Job ID = 1292876 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,945,035 reads read : 41,890,070 reads written : 41,890,070 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: 00:07:05 20945035 reads; of these: 20945035 (100.00%) were paired; of these: 16484228 (78.70%) aligned concordantly 0 times 3745031 (17.88%) aligned concordantly exactly 1 time 715776 (3.42%) aligned concordantly >1 times ---- 16484228 pairs aligned concordantly 0 times; of these: 55684 (0.34%) aligned discordantly 1 time ---- 16428544 pairs aligned 0 times concordantly or discordantly; of these: 32857088 mates make up the pairs; of these: 32771322 (99.74%) aligned 0 times 55036 (0.17%) aligned exactly 1 time 30730 (0.09%) aligned >1 times 21.77% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 542217 / 4514629 = 0.1201 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 @ Sun, 02 Jun 2019 21:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 21:16:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 21:16:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:16:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.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 # Paired-End mode is off INFO @ Sun, 02 Jun 2019 21:16:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:16:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:16:50: 1000000 INFO @ Sun, 02 Jun 2019 21:16:52: 1000000 INFO @ Sun, 02 Jun 2019 21:16:52: 1000000 INFO @ Sun, 02 Jun 2019 21:16:57: 2000000 INFO @ Sun, 02 Jun 2019 21:17:01: 2000000 INFO @ Sun, 02 Jun 2019 21:17:01: 2000000 INFO @ Sun, 02 Jun 2019 21:17:04: 3000000 INFO @ Sun, 02 Jun 2019 21:17:09: 3000000 INFO @ Sun, 02 Jun 2019 21:17:10: 3000000 INFO @ Sun, 02 Jun 2019 21:17:11: 4000000 INFO @ Sun, 02 Jun 2019 21:17:18: 4000000 INFO @ Sun, 02 Jun 2019 21:17:18: 5000000 INFO @ Sun, 02 Jun 2019 21:17:19: 4000000 INFO @ Sun, 02 Jun 2019 21:17:25: 6000000 INFO @ Sun, 02 Jun 2019 21:17:26: 5000000 INFO @ Sun, 02 Jun 2019 21:17:27: 5000000 INFO @ Sun, 02 Jun 2019 21:17:32: 7000000 INFO @ Sun, 02 Jun 2019 21:17:34: 6000000 INFO @ Sun, 02 Jun 2019 21:17:35: 6000000 INFO @ Sun, 02 Jun 2019 21:17:39: 8000000 INFO @ Sun, 02 Jun 2019 21:17:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:17:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:17:39: #1 total tags in treatment: 3920884 INFO @ Sun, 02 Jun 2019 21:17:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:17:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:17:39: #1 tags after filtering in treatment: 3776217 INFO @ Sun, 02 Jun 2019 21:17:39: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 21:17:39: #1 finished! INFO @ Sun, 02 Jun 2019 21:17:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:17:39: #2 number of paired peaks: 486 WARNING @ Sun, 02 Jun 2019 21:17:39: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 02 Jun 2019 21:17:39: start model_add_line... INFO @ Sun, 02 Jun 2019 21:17:39: start X-correlation... INFO @ Sun, 02 Jun 2019 21:17:39: end of X-cor INFO @ Sun, 02 Jun 2019 21:17:39: #2 finished! INFO @ Sun, 02 Jun 2019 21:17:39: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:17:39: #2 alternative fragment length(s) may be 160,182 bps INFO @ Sun, 02 Jun 2019 21:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10_model.r INFO @ Sun, 02 Jun 2019 21:17:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:17:43: 7000000 INFO @ Sun, 02 Jun 2019 21:17:43: 7000000 INFO @ Sun, 02 Jun 2019 21:17:51: 8000000 INFO @ Sun, 02 Jun 2019 21:17:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:17:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:17:51: #1 total tags in treatment: 3920884 INFO @ Sun, 02 Jun 2019 21:17:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:17:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:17:51: #1 tags after filtering in treatment: 3776217 INFO @ Sun, 02 Jun 2019 21:17:51: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 21:17:51: #1 finished! INFO @ Sun, 02 Jun 2019 21:17:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:17:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:17:52: 8000000 INFO @ Sun, 02 Jun 2019 21:17:52: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:17:52: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:17:52: #1 total tags in treatment: 3920884 INFO @ Sun, 02 Jun 2019 21:17:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:17:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:17:52: #2 number of paired peaks: 486 WARNING @ Sun, 02 Jun 2019 21:17:52: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 02 Jun 2019 21:17:52: start model_add_line... INFO @ Sun, 02 Jun 2019 21:17:52: #1 tags after filtering in treatment: 3776217 INFO @ Sun, 02 Jun 2019 21:17:52: #1 Redundant rate of treatment: 0.04 INFO @ Sun, 02 Jun 2019 21:17:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:17:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:17:52: start X-correlation... INFO @ Sun, 02 Jun 2019 21:17:52: end of X-cor INFO @ Sun, 02 Jun 2019 21:17:52: #2 finished! INFO @ Sun, 02 Jun 2019 21:17:52: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:17:52: #2 alternative fragment length(s) may be 160,182 bps INFO @ Sun, 02 Jun 2019 21:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05_model.r INFO @ Sun, 02 Jun 2019 21:17:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:17:52: #2 number of paired peaks: 486 WARNING @ Sun, 02 Jun 2019 21:17:52: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 02 Jun 2019 21:17:52: start model_add_line... INFO @ Sun, 02 Jun 2019 21:17:52: start X-correlation... INFO @ Sun, 02 Jun 2019 21:17:52: end of X-cor INFO @ Sun, 02 Jun 2019 21:17:52: #2 finished! INFO @ Sun, 02 Jun 2019 21:17:52: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 21:17:52: #2 alternative fragment length(s) may be 160,182 bps INFO @ Sun, 02 Jun 2019 21:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20_model.r INFO @ Sun, 02 Jun 2019 21:17:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:17:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:17:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:17:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.10_summits.bed INFO @ Sun, 02 Jun 2019 21:17:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:18:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:18:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.05_summits.bed INFO @ Sun, 02 Jun 2019 21:18:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996807/SRX4996807.20_summits.bed INFO @ Sun, 02 Jun 2019 21:18:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。