fragment length(s) may be 261 bps INFO @ Sat, 03 Jun 2017 04:41:43: #2.2 Generate R script for model : SRX1674097.20_model.r INFO @ Sat, 03 Jun 2017 04:41:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:43:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:43:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:44:35: #4 Write output xls file... SRX1674097.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:35: #4 Write peak in narrowPeak format file... SRX1674097.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:35: #4 Write summits bed file... SRX1674097.20_summits.bed INFO @ Sat, 03 Jun 2017 04:44:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7434 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:44:39: #4 Write output xls file... SRX1674097.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:39: #4 Write peak in narrowPeak format file... SRX1674097.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:39: #4 Write summits bed file... SRX1674097.10_summits.bed INFO @ Sat, 03 Jun 2017 04:44:39: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (12911 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write output xls file... SRX1674097.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write peak in narrowPeak format file... SRX1674097.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:44:50: #4 Write summits bed file... SRX1674097.05_summits.bed INFO @ Sat, 03 Jun 2017 04:44:50: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (18267 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。