Job ID = 1292370 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 37,064,952 reads read : 74,129,904 reads written : 74,129,904 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:51:43 37064952 reads; of these: 37064952 (100.00%) were paired; of these: 2374507 (6.41%) aligned concordantly 0 times 32419716 (87.47%) aligned concordantly exactly 1 time 2270729 (6.13%) aligned concordantly >1 times ---- 2374507 pairs aligned concordantly 0 times; of these: 578991 (24.38%) aligned discordantly 1 time ---- 1795516 pairs aligned 0 times concordantly or discordantly; of these: 3591032 mates make up the pairs; of these: 2819088 (78.50%) aligned 0 times 574059 (15.99%) aligned exactly 1 time 197885 (5.51%) aligned >1 times 96.20% overall alignment rate Time searching: 00:51:44 Overall time: 00:51:44 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 32 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] 14081718 / 35120177 = 0.4010 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 19:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.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 19:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.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 19:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.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 19:58:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:12: 1000000 INFO @ Sun, 02 Jun 2019 19:58:15: 1000000 INFO @ Sun, 02 Jun 2019 19:58:15: 1000000 INFO @ Sun, 02 Jun 2019 19:58:20: 2000000 INFO @ Sun, 02 Jun 2019 19:58:25: 2000000 INFO @ Sun, 02 Jun 2019 19:58:27: 2000000 INFO @ Sun, 02 Jun 2019 19:58:28: 3000000 INFO @ Sun, 02 Jun 2019 19:58:36: 3000000 INFO @ Sun, 02 Jun 2019 19:58:36: 4000000 INFO @ Sun, 02 Jun 2019 19:58:38: 3000000 INFO @ Sun, 02 Jun 2019 19:58:43: 5000000 INFO @ Sun, 02 Jun 2019 19:58:46: 4000000 INFO @ Sun, 02 Jun 2019 19:58:49: 4000000 INFO @ Sun, 02 Jun 2019 19:58:51: 6000000 INFO @ Sun, 02 Jun 2019 19:58:57: 5000000 INFO @ Sun, 02 Jun 2019 19:58:58: 7000000 INFO @ Sun, 02 Jun 2019 19:59:00: 5000000 INFO @ Sun, 02 Jun 2019 19:59:06: 8000000 INFO @ Sun, 02 Jun 2019 19:59:07: 6000000 INFO @ Sun, 02 Jun 2019 19:59:11: 6000000 INFO @ Sun, 02 Jun 2019 19:59:13: 9000000 INFO @ Sun, 02 Jun 2019 19:59:18: 7000000 INFO @ Sun, 02 Jun 2019 19:59:20: 10000000 INFO @ Sun, 02 Jun 2019 19:59:23: 7000000 INFO @ Sun, 02 Jun 2019 19:59:27: 11000000 INFO @ Sun, 02 Jun 2019 19:59:27: 8000000 INFO @ Sun, 02 Jun 2019 19:59:34: 12000000 INFO @ Sun, 02 Jun 2019 19:59:34: 8000000 INFO @ Sun, 02 Jun 2019 19:59:37: 9000000 INFO @ Sun, 02 Jun 2019 19:59:41: 13000000 INFO @ Sun, 02 Jun 2019 19:59:44: 9000000 INFO @ Sun, 02 Jun 2019 19:59:47: 10000000 INFO @ Sun, 02 Jun 2019 19:59:48: 14000000 INFO @ Sun, 02 Jun 2019 19:59:55: 15000000 INFO @ Sun, 02 Jun 2019 19:59:55: 10000000 INFO @ Sun, 02 Jun 2019 19:59:58: 11000000 INFO @ Sun, 02 Jun 2019 20:00:02: 16000000 INFO @ Sun, 02 Jun 2019 20:00:06: 11000000 INFO @ Sun, 02 Jun 2019 20:00:07: 12000000 INFO @ Sun, 02 Jun 2019 20:00:09: 17000000 INFO @ Sun, 02 Jun 2019 20:00:16: 18000000 INFO @ Sun, 02 Jun 2019 20:00:16: 12000000 INFO @ Sun, 02 Jun 2019 20:00:17: 13000000 INFO @ Sun, 02 Jun 2019 20:00:23: 19000000 INFO @ Sun, 02 Jun 2019 20:00:26: 13000000 INFO @ Sun, 02 Jun 2019 20:00:27: 14000000 INFO @ Sun, 02 Jun 2019 20:00:30: 20000000 INFO @ Sun, 02 Jun 2019 20:00:36: 15000000 INFO @ Sun, 02 Jun 2019 20:00:37: 14000000 INFO @ Sun, 02 Jun 2019 20:00:37: 21000000 INFO @ Sun, 02 Jun 2019 20:00:44: 22000000 INFO @ Sun, 02 Jun 2019 20:00:46: 16000000 INFO @ Sun, 02 Jun 2019 20:00:47: 15000000 INFO @ Sun, 02 Jun 2019 20:00:52: 23000000 INFO @ Sun, 02 Jun 2019 20:00:55: 17000000 INFO @ Sun, 02 Jun 2019 20:00:57: 16000000 INFO @ Sun, 02 Jun 2019 20:00:59: 24000000 INFO @ Sun, 02 Jun 2019 20:01:05: 18000000 INFO @ Sun, 02 Jun 2019 20:01:06: 25000000 INFO @ Sun, 02 Jun 2019 20:01:08: 17000000 INFO @ Sun, 02 Jun 2019 20:01:13: 26000000 INFO @ Sun, 02 Jun 2019 20:01:15: 19000000 INFO @ Sun, 02 Jun 2019 20:01:18: 18000000 INFO @ Sun, 02 Jun 2019 20:01:20: 27000000 INFO @ Sun, 02 Jun 2019 20:01:24: 20000000 INFO @ Sun, 02 Jun 2019 20:01:27: 28000000 INFO @ Sun, 02 Jun 2019 20:01:28: 19000000 INFO @ Sun, 02 Jun 2019 20:01:34: 21000000 INFO @ Sun, 02 Jun 2019 20:01:34: 29000000 INFO @ Sun, 02 Jun 2019 20:01:38: 20000000 INFO @ Sun, 02 Jun 2019 20:01:42: 30000000 INFO @ Sun, 02 Jun 2019 20:01:44: 22000000 INFO @ Sun, 02 Jun 2019 20:01:48: 21000000 INFO @ Sun, 02 Jun 2019 20:01:49: 31000000 INFO @ Sun, 02 Jun 2019 20:01:54: 23000000 INFO @ Sun, 02 Jun 2019 20:01:56: 32000000 INFO @ Sun, 02 Jun 2019 20:02:00: 22000000 INFO @ Sun, 02 Jun 2019 20:02:03: 33000000 INFO @ Sun, 02 Jun 2019 20:02:04: 24000000 INFO @ Sun, 02 Jun 2019 20:02:09: 34000000 INFO @ Sun, 02 Jun 2019 20:02:10: 23000000 INFO @ Sun, 02 Jun 2019 20:02:14: 25000000 INFO @ Sun, 02 Jun 2019 20:02:17: 35000000 INFO @ Sun, 02 Jun 2019 20:02:22: 24000000 INFO @ Sun, 02 Jun 2019 20:02:24: 36000000 INFO @ Sun, 02 Jun 2019 20:02:24: 26000000 INFO @ Sun, 02 Jun 2019 20:02:31: 37000000 INFO @ Sun, 02 Jun 2019 20:02:33: 25000000 INFO @ Sun, 02 Jun 2019 20:02:34: 27000000 INFO @ Sun, 02 Jun 2019 20:02:38: 38000000 INFO @ Sun, 02 Jun 2019 20:02:43: 26000000 INFO @ Sun, 02 Jun 2019 20:02:43: 28000000 INFO @ Sun, 02 Jun 2019 20:02:45: 39000000 INFO @ Sun, 02 Jun 2019 20:02:52: 40000000 INFO @ Sun, 02 Jun 2019 20:02:53: 29000000 INFO @ Sun, 02 Jun 2019 20:02:53: 27000000 INFO @ Sun, 02 Jun 2019 20:02:59: 41000000 INFO @ Sun, 02 Jun 2019 20:03:03: 30000000 INFO @ Sun, 02 Jun 2019 20:03:03: 28000000 INFO @ Sun, 02 Jun 2019 20:03:06: 42000000 INFO @ Sun, 02 Jun 2019 20:03:12: 31000000 INFO @ Sun, 02 Jun 2019 20:03:13: 43000000 INFO @ Sun, 02 Jun 2019 20:03:13: 29000000 INFO @ Sun, 02 Jun 2019 20:03:14: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:03:14: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:03:14: #1 total tags in treatment: 20678351 INFO @ Sun, 02 Jun 2019 20:03:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:03:14: #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 20:03:15: #1 tags after filtering in treatment: 17173968 INFO @ Sun, 02 Jun 2019 20:03:15: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:03:15: #1 finished! INFO @ Sun, 02 Jun 2019 20:03:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:03:17: #2 number of paired peaks: 680 WARNING @ Sun, 02 Jun 2019 20:03:17: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 02 Jun 2019 20:03:17: start model_add_line... INFO @ Sun, 02 Jun 2019 20:03:17: start X-correlation... INFO @ Sun, 02 Jun 2019 20:03:17: end of X-cor INFO @ Sun, 02 Jun 2019 20:03:17: #2 finished! INFO @ Sun, 02 Jun 2019 20:03:17: #2 predicted fragment length is 199 bps INFO @ Sun, 02 Jun 2019 20:03:17: #2 alternative fragment length(s) may be 4,199 bps INFO @ Sun, 02 Jun 2019 20:03:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10_model.r INFO @ Sun, 02 Jun 2019 20:03:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:03:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:03:21: 32000000 INFO @ Sun, 02 Jun 2019 20:03:24: 30000000 INFO @ Sun, 02 Jun 2019 20:03:31: 33000000 INFO @ Sun, 02 Jun 2019 20:03:33: 31000000 INFO @ Sun, 02 Jun 2019 20:03:40: 34000000 INFO @ Sun, 02 Jun 2019 20:03:43: 32000000 INFO @ Sun, 02 Jun 2019 20:03:51: 35000000 INFO @ Sun, 02 Jun 2019 20:03:53: 33000000 INFO @ Sun, 02 Jun 2019 20:04:01: 36000000 INFO @ Sun, 02 Jun 2019 20:04:04: 34000000 INFO @ Sun, 02 Jun 2019 20:04:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:04:10: 37000000 INFO @ Sun, 02 Jun 2019 20:04:15: 35000000 INFO @ Sun, 02 Jun 2019 20:04:20: 38000000 INFO @ Sun, 02 Jun 2019 20:04:25: 36000000 INFO @ Sun, 02 Jun 2019 20:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:04:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:04:29: 39000000 INFO @ Sun, 02 Jun 2019 20:04:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.10_summits.bed INFO @ Sun, 02 Jun 2019 20:04:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2667 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:04:35: 37000000 INFO @ Sun, 02 Jun 2019 20:04:38: 40000000 INFO @ Sun, 02 Jun 2019 20:04:45: 38000000 INFO @ Sun, 02 Jun 2019 20:04:48: 41000000 INFO @ Sun, 02 Jun 2019 20:04:55: 39000000 INFO @ Sun, 02 Jun 2019 20:04:57: 42000000 INFO @ Sun, 02 Jun 2019 20:05:05: 40000000 INFO @ Sun, 02 Jun 2019 20:05:07: 43000000 INFO @ Sun, 02 Jun 2019 20:05:08: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:05:08: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:05:08: #1 total tags in treatment: 20678351 INFO @ Sun, 02 Jun 2019 20:05:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:08: #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 20:05:09: #1 tags after filtering in treatment: 17173968 INFO @ Sun, 02 Jun 2019 20:05:09: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:05:09: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:10: #2 number of paired peaks: 680 WARNING @ Sun, 02 Jun 2019 20:05:10: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 02 Jun 2019 20:05:10: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:10: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:10: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:10: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:10: #2 predicted fragment length is 199 bps INFO @ Sun, 02 Jun 2019 20:05:10: #2 alternative fragment length(s) may be 4,199 bps INFO @ Sun, 02 Jun 2019 20:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20_model.r INFO @ Sun, 02 Jun 2019 20:05:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:14: 41000000 INFO @ Sun, 02 Jun 2019 20:05:24: 42000000 INFO @ Sun, 02 Jun 2019 20:05:33: 43000000 INFO @ Sun, 02 Jun 2019 20:05:34: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 20:05:34: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 20:05:34: #1 total tags in treatment: 20678351 INFO @ Sun, 02 Jun 2019 20:05:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:34: #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 20:05:35: #1 tags after filtering in treatment: 17173968 INFO @ Sun, 02 Jun 2019 20:05:35: #1 Redundant rate of treatment: 0.17 INFO @ Sun, 02 Jun 2019 20:05:35: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:36: #2 number of paired peaks: 680 WARNING @ Sun, 02 Jun 2019 20:05:36: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 02 Jun 2019 20:05:36: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:37: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:37: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:37: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:37: #2 predicted fragment length is 199 bps INFO @ Sun, 02 Jun 2019 20:05:37: #2 alternative fragment length(s) may be 4,199 bps INFO @ Sun, 02 Jun 2019 20:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05_model.r INFO @ Sun, 02 Jun 2019 20:05:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.20_summits.bed INFO @ Sun, 02 Jun 2019 20:06:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1212 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:06:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:06:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:06:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:06:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3733157/SRX3733157.05_summits.bed INFO @ Sun, 02 Jun 2019 20:06:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4755 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。