Job ID = 1292877 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,457,303 reads read : 32,914,606 reads written : 32,914,606 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: 00:17:40 16457303 reads; of these: 16457303 (100.00%) were paired; of these: 3086340 (18.75%) aligned concordantly 0 times 11174168 (67.90%) aligned concordantly exactly 1 time 2196795 (13.35%) aligned concordantly >1 times ---- 3086340 pairs aligned concordantly 0 times; of these: 1140926 (36.97%) aligned discordantly 1 time ---- 1945414 pairs aligned 0 times concordantly or discordantly; of these: 3890828 mates make up the pairs; of these: 3289816 (84.55%) aligned 0 times 293183 (7.54%) aligned exactly 1 time 307829 (7.91%) aligned >1 times 90.00% overall alignment rate Time searching: 00:17:40 Overall time: 00:17:40 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 16 files... [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] 4147649 / 14502708 = 0.2860 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 21:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.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 21:29:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.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 21:29:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.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 21:29:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:35: 1000000 INFO @ Sun, 02 Jun 2019 21:29:36: 1000000 INFO @ Sun, 02 Jun 2019 21:29:37: 1000000 INFO @ Sun, 02 Jun 2019 21:29:42: 2000000 INFO @ Sun, 02 Jun 2019 21:29:45: 2000000 INFO @ Sun, 02 Jun 2019 21:29:45: 2000000 INFO @ Sun, 02 Jun 2019 21:29:49: 3000000 INFO @ Sun, 02 Jun 2019 21:29:52: 3000000 INFO @ Sun, 02 Jun 2019 21:29:53: 3000000 INFO @ Sun, 02 Jun 2019 21:29:56: 4000000 INFO @ Sun, 02 Jun 2019 21:30:00: 4000000 INFO @ Sun, 02 Jun 2019 21:30:02: 4000000 INFO @ Sun, 02 Jun 2019 21:30:03: 5000000 INFO @ Sun, 02 Jun 2019 21:30:08: 5000000 INFO @ Sun, 02 Jun 2019 21:30:10: 6000000 INFO @ Sun, 02 Jun 2019 21:30:10: 5000000 INFO @ Sun, 02 Jun 2019 21:30:16: 6000000 INFO @ Sun, 02 Jun 2019 21:30:17: 7000000 INFO @ Sun, 02 Jun 2019 21:30:18: 6000000 INFO @ Sun, 02 Jun 2019 21:30:24: 8000000 INFO @ Sun, 02 Jun 2019 21:30:24: 7000000 INFO @ Sun, 02 Jun 2019 21:30:26: 7000000 INFO @ Sun, 02 Jun 2019 21:30:30: 9000000 INFO @ Sun, 02 Jun 2019 21:30:32: 8000000 INFO @ Sun, 02 Jun 2019 21:30:35: 8000000 INFO @ Sun, 02 Jun 2019 21:30:37: 10000000 INFO @ Sun, 02 Jun 2019 21:30:39: 9000000 INFO @ Sun, 02 Jun 2019 21:30:43: 9000000 INFO @ Sun, 02 Jun 2019 21:30:44: 11000000 INFO @ Sun, 02 Jun 2019 21:30:47: 10000000 INFO @ Sun, 02 Jun 2019 21:30:51: 12000000 INFO @ Sun, 02 Jun 2019 21:30:52: 10000000 INFO @ Sun, 02 Jun 2019 21:30:55: 11000000 INFO @ Sun, 02 Jun 2019 21:30:58: 13000000 INFO @ Sun, 02 Jun 2019 21:31:00: 11000000 INFO @ Sun, 02 Jun 2019 21:31:04: 12000000 INFO @ Sun, 02 Jun 2019 21:31:04: 14000000 INFO @ Sun, 02 Jun 2019 21:31:09: 12000000 INFO @ Sun, 02 Jun 2019 21:31:11: 15000000 INFO @ Sun, 02 Jun 2019 21:31:11: 13000000 INFO @ Sun, 02 Jun 2019 21:31:16: 13000000 INFO @ Sun, 02 Jun 2019 21:31:17: 16000000 INFO @ Sun, 02 Jun 2019 21:31:19: 14000000 INFO @ Sun, 02 Jun 2019 21:31:24: 17000000 INFO @ Sun, 02 Jun 2019 21:31:24: 14000000 INFO @ Sun, 02 Jun 2019 21:31:26: 15000000 INFO @ Sun, 02 Jun 2019 21:31:30: 18000000 INFO @ Sun, 02 Jun 2019 21:31:32: 15000000 INFO @ Sun, 02 Jun 2019 21:31:33: 16000000 INFO @ Sun, 02 Jun 2019 21:31:36: 19000000 INFO @ Sun, 02 Jun 2019 21:31:39: 16000000 INFO @ Sun, 02 Jun 2019 21:31:41: 17000000 INFO @ Sun, 02 Jun 2019 21:31:43: 20000000 INFO @ Sun, 02 Jun 2019 21:31:47: 17000000 INFO @ Sun, 02 Jun 2019 21:31:48: 18000000 INFO @ Sun, 02 Jun 2019 21:31:49: 21000000 INFO @ Sun, 02 Jun 2019 21:31:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:31:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:31:51: #1 total tags in treatment: 9382937 INFO @ Sun, 02 Jun 2019 21:31:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:51: #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 21:31:52: #1 tags after filtering in treatment: 8652992 INFO @ Sun, 02 Jun 2019 21:31:52: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:31:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:53: #2 number of paired peaks: 565 WARNING @ Sun, 02 Jun 2019 21:31:53: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:53: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:53: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 21:31:53: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 21:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10_model.r INFO @ Sun, 02 Jun 2019 21:31:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:54: 18000000 INFO @ Sun, 02 Jun 2019 21:31:55: 19000000 INFO @ Sun, 02 Jun 2019 21:32:02: 19000000 INFO @ Sun, 02 Jun 2019 21:32:02: 20000000 INFO @ Sun, 02 Jun 2019 21:32:10: 21000000 INFO @ Sun, 02 Jun 2019 21:32:10: 20000000 INFO @ Sun, 02 Jun 2019 21:32:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:32:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:32:12: #1 total tags in treatment: 9382937 INFO @ Sun, 02 Jun 2019 21:32:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:32:12: #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 21:32:12: #1 tags after filtering in treatment: 8652992 INFO @ Sun, 02 Jun 2019 21:32:12: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:32:12: #1 finished! INFO @ Sun, 02 Jun 2019 21:32:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:32:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:32:13: #2 number of paired peaks: 565 WARNING @ Sun, 02 Jun 2019 21:32:13: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 02 Jun 2019 21:32:13: start model_add_line... INFO @ Sun, 02 Jun 2019 21:32:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:32:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:32:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:32:13: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 21:32:13: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 21:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20_model.r INFO @ Sun, 02 Jun 2019 21:32:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:32:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:32:17: 21000000 INFO @ Sun, 02 Jun 2019 21:32:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:20: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:32:20: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:32:20: #1 total tags in treatment: 9382937 INFO @ Sun, 02 Jun 2019 21:32:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:32:20: #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 21:32:20: #1 tags after filtering in treatment: 8652992 INFO @ Sun, 02 Jun 2019 21:32:20: #1 Redundant rate of treatment: 0.08 INFO @ Sun, 02 Jun 2019 21:32:20: #1 finished! INFO @ Sun, 02 Jun 2019 21:32:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:32:21: #2 number of paired peaks: 565 WARNING @ Sun, 02 Jun 2019 21:32:21: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 02 Jun 2019 21:32:21: start model_add_line... INFO @ Sun, 02 Jun 2019 21:32:21: start X-correlation... INFO @ Sun, 02 Jun 2019 21:32:21: end of X-cor INFO @ Sun, 02 Jun 2019 21:32:21: #2 finished! INFO @ Sun, 02 Jun 2019 21:32:21: #2 predicted fragment length is 148 bps INFO @ Sun, 02 Jun 2019 21:32:21: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sun, 02 Jun 2019 21:32:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05_model.r INFO @ Sun, 02 Jun 2019 21:32:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:32:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:32:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.10_summits.bed INFO @ Sun, 02 Jun 2019 21:32:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:39: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.20_summits.bed INFO @ Sun, 02 Jun 2019 21:32:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996808/SRX4996808.05_summits.bed INFO @ Sun, 02 Jun 2019 21:32:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (431 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。