Job ID = 1292010 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,146,525 reads read : 42,293,050 reads written : 42,293,050 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: 00:22:40 21146525 reads; of these: 21146525 (100.00%) were paired; of these: 1215773 (5.75%) aligned concordantly 0 times 17135700 (81.03%) aligned concordantly exactly 1 time 2795052 (13.22%) aligned concordantly >1 times ---- 1215773 pairs aligned concordantly 0 times; of these: 690477 (56.79%) aligned discordantly 1 time ---- 525296 pairs aligned 0 times concordantly or discordantly; of these: 1050592 mates make up the pairs; of these: 607068 (57.78%) aligned 0 times 261611 (24.90%) aligned exactly 1 time 181913 (17.32%) aligned >1 times 98.56% overall alignment rate Time searching: 00:22:40 Overall time: 00:22:40 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 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] 355266 / 20610749 = 0.0172 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 17:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.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 17:57:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:57:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.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 17:57:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:57:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.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 17:57:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:57:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:00: 1000000 INFO @ Sun, 02 Jun 2019 17:58:03: 1000000 INFO @ Sun, 02 Jun 2019 17:58:03: 1000000 INFO @ Sun, 02 Jun 2019 17:58:08: 2000000 INFO @ Sun, 02 Jun 2019 17:58:14: 2000000 INFO @ Sun, 02 Jun 2019 17:58:15: 2000000 INFO @ Sun, 02 Jun 2019 17:58:17: 3000000 INFO @ Sun, 02 Jun 2019 17:58:24: 3000000 INFO @ Sun, 02 Jun 2019 17:58:25: 4000000 INFO @ Sun, 02 Jun 2019 17:58:27: 3000000 INFO @ Sun, 02 Jun 2019 17:58:33: 5000000 INFO @ Sun, 02 Jun 2019 17:58:34: 4000000 INFO @ Sun, 02 Jun 2019 17:58:38: 4000000 INFO @ Sun, 02 Jun 2019 17:58:41: 6000000 INFO @ Sun, 02 Jun 2019 17:58:45: 5000000 INFO @ Sun, 02 Jun 2019 17:58:49: 7000000 INFO @ Sun, 02 Jun 2019 17:58:49: 5000000 INFO @ Sun, 02 Jun 2019 17:58:55: 6000000 INFO @ Sun, 02 Jun 2019 17:58:57: 8000000 INFO @ Sun, 02 Jun 2019 17:59:02: 6000000 INFO @ Sun, 02 Jun 2019 17:59:06: 7000000 INFO @ Sun, 02 Jun 2019 17:59:06: 9000000 INFO @ Sun, 02 Jun 2019 17:59:14: 7000000 INFO @ Sun, 02 Jun 2019 17:59:14: 10000000 INFO @ Sun, 02 Jun 2019 17:59:16: 8000000 INFO @ Sun, 02 Jun 2019 17:59:22: 11000000 INFO @ Sun, 02 Jun 2019 17:59:25: 8000000 INFO @ Sun, 02 Jun 2019 17:59:27: 9000000 INFO @ Sun, 02 Jun 2019 17:59:30: 12000000 INFO @ Sun, 02 Jun 2019 17:59:37: 9000000 INFO @ Sun, 02 Jun 2019 17:59:37: 10000000 INFO @ Sun, 02 Jun 2019 17:59:38: 13000000 INFO @ Sun, 02 Jun 2019 17:59:46: 14000000 INFO @ Sun, 02 Jun 2019 17:59:48: 10000000 INFO @ Sun, 02 Jun 2019 17:59:49: 11000000 INFO @ Sun, 02 Jun 2019 17:59:54: 15000000 INFO @ Sun, 02 Jun 2019 17:59:59: 11000000 INFO @ Sun, 02 Jun 2019 18:00:00: 12000000 INFO @ Sun, 02 Jun 2019 18:00:02: 16000000 INFO @ Sun, 02 Jun 2019 18:00:10: 12000000 INFO @ Sun, 02 Jun 2019 18:00:10: 17000000 INFO @ Sun, 02 Jun 2019 18:00:11: 13000000 INFO @ Sun, 02 Jun 2019 18:00:18: 18000000 INFO @ Sun, 02 Jun 2019 18:00:21: 13000000 INFO @ Sun, 02 Jun 2019 18:00:22: 14000000 INFO @ Sun, 02 Jun 2019 18:00:26: 19000000 INFO @ Sun, 02 Jun 2019 18:00:33: 14000000 INFO @ Sun, 02 Jun 2019 18:00:34: 20000000 INFO @ Sun, 02 Jun 2019 18:00:35: 15000000 INFO @ Sun, 02 Jun 2019 18:00:42: 21000000 INFO @ Sun, 02 Jun 2019 18:00:43: 15000000 INFO @ Sun, 02 Jun 2019 18:00:45: 16000000 INFO @ Sun, 02 Jun 2019 18:00:50: 22000000 INFO @ Sun, 02 Jun 2019 18:00:53: 16000000 INFO @ Sun, 02 Jun 2019 18:00:55: 17000000 INFO @ Sun, 02 Jun 2019 18:00:58: 23000000 INFO @ Sun, 02 Jun 2019 18:01:04: 17000000 INFO @ Sun, 02 Jun 2019 18:01:06: 18000000 INFO @ Sun, 02 Jun 2019 18:01:06: 24000000 INFO @ Sun, 02 Jun 2019 18:01:14: 25000000 INFO @ Sun, 02 Jun 2019 18:01:15: 18000000 INFO @ Sun, 02 Jun 2019 18:01:17: 19000000 INFO @ Sun, 02 Jun 2019 18:01:22: 26000000 INFO @ Sun, 02 Jun 2019 18:01:26: 19000000 INFO @ Sun, 02 Jun 2019 18:01:28: 20000000 INFO @ Sun, 02 Jun 2019 18:01:30: 27000000 INFO @ Sun, 02 Jun 2019 18:01:36: 20000000 INFO @ Sun, 02 Jun 2019 18:01:38: 28000000 INFO @ Sun, 02 Jun 2019 18:01:39: 21000000 INFO @ Sun, 02 Jun 2019 18:01:46: 29000000 INFO @ Sun, 02 Jun 2019 18:01:47: 21000000 INFO @ Sun, 02 Jun 2019 18:01:50: 22000000 INFO @ Sun, 02 Jun 2019 18:01:54: 30000000 INFO @ Sun, 02 Jun 2019 18:01:59: 22000000 INFO @ Sun, 02 Jun 2019 18:02:02: 23000000 INFO @ Sun, 02 Jun 2019 18:02:02: 31000000 INFO @ Sun, 02 Jun 2019 18:02:10: 23000000 INFO @ Sun, 02 Jun 2019 18:02:10: 32000000 INFO @ Sun, 02 Jun 2019 18:02:13: 24000000 INFO @ Sun, 02 Jun 2019 18:02:18: 33000000 INFO @ Sun, 02 Jun 2019 18:02:20: 24000000 INFO @ Sun, 02 Jun 2019 18:02:24: 25000000 INFO @ Sun, 02 Jun 2019 18:02:25: 34000000 INFO @ Sun, 02 Jun 2019 18:02:31: 25000000 INFO @ Sun, 02 Jun 2019 18:02:33: 35000000 INFO @ Sun, 02 Jun 2019 18:02:35: 26000000 INFO @ Sun, 02 Jun 2019 18:02:41: 36000000 INFO @ Sun, 02 Jun 2019 18:02:41: 26000000 INFO @ Sun, 02 Jun 2019 18:02:46: 27000000 INFO @ Sun, 02 Jun 2019 18:02:49: 37000000 INFO @ Sun, 02 Jun 2019 18:02:52: 27000000 INFO @ Sun, 02 Jun 2019 18:02:57: 28000000 INFO @ Sun, 02 Jun 2019 18:02:57: 38000000 INFO @ Sun, 02 Jun 2019 18:03:02: 28000000 INFO @ Sun, 02 Jun 2019 18:03:05: 39000000 INFO @ Sun, 02 Jun 2019 18:03:08: 29000000 INFO @ Sun, 02 Jun 2019 18:03:13: 29000000 INFO @ Sun, 02 Jun 2019 18:03:13: 40000000 INFO @ Sun, 02 Jun 2019 18:03:19: 30000000 INFO @ Sun, 02 Jun 2019 18:03:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:03:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:03:21: #1 total tags in treatment: 19579765 INFO @ Sun, 02 Jun 2019 18:03:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:03:21: #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 18:03:22: #1 tags after filtering in treatment: 17554530 INFO @ Sun, 02 Jun 2019 18:03:22: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:03:22: #1 finished! INFO @ Sun, 02 Jun 2019 18:03:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:03:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:03:23: #2 number of paired peaks: 284 WARNING @ Sun, 02 Jun 2019 18:03:23: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sun, 02 Jun 2019 18:03:23: start model_add_line... INFO @ Sun, 02 Jun 2019 18:03:24: start X-correlation... INFO @ Sun, 02 Jun 2019 18:03:24: end of X-cor INFO @ Sun, 02 Jun 2019 18:03:24: #2 finished! INFO @ Sun, 02 Jun 2019 18:03:24: #2 predicted fragment length is 113 bps INFO @ Sun, 02 Jun 2019 18:03:24: #2 alternative fragment length(s) may be 4,113,133 bps INFO @ Sun, 02 Jun 2019 18:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05_model.r INFO @ Sun, 02 Jun 2019 18:03:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:03:24: 30000000 INFO @ Sun, 02 Jun 2019 18:03:30: 31000000 INFO @ Sun, 02 Jun 2019 18:03:35: 31000000 INFO @ Sun, 02 Jun 2019 18:03:41: 32000000 INFO @ Sun, 02 Jun 2019 18:03:46: 32000000 INFO @ Sun, 02 Jun 2019 18:03:51: 33000000 INFO @ Sun, 02 Jun 2019 18:03:56: 33000000 INFO @ Sun, 02 Jun 2019 18:04:02: 34000000 INFO @ Sun, 02 Jun 2019 18:04:07: 34000000 INFO @ Sun, 02 Jun 2019 18:04:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:04:12: 35000000 INFO @ Sun, 02 Jun 2019 18:04:16: 35000000 INFO @ Sun, 02 Jun 2019 18:04:22: 36000000 INFO @ Sun, 02 Jun 2019 18:04:24: 36000000 INFO @ Sun, 02 Jun 2019 18:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.05_summits.bed INFO @ Sun, 02 Jun 2019 18:04:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:04:32: 37000000 INFO @ Sun, 02 Jun 2019 18:04:32: 37000000 INFO @ Sun, 02 Jun 2019 18:04:41: 38000000 INFO @ Sun, 02 Jun 2019 18:04:42: 38000000 INFO @ Sun, 02 Jun 2019 18:04:50: 39000000 INFO @ Sun, 02 Jun 2019 18:04:52: 39000000 INFO @ Sun, 02 Jun 2019 18:04:58: 40000000 INFO @ Sun, 02 Jun 2019 18:05:01: 40000000 INFO @ Sun, 02 Jun 2019 18:05:05: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:05:05: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:05:05: #1 total tags in treatment: 19579765 INFO @ Sun, 02 Jun 2019 18:05:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:05: #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 18:05:06: #1 tags after filtering in treatment: 17554530 INFO @ Sun, 02 Jun 2019 18:05:06: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:05:06: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:08: #2 number of paired peaks: 284 WARNING @ Sun, 02 Jun 2019 18:05:08: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sun, 02 Jun 2019 18:05:08: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:08: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:08: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:08: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:08: #2 predicted fragment length is 113 bps INFO @ Sun, 02 Jun 2019 18:05:08: #2 alternative fragment length(s) may be 4,113,133 bps INFO @ Sun, 02 Jun 2019 18:05:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10_model.r INFO @ Sun, 02 Jun 2019 18:05:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:10: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:05:10: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:05:10: #1 total tags in treatment: 19579765 INFO @ Sun, 02 Jun 2019 18:05:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:05:10: #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 18:05:11: #1 tags after filtering in treatment: 17554530 INFO @ Sun, 02 Jun 2019 18:05:11: #1 Redundant rate of treatment: 0.10 INFO @ Sun, 02 Jun 2019 18:05:11: #1 finished! INFO @ Sun, 02 Jun 2019 18:05:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:05:13: #2 number of paired peaks: 284 WARNING @ Sun, 02 Jun 2019 18:05:13: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Sun, 02 Jun 2019 18:05:13: start model_add_line... INFO @ Sun, 02 Jun 2019 18:05:13: start X-correlation... INFO @ Sun, 02 Jun 2019 18:05:13: end of X-cor INFO @ Sun, 02 Jun 2019 18:05:13: #2 finished! INFO @ Sun, 02 Jun 2019 18:05:13: #2 predicted fragment length is 113 bps INFO @ Sun, 02 Jun 2019 18:05:13: #2 alternative fragment length(s) may be 4,113,133 bps INFO @ Sun, 02 Jun 2019 18:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20_model.r INFO @ Sun, 02 Jun 2019 18:05:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:05:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:05:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.10_summits.bed INFO @ Sun, 02 Jun 2019 18:06:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2978706/SRX2978706.20_summits.bed INFO @ Sun, 02 Jun 2019 18:06:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (233 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。