Job ID = 1292883 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,918,230 reads read : 37,836,460 reads written : 37,836,460 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: 00:20:30 18918230 reads; of these: 18918230 (100.00%) were paired; of these: 979378 (5.18%) aligned concordantly 0 times 15342448 (81.10%) aligned concordantly exactly 1 time 2596404 (13.72%) aligned concordantly >1 times ---- 979378 pairs aligned concordantly 0 times; of these: 488249 (49.85%) aligned discordantly 1 time ---- 491129 pairs aligned 0 times concordantly or discordantly; of these: 982258 mates make up the pairs; of these: 573124 (58.35%) aligned 0 times 251721 (25.63%) aligned exactly 1 time 157413 (16.03%) aligned >1 times 98.49% overall alignment rate Time searching: 00:20:30 Overall time: 00:20:30 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] 310650 / 18415834 = 0.0169 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 21:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.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 21:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.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 21:39:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.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 21:39:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:39:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:39:51: 1000000 INFO @ Sun, 02 Jun 2019 21:39:52: 1000000 INFO @ Sun, 02 Jun 2019 21:39:54: 1000000 INFO @ Sun, 02 Jun 2019 21:39:58: 2000000 INFO @ Sun, 02 Jun 2019 21:40:00: 2000000 INFO @ Sun, 02 Jun 2019 21:40:04: 2000000 INFO @ Sun, 02 Jun 2019 21:40:06: 3000000 INFO @ Sun, 02 Jun 2019 21:40:09: 3000000 INFO @ Sun, 02 Jun 2019 21:40:13: 4000000 INFO @ Sun, 02 Jun 2019 21:40:16: 3000000 INFO @ Sun, 02 Jun 2019 21:40:17: 4000000 INFO @ Sun, 02 Jun 2019 21:40:21: 5000000 INFO @ Sun, 02 Jun 2019 21:40:26: 5000000 INFO @ Sun, 02 Jun 2019 21:40:27: 4000000 INFO @ Sun, 02 Jun 2019 21:40:28: 6000000 INFO @ Sun, 02 Jun 2019 21:40:34: 6000000 INFO @ Sun, 02 Jun 2019 21:40:35: 7000000 INFO @ Sun, 02 Jun 2019 21:40:38: 5000000 INFO @ Sun, 02 Jun 2019 21:40:42: 7000000 INFO @ Sun, 02 Jun 2019 21:40:43: 8000000 INFO @ Sun, 02 Jun 2019 21:40:49: 6000000 INFO @ Sun, 02 Jun 2019 21:40:51: 9000000 INFO @ Sun, 02 Jun 2019 21:40:51: 8000000 INFO @ Sun, 02 Jun 2019 21:40:59: 10000000 INFO @ Sun, 02 Jun 2019 21:41:00: 7000000 INFO @ Sun, 02 Jun 2019 21:41:01: 9000000 INFO @ Sun, 02 Jun 2019 21:41:07: 11000000 INFO @ Sun, 02 Jun 2019 21:41:10: 10000000 INFO @ Sun, 02 Jun 2019 21:41:11: 8000000 INFO @ Sun, 02 Jun 2019 21:41:14: 12000000 INFO @ Sun, 02 Jun 2019 21:41:19: 11000000 INFO @ Sun, 02 Jun 2019 21:41:21: 13000000 INFO @ Sun, 02 Jun 2019 21:41:22: 9000000 INFO @ Sun, 02 Jun 2019 21:41:27: 12000000 INFO @ Sun, 02 Jun 2019 21:41:29: 14000000 INFO @ Sun, 02 Jun 2019 21:41:33: 10000000 INFO @ Sun, 02 Jun 2019 21:41:36: 13000000 INFO @ Sun, 02 Jun 2019 21:41:37: 15000000 INFO @ Sun, 02 Jun 2019 21:41:44: 11000000 INFO @ Sun, 02 Jun 2019 21:41:44: 14000000 INFO @ Sun, 02 Jun 2019 21:41:44: 16000000 INFO @ Sun, 02 Jun 2019 21:41:51: 17000000 INFO @ Sun, 02 Jun 2019 21:41:52: 15000000 INFO @ Sun, 02 Jun 2019 21:41:55: 12000000 INFO @ Sun, 02 Jun 2019 21:41:59: 18000000 INFO @ Sun, 02 Jun 2019 21:42:01: 16000000 INFO @ Sun, 02 Jun 2019 21:42:06: 13000000 INFO @ Sun, 02 Jun 2019 21:42:06: 19000000 INFO @ Sun, 02 Jun 2019 21:42:09: 17000000 INFO @ Sun, 02 Jun 2019 21:42:13: 20000000 INFO @ Sun, 02 Jun 2019 21:42:17: 14000000 INFO @ Sun, 02 Jun 2019 21:42:18: 18000000 INFO @ Sun, 02 Jun 2019 21:42:21: 21000000 INFO @ Sun, 02 Jun 2019 21:42:26: 19000000 INFO @ Sun, 02 Jun 2019 21:42:28: 15000000 INFO @ Sun, 02 Jun 2019 21:42:28: 22000000 INFO @ Sun, 02 Jun 2019 21:42:34: 20000000 INFO @ Sun, 02 Jun 2019 21:42:36: 23000000 INFO @ Sun, 02 Jun 2019 21:42:39: 16000000 INFO @ Sun, 02 Jun 2019 21:42:43: 21000000 INFO @ Sun, 02 Jun 2019 21:42:44: 24000000 INFO @ Sun, 02 Jun 2019 21:42:50: 17000000 INFO @ Sun, 02 Jun 2019 21:42:52: 25000000 INFO @ Sun, 02 Jun 2019 21:42:53: 22000000 INFO @ Sun, 02 Jun 2019 21:43:00: 26000000 INFO @ Sun, 02 Jun 2019 21:43:00: 18000000 INFO @ Sun, 02 Jun 2019 21:43:02: 23000000 INFO @ Sun, 02 Jun 2019 21:43:07: 27000000 INFO @ Sun, 02 Jun 2019 21:43:10: 24000000 INFO @ Sun, 02 Jun 2019 21:43:11: 19000000 INFO @ Sun, 02 Jun 2019 21:43:14: 28000000 INFO @ Sun, 02 Jun 2019 21:43:19: 25000000 INFO @ Sun, 02 Jun 2019 21:43:22: 29000000 INFO @ Sun, 02 Jun 2019 21:43:23: 20000000 INFO @ Sun, 02 Jun 2019 21:43:27: 26000000 INFO @ Sun, 02 Jun 2019 21:43:29: 30000000 INFO @ Sun, 02 Jun 2019 21:43:33: 21000000 INFO @ Sun, 02 Jun 2019 21:43:36: 27000000 INFO @ Sun, 02 Jun 2019 21:43:36: 31000000 INFO @ Sun, 02 Jun 2019 21:43:44: 28000000 INFO @ Sun, 02 Jun 2019 21:43:44: 32000000 INFO @ Sun, 02 Jun 2019 21:43:44: 22000000 INFO @ Sun, 02 Jun 2019 21:43:52: 33000000 INFO @ Sun, 02 Jun 2019 21:43:52: 29000000 INFO @ Sun, 02 Jun 2019 21:43:55: 23000000 INFO @ Sun, 02 Jun 2019 21:44:00: 34000000 INFO @ Sun, 02 Jun 2019 21:44:01: 30000000 INFO @ Sun, 02 Jun 2019 21:44:06: 24000000 INFO @ Sun, 02 Jun 2019 21:44:08: 35000000 INFO @ Sun, 02 Jun 2019 21:44:09: 31000000 INFO @ Sun, 02 Jun 2019 21:44:16: 36000000 INFO @ Sun, 02 Jun 2019 21:44:17: 25000000 INFO @ Sun, 02 Jun 2019 21:44:18: 32000000 INFO @ Sun, 02 Jun 2019 21:44:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:44:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:44:21: #1 total tags in treatment: 17631217 INFO @ Sun, 02 Jun 2019 21:44:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:21: #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 21:44:22: #1 tags after filtering in treatment: 16048733 INFO @ Sun, 02 Jun 2019 21:44:22: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:44:22: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:23: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:44:23: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:23: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:23: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:23: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:23: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:23: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 21:44:23: #2 alternative fragment length(s) may be 3,110 bps INFO @ Sun, 02 Jun 2019 21:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10_model.r INFO @ Sun, 02 Jun 2019 21:44:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:26: 33000000 INFO @ Sun, 02 Jun 2019 21:44:27: 26000000 INFO @ Sun, 02 Jun 2019 21:44:35: 34000000 INFO @ Sun, 02 Jun 2019 21:44:37: 27000000 INFO @ Sun, 02 Jun 2019 21:44:43: 35000000 INFO @ Sun, 02 Jun 2019 21:44:47: 28000000 INFO @ Sun, 02 Jun 2019 21:44:51: 36000000 INFO @ Sun, 02 Jun 2019 21:44:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:44:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:44:56: #1 total tags in treatment: 17631217 INFO @ Sun, 02 Jun 2019 21:44:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:56: #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 21:44:56: #1 tags after filtering in treatment: 16048733 INFO @ Sun, 02 Jun 2019 21:44:56: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:44:56: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:58: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:44:58: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:58: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:58: 29000000 INFO @ Sun, 02 Jun 2019 21:44:58: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:58: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:58: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:58: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 21:44:58: #2 alternative fragment length(s) may be 3,110 bps INFO @ Sun, 02 Jun 2019 21:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20_model.r INFO @ Sun, 02 Jun 2019 21:44:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:45:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:08: 30000000 INFO @ Sun, 02 Jun 2019 21:45:19: 31000000 INFO @ Sun, 02 Jun 2019 21:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.10_summits.bed INFO @ Sun, 02 Jun 2019 21:45:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:45:29: 32000000 INFO @ Sun, 02 Jun 2019 21:45:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:40: 33000000 INFO @ Sun, 02 Jun 2019 21:45:51: 34000000 INFO @ Sun, 02 Jun 2019 21:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.20_summits.bed INFO @ Sun, 02 Jun 2019 21:45:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:46:00: 35000000 INFO @ Sun, 02 Jun 2019 21:46:10: 36000000 INFO @ Sun, 02 Jun 2019 21:46:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:46:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:46:17: #1 total tags in treatment: 17631217 INFO @ Sun, 02 Jun 2019 21:46:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:46:17: #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 21:46:17: #1 tags after filtering in treatment: 16048733 INFO @ Sun, 02 Jun 2019 21:46:17: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:46:17: #1 finished! INFO @ Sun, 02 Jun 2019 21:46:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:46:19: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:46:19: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:46:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:46:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:46:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:46:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:46:19: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 21:46:19: #2 alternative fragment length(s) may be 3,110 bps INFO @ Sun, 02 Jun 2019 21:46:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05_model.r INFO @ Sun, 02 Jun 2019 21:46:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:46:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996814/SRX4996814.05_summits.bed INFO @ Sun, 02 Jun 2019 21:47:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (493 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。