Job ID = 9025467 sra ファイルのダウンロード中... Completed: 566821K bytes transferred in 7 seconds (604641K bits/sec), in 2 files, 3 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 20110 0 20110 0 0 2433 0 --:--:-- 0:00:08 --:--:-- 10817 100 51966 0 51966 0 0 5612 0 --:--:-- 0:00:09 --:--:-- 18201 100 57796 0 57796 0 0 6241 0 --:--:-- 0:00:09 --:--:-- 20236 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 8044123 spots for /home/okishinya/chipatlas/results/ce10/SRX1099840/SRR2105911.sra Written 8044123 spots total Written 9962719 spots for /home/okishinya/chipatlas/results/ce10/SRX1099840/SRR2105912.sra Written 9962719 spots total 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: 00:04:27 18006842 reads; of these: 18006842 (100.00%) were unpaired; of these: 1621931 (9.01%) aligned 0 times 14111790 (78.37%) aligned exactly 1 time 2273121 (12.62%) aligned >1 times 90.99% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 5988084 / 16384911 = 0.3655 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 04:05:54: # Command line: callpeak -t SRX1099840.bam -f BAM -g ce -n SRX1099840.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1099840.20 # format = BAM # ChIP-seq file = ['SRX1099840.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 04:05:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:54: # Command line: callpeak -t SRX1099840.bam -f BAM -g ce -n SRX1099840.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1099840.05 # format = BAM # ChIP-seq file = ['SRX1099840.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 04:05:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:54: # Command line: callpeak -t SRX1099840.bam -f BAM -g ce -n SRX1099840.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1099840.10 # format = BAM # ChIP-seq file = ['SRX1099840.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 04:05:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:05:54: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:05:54: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:06:00: 1000000 INFO @ Sat, 03 Jun 2017 04:06:00: 1000000 INFO @ Sat, 03 Jun 2017 04:06:00: 1000000 INFO @ Sat, 03 Jun 2017 04:06:06: 2000000 INFO @ Sat, 03 Jun 2017 04:06:06: 2000000 INFO @ Sat, 03 Jun 2017 04:06:06: 2000000 INFO @ Sat, 03 Jun 2017 04:06:11: 3000000 INFO @ Sat, 03 Jun 2017 04:06:11: 3000000 INFO @ Sat, 03 Jun 2017 04:06:12: 3000000 INFO @ Sat, 03 Jun 2017 04:06:18: 4000000 INFO @ Sat, 03 Jun 2017 04:06:18: 4000000 INFO @ Sat, 03 Jun 2017 04:06:18: 4000000 INFO @ Sat, 03 Jun 2017 04:06:24: 5000000 INFO @ Sat, 03 Jun 2017 04:06:25: 5000000 INFO @ Sat, 03 Jun 2017 04:06:25: 5000000 INFO @ Sat, 03 Jun 2017 04:06:31: 6000000 INFO @ Sat, 03 Jun 2017 04:06:31: 6000000 INFO @ Sat, 03 Jun 2017 04:06:32: 6000000 INFO @ Sat, 03 Jun 2017 04:06:38: 7000000 INFO @ Sat, 03 Jun 2017 04:06:38: 7000000 INFO @ Sat, 03 Jun 2017 04:06:39: 7000000 INFO @ Sat, 03 Jun 2017 04:06:45: 8000000 INFO @ Sat, 03 Jun 2017 04:06:45: 8000000 INFO @ Sat, 03 Jun 2017 04:06:46: 8000000 INFO @ Sat, 03 Jun 2017 04:06:52: 9000000 INFO @ Sat, 03 Jun 2017 04:06:52: 9000000 INFO @ Sat, 03 Jun 2017 04:06:54: 9000000 INFO @ Sat, 03 Jun 2017 04:06:58: 10000000 INFO @ Sat, 03 Jun 2017 04:06:59: 10000000 INFO @ Sat, 03 Jun 2017 04:07:01: 10000000 INFO @ Sat, 03 Jun 2017 04:07:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:07:01: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:07:01: #1 total tags in treatment: 10396827 INFO @ Sat, 03 Jun 2017 04:07:01: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:01: #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 04:07:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:07:02: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:07:02: #1 total tags in treatment: 10396827 INFO @ Sat, 03 Jun 2017 04:07:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:02: #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 04:07:03: #1 tags after filtering in treatment: 10395178 INFO @ Sat, 03 Jun 2017 04:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:03: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:03: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:04: #1 tags after filtering in treatment: 10395178 INFO @ Sat, 03 Jun 2017 04:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:04: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:04: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:04: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 04:07:04: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 04:07:04: #1 total tags in treatment: 10396827 INFO @ Sat, 03 Jun 2017 04:07:04: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:07:04: #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 04:07:05: #2 number of paired peaks: 1045 INFO @ Sat, 03 Jun 2017 04:07:05: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:05: #2 number of paired peaks: 1045 INFO @ Sat, 03 Jun 2017 04:07:05: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:06: #1 tags after filtering in treatment: 10395178 INFO @ Sat, 03 Jun 2017 04:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 04:07:06: #1 finished! INFO @ Sat, 03 Jun 2017 04:07:06: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:07:08: #2 number of paired peaks: 1045 INFO @ Sat, 03 Jun 2017 04:07:08: start model_add_line... INFO @ Sat, 03 Jun 2017 04:07:15: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:15: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:15: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:15: #2 predicted fragment length is 201 bps INFO @ Sat, 03 Jun 2017 04:07:15: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 03 Jun 2017 04:07:15: #2.2 Generate R script for model : SRX1099840.20_model.r INFO @ Sat, 03 Jun 2017 04:07:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:15: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:15: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:15: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:15: #2 predicted fragment length is 201 bps INFO @ Sat, 03 Jun 2017 04:07:15: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 03 Jun 2017 04:07:15: #2.2 Generate R script for model : SRX1099840.10_model.r INFO @ Sat, 03 Jun 2017 04:07:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:07:18: start X-correlation... INFO @ Sat, 03 Jun 2017 04:07:18: end of X-cor INFO @ Sat, 03 Jun 2017 04:07:18: #2 finished! INFO @ Sat, 03 Jun 2017 04:07:18: #2 predicted fragment length is 201 bps INFO @ Sat, 03 Jun 2017 04:07:18: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 03 Jun 2017 04:07:18: #2.2 Generate R script for model : SRX1099840.05_model.r INFO @ Sat, 03 Jun 2017 04:07:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:08:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:08:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write output xls file... SRX1099840.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write peak in narrowPeak format file... SRX1099840.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write summits bed file... SRX1099840.10_summits.bed INFO @ Sat, 03 Jun 2017 04:09:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2754 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write output xls file... SRX1099840.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write peak in narrowPeak format file... SRX1099840.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:03: #4 Write summits bed file... SRX1099840.20_summits.bed INFO @ Sat, 03 Jun 2017 04:09:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1514 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:09:09: #4 Write output xls file... SRX1099840.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:09:09: #4 Write peak in narrowPeak format file... SRX1099840.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:09:09: #4 Write summits bed file... SRX1099840.05_summits.bed INFO @ Sat, 03 Jun 2017 04:09:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4541 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。