Job ID = 9041710 sra ファイルのダウンロード中... Completed: 1880742K bytes transferred in 16 seconds (947271K 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 --:--:-- 0:00:07 --:--:-- 0 100 14324 0 14324 0 0 1839 0 --:--:-- 0:00:07 --:--:-- 10195 100 46173 0 46173 0 0 5359 0 --:--:-- 0:00:08 --:--:-- 20659 100 102k 0 102k 0 0 11108 0 --:--:-- 0:00:09 --:--:-- 34250 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 56523575 spots for /home/okishinya/chipatlas/results/dm3/SRX1361358/SRR2749796.sra Written 56523575 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: 00:11:51 56523575 reads; of these: 56523575 (100.00%) were unpaired; of these: 3285463 (5.81%) aligned 0 times 37060038 (65.57%) aligned exactly 1 time 16178074 (28.62%) aligned >1 times 94.19% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 27739503 / 53238112 = 0.5210 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 @ Mon, 05 Jun 2017 01:58:45: # Command line: callpeak -t SRX1361358.bam -f BAM -g dm -n SRX1361358.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361358.05 # format = BAM # ChIP-seq file = ['SRX1361358.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 01:58:45: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:58:45: # Command line: callpeak -t SRX1361358.bam -f BAM -g dm -n SRX1361358.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361358.10 # format = BAM # ChIP-seq file = ['SRX1361358.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 01:58:45: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:58:45: # Command line: callpeak -t SRX1361358.bam -f BAM -g dm -n SRX1361358.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361358.20 # format = BAM # ChIP-seq file = ['SRX1361358.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 05 Jun 2017 01:58:45: #1 read tag files... INFO @ Mon, 05 Jun 2017 01:58:45: #1 read treatment tags... INFO @ Mon, 05 Jun 2017 01:58:51: 1000000 INFO @ Mon, 05 Jun 2017 01:58:51: 1000000 INFO @ Mon, 05 Jun 2017 01:58:51: 1000000 INFO @ Mon, 05 Jun 2017 01:58:57: 2000000 INFO @ Mon, 05 Jun 2017 01:58:57: 2000000 INFO @ Mon, 05 Jun 2017 01:58:57: 2000000 INFO @ Mon, 05 Jun 2017 01:59:03: 3000000 INFO @ Mon, 05 Jun 2017 01:59:03: 3000000 INFO @ Mon, 05 Jun 2017 01:59:03: 3000000 INFO @ Mon, 05 Jun 2017 01:59:09: 4000000 INFO @ Mon, 05 Jun 2017 01:59:09: 4000000 INFO @ Mon, 05 Jun 2017 01:59:09: 4000000 INFO @ Mon, 05 Jun 2017 01:59:15: 5000000 INFO @ Mon, 05 Jun 2017 01:59:15: 5000000 INFO @ Mon, 05 Jun 2017 01:59:16: 5000000 INFO @ Mon, 05 Jun 2017 01:59:21: 6000000 INFO @ Mon, 05 Jun 2017 01:59:21: 6000000 INFO @ Mon, 05 Jun 2017 01:59:22: 6000000 INFO @ Mon, 05 Jun 2017 01:59:27: 7000000 INFO @ Mon, 05 Jun 2017 01:59:27: 7000000 INFO @ Mon, 05 Jun 2017 01:59:28: 7000000 INFO @ Mon, 05 Jun 2017 01:59:33: 8000000 INFO @ Mon, 05 Jun 2017 01:59:34: 8000000 INFO @ Mon, 05 Jun 2017 01:59:35: 8000000 INFO @ Mon, 05 Jun 2017 01:59:39: 9000000 INFO @ Mon, 05 Jun 2017 01:59:40: 9000000 INFO @ Mon, 05 Jun 2017 01:59:41: 9000000 INFO @ Mon, 05 Jun 2017 01:59:45: 10000000 INFO @ Mon, 05 Jun 2017 01:59:46: 10000000 INFO @ Mon, 05 Jun 2017 01:59:47: 10000000 INFO @ Mon, 05 Jun 2017 01:59:51: 11000000 INFO @ Mon, 05 Jun 2017 01:59:52: 11000000 INFO @ Mon, 05 Jun 2017 01:59:53: 11000000 INFO @ Mon, 05 Jun 2017 01:59:57: 12000000 INFO @ Mon, 05 Jun 2017 01:59:58: 12000000 INFO @ Mon, 05 Jun 2017 02:00:00: 12000000 INFO @ Mon, 05 Jun 2017 02:00:03: 13000000 INFO @ Mon, 05 Jun 2017 02:00:04: 13000000 INFO @ Mon, 05 Jun 2017 02:00:06: 13000000 INFO @ Mon, 05 Jun 2017 02:00:09: 14000000 INFO @ Mon, 05 Jun 2017 02:00:10: 14000000 INFO @ Mon, 05 Jun 2017 02:00:12: 14000000 INFO @ Mon, 05 Jun 2017 02:00:15: 15000000 INFO @ Mon, 05 Jun 2017 02:00:16: 15000000 INFO @ Mon, 05 Jun 2017 02:00:18: 15000000 INFO @ Mon, 05 Jun 2017 02:00:21: 16000000 INFO @ Mon, 05 Jun 2017 02:00:23: 16000000 INFO @ Mon, 05 Jun 2017 02:00:25: 16000000 INFO @ Mon, 05 Jun 2017 02:00:27: 17000000 INFO @ Mon, 05 Jun 2017 02:00:29: 17000000 INFO @ Mon, 05 Jun 2017 02:00:31: 17000000 INFO @ Mon, 05 Jun 2017 02:00:33: 18000000 INFO @ Mon, 05 Jun 2017 02:00:35: 18000000 INFO @ Mon, 05 Jun 2017 02:00:37: 18000000 INFO @ Mon, 05 Jun 2017 02:00:39: 19000000 INFO @ Mon, 05 Jun 2017 02:00:41: 19000000 INFO @ Mon, 05 Jun 2017 02:00:44: 19000000 INFO @ Mon, 05 Jun 2017 02:00:45: 20000000 INFO @ Mon, 05 Jun 2017 02:00:47: 20000000 INFO @ Mon, 05 Jun 2017 02:00:50: 20000000 INFO @ Mon, 05 Jun 2017 02:00:51: 21000000 INFO @ Mon, 05 Jun 2017 02:00:53: 21000000 INFO @ Mon, 05 Jun 2017 02:00:56: 21000000 INFO @ Mon, 05 Jun 2017 02:00:57: 22000000 INFO @ Mon, 05 Jun 2017 02:00:59: 22000000 INFO @ Mon, 05 Jun 2017 02:01:02: 22000000 INFO @ Mon, 05 Jun 2017 02:01:03: 23000000 INFO @ Mon, 05 Jun 2017 02:01:06: 23000000 INFO @ Mon, 05 Jun 2017 02:01:09: 23000000 INFO @ Mon, 05 Jun 2017 02:01:09: 24000000 INFO @ Mon, 05 Jun 2017 02:01:12: 24000000 INFO @ Mon, 05 Jun 2017 02:01:15: 25000000 INFO @ Mon, 05 Jun 2017 02:01:15: 24000000 INFO @ Mon, 05 Jun 2017 02:01:18: 25000000 INFO @ Mon, 05 Jun 2017 02:01:19: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:01:19: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:01:19: #1 total tags in treatment: 25498609 INFO @ Mon, 05 Jun 2017 02:01:19: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:01:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:01:22: 25000000 INFO @ Mon, 05 Jun 2017 02:01:22: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:01:22: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:01:22: #1 total tags in treatment: 25498609 INFO @ Mon, 05 Jun 2017 02:01:22: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:01:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:01:23: #1 tags after filtering in treatment: 25487728 INFO @ Mon, 05 Jun 2017 02:01:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:01:23: #1 finished! INFO @ Mon, 05 Jun 2017 02:01:23: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:01:25: #1 tag size is determined as 50 bps INFO @ Mon, 05 Jun 2017 02:01:25: #1 tag size = 50 INFO @ Mon, 05 Jun 2017 02:01:25: #1 total tags in treatment: 25498609 INFO @ Mon, 05 Jun 2017 02:01:25: #1 user defined the maximum tags... INFO @ Mon, 05 Jun 2017 02:01:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Jun 2017 02:01:27: #1 tags after filtering in treatment: 25487728 INFO @ Mon, 05 Jun 2017 02:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:01:27: #1 finished! INFO @ Mon, 05 Jun 2017 02:01:27: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:01:27: #2 number of paired peaks: 367 WARNING @ Mon, 05 Jun 2017 02:01:27: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 05 Jun 2017 02:01:27: start model_add_line... INFO @ Mon, 05 Jun 2017 02:01:30: #1 tags after filtering in treatment: 25487728 INFO @ Mon, 05 Jun 2017 02:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Jun 2017 02:01:30: #1 finished! INFO @ Mon, 05 Jun 2017 02:01:30: #2 Build Peak Model... INFO @ Mon, 05 Jun 2017 02:01:31: #2 number of paired peaks: 367 WARNING @ Mon, 05 Jun 2017 02:01:31: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 05 Jun 2017 02:01:31: start model_add_line... INFO @ Mon, 05 Jun 2017 02:01:34: #2 number of paired peaks: 367 WARNING @ Mon, 05 Jun 2017 02:01:34: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Mon, 05 Jun 2017 02:01:34: start model_add_line... INFO @ Mon, 05 Jun 2017 02:01:35: start X-correlation... INFO @ Mon, 05 Jun 2017 02:01:35: end of X-cor INFO @ Mon, 05 Jun 2017 02:01:35: #2 finished! INFO @ Mon, 05 Jun 2017 02:01:35: #2 predicted fragment length is 155 bps INFO @ Mon, 05 Jun 2017 02:01:35: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 05 Jun 2017 02:01:35: #2.2 Generate R script for model : SRX1361358.20_model.r INFO @ Mon, 05 Jun 2017 02:01:35: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:01:39: start X-correlation... INFO @ Mon, 05 Jun 2017 02:01:39: end of X-cor INFO @ Mon, 05 Jun 2017 02:01:39: #2 finished! INFO @ Mon, 05 Jun 2017 02:01:39: #2 predicted fragment length is 155 bps INFO @ Mon, 05 Jun 2017 02:01:39: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 05 Jun 2017 02:01:39: #2.2 Generate R script for model : SRX1361358.10_model.r INFO @ Mon, 05 Jun 2017 02:01:39: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:01:42: start X-correlation... INFO @ Mon, 05 Jun 2017 02:01:42: end of X-cor INFO @ Mon, 05 Jun 2017 02:01:42: #2 finished! INFO @ Mon, 05 Jun 2017 02:01:42: #2 predicted fragment length is 155 bps INFO @ Mon, 05 Jun 2017 02:01:42: #2 alternative fragment length(s) may be 155 bps INFO @ Mon, 05 Jun 2017 02:01:42: #2.2 Generate R script for model : SRX1361358.05_model.r INFO @ Mon, 05 Jun 2017 02:01:42: #3 Call peaks... INFO @ Mon, 05 Jun 2017 02:01:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Jun 2017 02:03:43: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:03:43: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:03:51: #3 Call peaks for each chromosome... INFO @ Mon, 05 Jun 2017 02:05:17: #4 Write output xls file... SRX1361358.20_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:17: #4 Write peak in narrowPeak format file... SRX1361358.20_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:17: #4 Write summits bed file... SRX1361358.20_summits.bed INFO @ Mon, 05 Jun 2017 02:05:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5203 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:05:26: #4 Write output xls file... SRX1361358.10_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:26: #4 Write peak in narrowPeak format file... SRX1361358.10_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:26: #4 Write summits bed file... SRX1361358.10_summits.bed INFO @ Mon, 05 Jun 2017 02:05:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8018 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 05 Jun 2017 02:05:45: #4 Write output xls file... SRX1361358.05_peaks.xls INFO @ Mon, 05 Jun 2017 02:05:45: #4 Write peak in narrowPeak format file... SRX1361358.05_peaks.narrowPeak INFO @ Mon, 05 Jun 2017 02:05:45: #4 Write summits bed file... SRX1361358.05_summits.bed INFO @ Mon, 05 Jun 2017 02:05:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13036 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。