Job ID = 4303138 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 34,656,544 reads read : 69,313,088 reads written : 69,313,088 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1554221.sra.cache’: No such file or directory 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: 01:09:07 34656544 reads; of these: 34656544 (100.00%) were paired; of these: 8579510 (24.76%) aligned concordantly 0 times 19531170 (56.36%) aligned concordantly exactly 1 time 6545864 (18.89%) aligned concordantly >1 times ---- 8579510 pairs aligned concordantly 0 times; of these: 578510 (6.74%) aligned discordantly 1 time ---- 8001000 pairs aligned 0 times concordantly or discordantly; of these: 16002000 mates make up the pairs; of these: 14853008 (92.82%) aligned 0 times 665496 (4.16%) aligned exactly 1 time 483496 (3.02%) aligned >1 times 78.57% overall alignment rate Time searching: 01:09:07 Overall time: 01:09:07 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 21011890 / 26637354 = 0.7888 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 02:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.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 # Paired-End mode is off INFO @ Thu, 12 Dec 2019 02:11:56: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:11:56: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:12:01: 1000000 INFO @ Thu, 12 Dec 2019 02:12:06: 2000000 INFO @ Thu, 12 Dec 2019 02:12:12: 3000000 INFO @ Thu, 12 Dec 2019 02:12:18: 4000000 INFO @ Thu, 12 Dec 2019 02:12:23: 5000000 INFO @ Thu, 12 Dec 2019 02:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.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 # Paired-End mode is off INFO @ Thu, 12 Dec 2019 02:12:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:12:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:12:29: 6000000 INFO @ Thu, 12 Dec 2019 02:12:31: 1000000 INFO @ Thu, 12 Dec 2019 02:12:36: 7000000 INFO @ Thu, 12 Dec 2019 02:12:36: 2000000 INFO @ Thu, 12 Dec 2019 02:12:42: 8000000 INFO @ Thu, 12 Dec 2019 02:12:43: 3000000 INFO @ Thu, 12 Dec 2019 02:12:48: 9000000 INFO @ Thu, 12 Dec 2019 02:12:48: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 02:12:54: 5000000 INFO @ Thu, 12 Dec 2019 02:12:54: 10000000 INFO @ Thu, 12 Dec 2019 02:12:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.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 # Paired-End mode is off INFO @ Thu, 12 Dec 2019 02:12:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:12:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:13:00: 6000000 INFO @ Thu, 12 Dec 2019 02:13:01: 11000000 INFO @ Thu, 12 Dec 2019 02:13:01: 1000000 INFO @ Thu, 12 Dec 2019 02:13:07: 7000000 INFO @ Thu, 12 Dec 2019 02:13:08: 2000000 INFO @ Thu, 12 Dec 2019 02:13:08: 12000000 INFO @ Thu, 12 Dec 2019 02:13:11: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:13:11: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:13:11: #1 total tags in treatment: 5454710 INFO @ Thu, 12 Dec 2019 02:13:11: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:13:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:13:11: #1 tags after filtering in treatment: 5193830 INFO @ Thu, 12 Dec 2019 02:13:11: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:13:11: #1 finished! INFO @ Thu, 12 Dec 2019 02:13:11: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:13:12: #2 number of paired peaks: 2463 INFO @ Thu, 12 Dec 2019 02:13:12: start model_add_line... INFO @ Thu, 12 Dec 2019 02:13:12: start X-correlation... INFO @ Thu, 12 Dec 2019 02:13:12: end of X-cor INFO @ Thu, 12 Dec 2019 02:13:12: #2 finished! INFO @ Thu, 12 Dec 2019 02:13:12: #2 predicted fragment length is 167 bps INFO @ Thu, 12 Dec 2019 02:13:12: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 12 Dec 2019 02:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05_model.r INFO @ Thu, 12 Dec 2019 02:13:12: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:13:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:13:13: 8000000 INFO @ Thu, 12 Dec 2019 02:13:14: 3000000 INFO @ Thu, 12 Dec 2019 02:13:19: 9000000 INFO @ Thu, 12 Dec 2019 02:13:21: 4000000 INFO @ Thu, 12 Dec 2019 02:13:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:13:24: 10000000 INFO @ Thu, 12 Dec 2019 02:13:27: 5000000 INFO @ Thu, 12 Dec 2019 02:13:30: 11000000 INFO @ Thu, 12 Dec 2019 02:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05_peaks.xls INFO @ Thu, 12 Dec 2019 02:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.05_summits.bed INFO @ Thu, 12 Dec 2019 02:13:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5048 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 02:13:34: 6000000 INFO @ Thu, 12 Dec 2019 02:13:36: 12000000 INFO @ Thu, 12 Dec 2019 02:13:38: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:13:38: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:13:38: #1 total tags in treatment: 5454710 INFO @ Thu, 12 Dec 2019 02:13:38: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:13:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:13:39: #1 tags after filtering in treatment: 5193830 INFO @ Thu, 12 Dec 2019 02:13:39: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:13:39: #1 finished! INFO @ Thu, 12 Dec 2019 02:13:39: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:13:39: #2 number of paired peaks: 2463 INFO @ Thu, 12 Dec 2019 02:13:39: start model_add_line... INFO @ Thu, 12 Dec 2019 02:13:39: start X-correlation... INFO @ Thu, 12 Dec 2019 02:13:39: end of X-cor INFO @ Thu, 12 Dec 2019 02:13:39: #2 finished! INFO @ Thu, 12 Dec 2019 02:13:39: #2 predicted fragment length is 167 bps INFO @ Thu, 12 Dec 2019 02:13:39: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 12 Dec 2019 02:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10_model.r INFO @ Thu, 12 Dec 2019 02:13:39: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:13:40: 7000000 INFO @ Thu, 12 Dec 2019 02:13:46: 8000000 INFO @ Thu, 12 Dec 2019 02:13:51: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:13:51: 9000000 INFO @ Thu, 12 Dec 2019 02:13:57: 10000000 INFO @ Thu, 12 Dec 2019 02:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10_peaks.xls INFO @ Thu, 12 Dec 2019 02:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.10_summits.bed INFO @ Thu, 12 Dec 2019 02:13:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2938 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 02:14:02: 11000000 INFO @ Thu, 12 Dec 2019 02:14:08: 12000000 INFO @ Thu, 12 Dec 2019 02:14:10: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 02:14:10: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 02:14:10: #1 total tags in treatment: 5454710 INFO @ Thu, 12 Dec 2019 02:14:10: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:14:10: #1 tags after filtering in treatment: 5193830 INFO @ Thu, 12 Dec 2019 02:14:10: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 12 Dec 2019 02:14:10: #1 finished! INFO @ Thu, 12 Dec 2019 02:14:10: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:14:11: #2 number of paired peaks: 2463 INFO @ Thu, 12 Dec 2019 02:14:11: start model_add_line... INFO @ Thu, 12 Dec 2019 02:14:11: start X-correlation... INFO @ Thu, 12 Dec 2019 02:14:11: end of X-cor INFO @ Thu, 12 Dec 2019 02:14:11: #2 finished! INFO @ Thu, 12 Dec 2019 02:14:11: #2 predicted fragment length is 167 bps INFO @ Thu, 12 Dec 2019 02:14:11: #2 alternative fragment length(s) may be 167 bps INFO @ Thu, 12 Dec 2019 02:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20_model.r INFO @ Thu, 12 Dec 2019 02:14:11: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:14:23: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:14:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20_peaks.xls INFO @ Thu, 12 Dec 2019 02:14:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:14:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX683495/SRX683495.20_summits.bed INFO @ Thu, 12 Dec 2019 02:14:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1213 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。