Job ID = 1294807 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,980,213 reads read : 14,980,213 reads written : 14,980,213 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:37 14980213 reads; of these: 14980213 (100.00%) were unpaired; of these: 614397 (4.10%) aligned 0 times 9587245 (64.00%) aligned exactly 1 time 4778571 (31.90%) aligned >1 times 95.90% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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 8 files... [bam_rmdupse_core] 2407224 / 14365816 = 0.1676 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, 03 Jun 2019 10:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.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 @ Mon, 03 Jun 2019 10:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.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 @ Mon, 03 Jun 2019 10:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:25:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.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 @ Mon, 03 Jun 2019 10:25:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:25:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:25:32: 1000000 INFO @ Mon, 03 Jun 2019 10:25:33: 1000000 INFO @ Mon, 03 Jun 2019 10:25:33: 1000000 INFO @ Mon, 03 Jun 2019 10:25:39: 2000000 INFO @ Mon, 03 Jun 2019 10:25:41: 2000000 INFO @ Mon, 03 Jun 2019 10:25:41: 2000000 INFO @ Mon, 03 Jun 2019 10:25:46: 3000000 INFO @ Mon, 03 Jun 2019 10:25:49: 3000000 INFO @ Mon, 03 Jun 2019 10:25:49: 3000000 INFO @ Mon, 03 Jun 2019 10:25:53: 4000000 INFO @ Mon, 03 Jun 2019 10:25:57: 4000000 INFO @ Mon, 03 Jun 2019 10:25:57: 4000000 INFO @ Mon, 03 Jun 2019 10:26:01: 5000000 INFO @ Mon, 03 Jun 2019 10:26:05: 5000000 INFO @ Mon, 03 Jun 2019 10:26:05: 5000000 INFO @ Mon, 03 Jun 2019 10:26:08: 6000000 INFO @ Mon, 03 Jun 2019 10:26:13: 6000000 INFO @ Mon, 03 Jun 2019 10:26:13: 6000000 INFO @ Mon, 03 Jun 2019 10:26:15: 7000000 INFO @ Mon, 03 Jun 2019 10:26:21: 7000000 INFO @ Mon, 03 Jun 2019 10:26:21: 7000000 INFO @ Mon, 03 Jun 2019 10:26:22: 8000000 INFO @ Mon, 03 Jun 2019 10:26:29: 9000000 INFO @ Mon, 03 Jun 2019 10:26:29: 8000000 INFO @ Mon, 03 Jun 2019 10:26:29: 8000000 INFO @ Mon, 03 Jun 2019 10:26:36: 10000000 INFO @ Mon, 03 Jun 2019 10:26:37: 9000000 INFO @ Mon, 03 Jun 2019 10:26:37: 9000000 INFO @ Mon, 03 Jun 2019 10:26:43: 11000000 INFO @ Mon, 03 Jun 2019 10:26:45: 10000000 INFO @ Mon, 03 Jun 2019 10:26:45: 10000000 INFO @ Mon, 03 Jun 2019 10:26:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:26:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:26:50: #1 total tags in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:26:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:26:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:26:50: #1 tags after filtering in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:26:50: #1 finished! INFO @ Mon, 03 Jun 2019 10:26:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:26:51: #2 number of paired peaks: 680 WARNING @ Mon, 03 Jun 2019 10:26:51: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Mon, 03 Jun 2019 10:26:51: start model_add_line... INFO @ Mon, 03 Jun 2019 10:26:51: start X-correlation... INFO @ Mon, 03 Jun 2019 10:26:51: end of X-cor INFO @ Mon, 03 Jun 2019 10:26:51: #2 finished! INFO @ Mon, 03 Jun 2019 10:26:51: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 10:26:51: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 10:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20_model.r INFO @ Mon, 03 Jun 2019 10:26:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:26:53: 11000000 INFO @ Mon, 03 Jun 2019 10:26:53: 11000000 INFO @ Mon, 03 Jun 2019 10:27:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:27:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:27:00: #1 total tags in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:27:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:27:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:27:00: #1 tags after filtering in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:27:00: #1 finished! INFO @ Mon, 03 Jun 2019 10:27:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:27:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:27:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:27:01: #1 total tags in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:27:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:27:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 10:27:01: #1 tags after filtering in treatment: 11958592 INFO @ Mon, 03 Jun 2019 10:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:27:01: #1 finished! INFO @ Mon, 03 Jun 2019 10:27:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:27:02: #2 number of paired peaks: 680 WARNING @ Mon, 03 Jun 2019 10:27:02: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Mon, 03 Jun 2019 10:27:02: start model_add_line... INFO @ Mon, 03 Jun 2019 10:27:02: start X-correlation... INFO @ Mon, 03 Jun 2019 10:27:02: end of X-cor INFO @ Mon, 03 Jun 2019 10:27:02: #2 finished! INFO @ Mon, 03 Jun 2019 10:27:02: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 10:27:02: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 10:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10_model.r INFO @ Mon, 03 Jun 2019 10:27:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:27:02: #2 number of paired peaks: 680 WARNING @ Mon, 03 Jun 2019 10:27:02: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Mon, 03 Jun 2019 10:27:02: start model_add_line... INFO @ Mon, 03 Jun 2019 10:27:02: start X-correlation... INFO @ Mon, 03 Jun 2019 10:27:02: end of X-cor INFO @ Mon, 03 Jun 2019 10:27:02: #2 finished! INFO @ Mon, 03 Jun 2019 10:27:02: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 10:27:02: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 10:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05_model.r INFO @ Mon, 03 Jun 2019 10:27:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:27:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:27:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:27:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:27:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:27:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:27:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.20_summits.bed INFO @ Mon, 03 Jun 2019 10:27:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2463 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.10_summits.bed INFO @ Mon, 03 Jun 2019 10:27:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3802 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287891/SRX287891.05_summits.bed INFO @ Mon, 03 Jun 2019 10:27:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5759 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。