Job ID = 1290581 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,963,826 reads read : 25,927,652 reads written : 25,927,652 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: 00:14:05 12963826 reads; of these: 12963826 (100.00%) were paired; of these: 598479 (4.62%) aligned concordantly 0 times 10606310 (81.81%) aligned concordantly exactly 1 time 1759037 (13.57%) aligned concordantly >1 times ---- 598479 pairs aligned concordantly 0 times; of these: 337785 (56.44%) aligned discordantly 1 time ---- 260694 pairs aligned 0 times concordantly or discordantly; of these: 521388 mates make up the pairs; of these: 233376 (44.76%) aligned 0 times 159679 (30.63%) aligned exactly 1 time 128333 (24.61%) aligned >1 times 99.10% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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_sort_core] merging from 12 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] 182834 / 12612426 = 0.0145 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, 01 Jun 2019 22:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.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 @ Sat, 01 Jun 2019 22:09:26: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:26: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.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 @ Sat, 01 Jun 2019 22:09:26: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:26: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.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 @ Sat, 01 Jun 2019 22:09:26: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:09:26: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:09:34: 1000000 INFO @ Sat, 01 Jun 2019 22:09:34: 1000000 INFO @ Sat, 01 Jun 2019 22:09:35: 1000000 INFO @ Sat, 01 Jun 2019 22:09:40: 2000000 INFO @ Sat, 01 Jun 2019 22:09:41: 2000000 INFO @ Sat, 01 Jun 2019 22:09:44: 2000000 INFO @ Sat, 01 Jun 2019 22:09:47: 3000000 INFO @ Sat, 01 Jun 2019 22:09:49: 3000000 INFO @ Sat, 01 Jun 2019 22:09:53: 4000000 INFO @ Sat, 01 Jun 2019 22:09:54: 3000000 INFO @ Sat, 01 Jun 2019 22:09:57: 4000000 INFO @ Sat, 01 Jun 2019 22:10:00: 5000000 INFO @ Sat, 01 Jun 2019 22:10:03: 4000000 INFO @ Sat, 01 Jun 2019 22:10:04: 5000000 INFO @ Sat, 01 Jun 2019 22:10:06: 6000000 INFO @ Sat, 01 Jun 2019 22:10:11: 5000000 INFO @ Sat, 01 Jun 2019 22:10:12: 6000000 INFO @ Sat, 01 Jun 2019 22:10:13: 7000000 INFO @ Sat, 01 Jun 2019 22:10:18: 6000000 INFO @ Sat, 01 Jun 2019 22:10:19: 7000000 INFO @ Sat, 01 Jun 2019 22:10:20: 8000000 INFO @ Sat, 01 Jun 2019 22:10:26: 7000000 INFO @ Sat, 01 Jun 2019 22:10:26: 8000000 INFO @ Sat, 01 Jun 2019 22:10:27: 9000000 INFO @ Sat, 01 Jun 2019 22:10:33: 9000000 INFO @ Sat, 01 Jun 2019 22:10:34: 8000000 INFO @ Sat, 01 Jun 2019 22:10:34: 10000000 INFO @ Sat, 01 Jun 2019 22:10:41: 10000000 INFO @ Sat, 01 Jun 2019 22:10:41: 11000000 INFO @ Sat, 01 Jun 2019 22:10:42: 9000000 INFO @ Sat, 01 Jun 2019 22:10:48: 11000000 INFO @ Sat, 01 Jun 2019 22:10:48: 12000000 INFO @ Sat, 01 Jun 2019 22:10:49: 10000000 INFO @ Sat, 01 Jun 2019 22:10:55: 13000000 INFO @ Sat, 01 Jun 2019 22:10:55: 12000000 INFO @ Sat, 01 Jun 2019 22:10:57: 11000000 INFO @ Sat, 01 Jun 2019 22:11:01: 14000000 INFO @ Sat, 01 Jun 2019 22:11:01: 13000000 INFO @ Sat, 01 Jun 2019 22:11:05: 12000000 INFO @ Sat, 01 Jun 2019 22:11:08: 15000000 INFO @ Sat, 01 Jun 2019 22:11:08: 14000000 INFO @ Sat, 01 Jun 2019 22:11:12: 13000000 INFO @ Sat, 01 Jun 2019 22:11:15: 16000000 INFO @ Sat, 01 Jun 2019 22:11:15: 15000000 INFO @ Sat, 01 Jun 2019 22:11:20: 14000000 INFO @ Sat, 01 Jun 2019 22:11:22: 17000000 INFO @ Sat, 01 Jun 2019 22:11:22: 16000000 INFO @ Sat, 01 Jun 2019 22:11:27: 15000000 INFO @ Sat, 01 Jun 2019 22:11:28: 18000000 INFO @ Sat, 01 Jun 2019 22:11:29: 17000000 INFO @ Sat, 01 Jun 2019 22:11:35: 16000000 INFO @ Sat, 01 Jun 2019 22:11:35: 19000000 INFO @ Sat, 01 Jun 2019 22:11:35: 18000000 INFO @ Sat, 01 Jun 2019 22:11:41: 20000000 INFO @ Sat, 01 Jun 2019 22:11:42: 17000000 INFO @ Sat, 01 Jun 2019 22:11:42: 19000000 INFO @ Sat, 01 Jun 2019 22:11:47: 21000000 INFO @ Sat, 01 Jun 2019 22:11:49: 20000000 INFO @ Sat, 01 Jun 2019 22:11:49: 18000000 INFO @ Sat, 01 Jun 2019 22:11:53: 22000000 INFO @ Sat, 01 Jun 2019 22:11:55: 21000000 INFO @ Sat, 01 Jun 2019 22:11:57: 19000000 INFO @ Sat, 01 Jun 2019 22:11:59: 23000000 INFO @ Sat, 01 Jun 2019 22:12:01: 22000000 INFO @ Sat, 01 Jun 2019 22:12:04: 20000000 INFO @ Sat, 01 Jun 2019 22:12:05: 24000000 INFO @ Sat, 01 Jun 2019 22:12:08: 23000000 INFO @ Sat, 01 Jun 2019 22:12:11: 21000000 INFO @ Sat, 01 Jun 2019 22:12:11: 25000000 INFO @ Sat, 01 Jun 2019 22:12:14: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:12:14: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:12:14: #1 total tags in treatment: 12183799 INFO @ Sat, 01 Jun 2019 22:12:14: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:12:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:12:14: #1 tags after filtering in treatment: 11315034 INFO @ Sat, 01 Jun 2019 22:12:14: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:12:14: #1 finished! INFO @ Sat, 01 Jun 2019 22:12:14: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:12:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:12:14: 24000000 INFO @ Sat, 01 Jun 2019 22:12:15: #2 number of paired peaks: 339 WARNING @ Sat, 01 Jun 2019 22:12:15: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 01 Jun 2019 22:12:15: start model_add_line... INFO @ Sat, 01 Jun 2019 22:12:15: start X-correlation... INFO @ Sat, 01 Jun 2019 22:12:15: end of X-cor INFO @ Sat, 01 Jun 2019 22:12:15: #2 finished! INFO @ Sat, 01 Jun 2019 22:12:15: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 22:12:15: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 22:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20_model.r INFO @ Sat, 01 Jun 2019 22:12:15: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:12:18: 22000000 INFO @ Sat, 01 Jun 2019 22:12:21: 25000000 INFO @ Sat, 01 Jun 2019 22:12:23: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:12:23: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:12:23: #1 total tags in treatment: 12183799 INFO @ Sat, 01 Jun 2019 22:12:23: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:12:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:12:23: #1 tags after filtering in treatment: 11315034 INFO @ Sat, 01 Jun 2019 22:12:23: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:12:23: #1 finished! INFO @ Sat, 01 Jun 2019 22:12:23: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:12:24: #2 number of paired peaks: 339 WARNING @ Sat, 01 Jun 2019 22:12:24: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 01 Jun 2019 22:12:24: start model_add_line... INFO @ Sat, 01 Jun 2019 22:12:24: start X-correlation... INFO @ Sat, 01 Jun 2019 22:12:24: end of X-cor INFO @ Sat, 01 Jun 2019 22:12:24: #2 finished! INFO @ Sat, 01 Jun 2019 22:12:24: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 22:12:24: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 22:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10_model.r INFO @ Sat, 01 Jun 2019 22:12:24: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:12:25: 23000000 INFO @ Sat, 01 Jun 2019 22:12:32: 24000000 INFO @ Sat, 01 Jun 2019 22:12:39: 25000000 INFO @ Sat, 01 Jun 2019 22:12:42: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 22:12:42: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 22:12:42: #1 total tags in treatment: 12183799 INFO @ Sat, 01 Jun 2019 22:12:42: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:12:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:12:42: #1 tags after filtering in treatment: 11315034 INFO @ Sat, 01 Jun 2019 22:12:42: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 01 Jun 2019 22:12:42: #1 finished! INFO @ Sat, 01 Jun 2019 22:12:42: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:12:43: #2 number of paired peaks: 339 WARNING @ Sat, 01 Jun 2019 22:12:43: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sat, 01 Jun 2019 22:12:43: start model_add_line... INFO @ Sat, 01 Jun 2019 22:12:43: start X-correlation... INFO @ Sat, 01 Jun 2019 22:12:43: end of X-cor INFO @ Sat, 01 Jun 2019 22:12:43: #2 finished! INFO @ Sat, 01 Jun 2019 22:12:43: #2 predicted fragment length is 148 bps INFO @ Sat, 01 Jun 2019 22:12:43: #2 alternative fragment length(s) may be 4,148 bps INFO @ Sat, 01 Jun 2019 22:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05_model.r INFO @ Sat, 01 Jun 2019 22:12:43: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:12:47: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:12:55: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.20_summits.bed INFO @ Sat, 01 Jun 2019 22:13:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.10_summits.bed INFO @ Sat, 01 Jun 2019 22:13:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (277 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:13:15: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353662/SRX1353662.05_summits.bed INFO @ Sat, 01 Jun 2019 22:13:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (383 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。