Job ID = 1292879 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,332,188 reads read : 48,664,376 reads written : 48,664,376 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: 00:28:05 24332188 reads; of these: 24332188 (100.00%) were paired; of these: 2904895 (11.94%) aligned concordantly 0 times 17388187 (71.46%) aligned concordantly exactly 1 time 4039106 (16.60%) aligned concordantly >1 times ---- 2904895 pairs aligned concordantly 0 times; of these: 773836 (26.64%) aligned discordantly 1 time ---- 2131059 pairs aligned 0 times concordantly or discordantly; of these: 4262118 mates make up the pairs; of these: 3630168 (85.17%) aligned 0 times 357116 (8.38%) aligned exactly 1 time 274834 (6.45%) aligned >1 times 92.54% overall alignment rate Time searching: 00:28:05 Overall time: 00:28:05 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 20 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] 4830710 / 22188447 = 0.2177 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 21:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.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 21:49:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:49:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.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 21:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.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 21:49:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:49:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:49:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:49:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:49:46: 1000000 INFO @ Sun, 02 Jun 2019 21:49:48: 1000000 INFO @ Sun, 02 Jun 2019 21:49:48: 1000000 INFO @ Sun, 02 Jun 2019 21:49:53: 2000000 INFO @ Sun, 02 Jun 2019 21:49:56: 2000000 INFO @ Sun, 02 Jun 2019 21:49:57: 2000000 INFO @ Sun, 02 Jun 2019 21:50:00: 3000000 INFO @ Sun, 02 Jun 2019 21:50:05: 3000000 INFO @ Sun, 02 Jun 2019 21:50:05: 3000000 INFO @ Sun, 02 Jun 2019 21:50:07: 4000000 INFO @ Sun, 02 Jun 2019 21:50:14: 5000000 INFO @ Sun, 02 Jun 2019 21:50:14: 4000000 INFO @ Sun, 02 Jun 2019 21:50:14: 4000000 INFO @ Sun, 02 Jun 2019 21:50:21: 6000000 INFO @ Sun, 02 Jun 2019 21:50:23: 5000000 INFO @ Sun, 02 Jun 2019 21:50:23: 5000000 INFO @ Sun, 02 Jun 2019 21:50:28: 7000000 INFO @ Sun, 02 Jun 2019 21:50:32: 6000000 INFO @ Sun, 02 Jun 2019 21:50:32: 6000000 INFO @ Sun, 02 Jun 2019 21:50:35: 8000000 INFO @ Sun, 02 Jun 2019 21:50:41: 7000000 INFO @ Sun, 02 Jun 2019 21:50:41: 7000000 INFO @ Sun, 02 Jun 2019 21:50:42: 9000000 INFO @ Sun, 02 Jun 2019 21:50:49: 10000000 INFO @ Sun, 02 Jun 2019 21:50:50: 8000000 INFO @ Sun, 02 Jun 2019 21:50:50: 8000000 INFO @ Sun, 02 Jun 2019 21:50:55: 11000000 INFO @ Sun, 02 Jun 2019 21:50:58: 9000000 INFO @ Sun, 02 Jun 2019 21:50:58: 9000000 INFO @ Sun, 02 Jun 2019 21:51:02: 12000000 INFO @ Sun, 02 Jun 2019 21:51:07: 10000000 INFO @ Sun, 02 Jun 2019 21:51:07: 10000000 INFO @ Sun, 02 Jun 2019 21:51:09: 13000000 INFO @ Sun, 02 Jun 2019 21:51:16: 11000000 INFO @ Sun, 02 Jun 2019 21:51:16: 11000000 INFO @ Sun, 02 Jun 2019 21:51:16: 14000000 INFO @ Sun, 02 Jun 2019 21:51:23: 15000000 INFO @ Sun, 02 Jun 2019 21:51:24: 12000000 INFO @ Sun, 02 Jun 2019 21:51:24: 12000000 INFO @ Sun, 02 Jun 2019 21:51:30: 16000000 INFO @ Sun, 02 Jun 2019 21:51:33: 13000000 INFO @ Sun, 02 Jun 2019 21:51:33: 13000000 INFO @ Sun, 02 Jun 2019 21:51:37: 17000000 INFO @ Sun, 02 Jun 2019 21:51:42: 14000000 INFO @ Sun, 02 Jun 2019 21:51:42: 14000000 INFO @ Sun, 02 Jun 2019 21:51:44: 18000000 INFO @ Sun, 02 Jun 2019 21:51:51: 15000000 INFO @ Sun, 02 Jun 2019 21:51:51: 15000000 INFO @ Sun, 02 Jun 2019 21:51:51: 19000000 INFO @ Sun, 02 Jun 2019 21:51:58: 20000000 INFO @ Sun, 02 Jun 2019 21:51:59: 16000000 INFO @ Sun, 02 Jun 2019 21:52:00: 16000000 INFO @ Sun, 02 Jun 2019 21:52:05: 21000000 INFO @ Sun, 02 Jun 2019 21:52:08: 17000000 INFO @ Sun, 02 Jun 2019 21:52:08: 17000000 INFO @ Sun, 02 Jun 2019 21:52:11: 22000000 INFO @ Sun, 02 Jun 2019 21:52:17: 18000000 INFO @ Sun, 02 Jun 2019 21:52:17: 18000000 INFO @ Sun, 02 Jun 2019 21:52:18: 23000000 INFO @ Sun, 02 Jun 2019 21:52:25: 24000000 INFO @ Sun, 02 Jun 2019 21:52:26: 19000000 INFO @ Sun, 02 Jun 2019 21:52:26: 19000000 INFO @ Sun, 02 Jun 2019 21:52:32: 25000000 INFO @ Sun, 02 Jun 2019 21:52:34: 20000000 INFO @ Sun, 02 Jun 2019 21:52:35: 20000000 INFO @ Sun, 02 Jun 2019 21:52:38: 26000000 INFO @ Sun, 02 Jun 2019 21:52:43: 21000000 INFO @ Sun, 02 Jun 2019 21:52:43: 21000000 INFO @ Sun, 02 Jun 2019 21:52:45: 27000000 INFO @ Sun, 02 Jun 2019 21:52:51: 22000000 INFO @ Sun, 02 Jun 2019 21:52:52: 22000000 INFO @ Sun, 02 Jun 2019 21:52:52: 28000000 INFO @ Sun, 02 Jun 2019 21:52:58: 29000000 INFO @ Sun, 02 Jun 2019 21:53:00: 23000000 INFO @ Sun, 02 Jun 2019 21:53:00: 23000000 INFO @ Sun, 02 Jun 2019 21:53:05: 30000000 INFO @ Sun, 02 Jun 2019 21:53:08: 24000000 INFO @ Sun, 02 Jun 2019 21:53:08: 24000000 INFO @ Sun, 02 Jun 2019 21:53:12: 31000000 INFO @ Sun, 02 Jun 2019 21:53:17: 25000000 INFO @ Sun, 02 Jun 2019 21:53:17: 25000000 INFO @ Sun, 02 Jun 2019 21:53:19: 32000000 INFO @ Sun, 02 Jun 2019 21:53:25: 26000000 INFO @ Sun, 02 Jun 2019 21:53:25: 26000000 INFO @ Sun, 02 Jun 2019 21:53:25: 33000000 INFO @ Sun, 02 Jun 2019 21:53:32: 34000000 INFO @ Sun, 02 Jun 2019 21:53:33: 27000000 INFO @ Sun, 02 Jun 2019 21:53:34: 27000000 INFO @ Sun, 02 Jun 2019 21:53:39: 35000000 INFO @ Sun, 02 Jun 2019 21:53:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:53:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:53:42: #1 total tags in treatment: 16663408 INFO @ Sun, 02 Jun 2019 21:53:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:42: #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 21:53:42: 28000000 INFO @ Sun, 02 Jun 2019 21:53:42: #1 tags after filtering in treatment: 14655376 INFO @ Sun, 02 Jun 2019 21:53:42: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:53:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:42: 28000000 INFO @ Sun, 02 Jun 2019 21:53:43: #2 number of paired peaks: 480 WARNING @ Sun, 02 Jun 2019 21:53:43: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:43: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:53:43: #2 alternative fragment length(s) may be 3,105,126 bps INFO @ Sun, 02 Jun 2019 21:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20_model.r INFO @ Sun, 02 Jun 2019 21:53:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:50: 29000000 INFO @ Sun, 02 Jun 2019 21:53:50: 29000000 INFO @ Sun, 02 Jun 2019 21:53:58: 30000000 INFO @ Sun, 02 Jun 2019 21:53:58: 30000000 INFO @ Sun, 02 Jun 2019 21:54:06: 31000000 INFO @ Sun, 02 Jun 2019 21:54:07: 31000000 INFO @ Sun, 02 Jun 2019 21:54:14: 32000000 INFO @ Sun, 02 Jun 2019 21:54:15: 32000000 INFO @ Sun, 02 Jun 2019 21:54:23: 33000000 INFO @ Sun, 02 Jun 2019 21:54:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:23: 33000000 INFO @ Sun, 02 Jun 2019 21:54:31: 34000000 INFO @ Sun, 02 Jun 2019 21:54:31: 34000000 INFO @ Sun, 02 Jun 2019 21:54:39: 35000000 INFO @ Sun, 02 Jun 2019 21:54:39: 35000000 INFO @ Sun, 02 Jun 2019 21:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.20_summits.bed INFO @ Sun, 02 Jun 2019 21:54:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:54:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:54:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:54:42: #1 total tags in treatment: 16663408 INFO @ Sun, 02 Jun 2019 21:54:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:42: #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 21:54:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:54:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:54:42: #1 total tags in treatment: 16663408 INFO @ Sun, 02 Jun 2019 21:54:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:54:42: #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 21:54:42: #1 tags after filtering in treatment: 14655376 INFO @ Sun, 02 Jun 2019 21:54:42: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:54:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:43: #1 tags after filtering in treatment: 14655376 INFO @ Sun, 02 Jun 2019 21:54:43: #1 Redundant rate of treatment: 0.12 INFO @ Sun, 02 Jun 2019 21:54:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:54:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:54:44: #2 number of paired peaks: 480 WARNING @ Sun, 02 Jun 2019 21:54:44: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:44: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:44: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:44: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:54:44: #2 alternative fragment length(s) may be 3,105,126 bps INFO @ Sun, 02 Jun 2019 21:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05_model.r INFO @ Sun, 02 Jun 2019 21:54:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:54:44: #2 number of paired peaks: 480 WARNING @ Sun, 02 Jun 2019 21:54:44: Fewer paired peaks (480) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 480 pairs to build model! INFO @ Sun, 02 Jun 2019 21:54:44: start model_add_line... INFO @ Sun, 02 Jun 2019 21:54:44: start X-correlation... INFO @ Sun, 02 Jun 2019 21:54:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:54:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:54:44: #2 predicted fragment length is 126 bps INFO @ Sun, 02 Jun 2019 21:54:44: #2 alternative fragment length(s) may be 3,105,126 bps INFO @ Sun, 02 Jun 2019 21:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10_model.r INFO @ Sun, 02 Jun 2019 21:54:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:55:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.05_summits.bed INFO @ Sun, 02 Jun 2019 21:55:42: Done! INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996809/SRX4996809.10_summits.bed INFO @ Sun, 02 Jun 2019 21:55:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (372 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。