Job ID = 1292891 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,127,031 reads read : 50,254,062 reads written : 50,254,062 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: 00:27:49 25127031 reads; of these: 25127031 (100.00%) were paired; of these: 1252862 (4.99%) aligned concordantly 0 times 20401837 (81.19%) aligned concordantly exactly 1 time 3472332 (13.82%) aligned concordantly >1 times ---- 1252862 pairs aligned concordantly 0 times; of these: 581559 (46.42%) aligned discordantly 1 time ---- 671303 pairs aligned 0 times concordantly or discordantly; of these: 1342606 mates make up the pairs; of these: 861136 (64.14%) aligned 0 times 298726 (22.25%) aligned exactly 1 time 182744 (13.61%) aligned >1 times 98.29% overall alignment rate Time searching: 00:27:49 Overall time: 00:27:49 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 24 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] 341523 / 24440536 = 0.0140 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 21:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.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 21:56:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:56:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.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 21:56:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:56:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.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 21:56:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:56:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:56:28: 1000000 INFO @ Sun, 02 Jun 2019 21:56:29: 1000000 INFO @ Sun, 02 Jun 2019 21:56:30: 1000000 INFO @ Sun, 02 Jun 2019 21:56:34: 2000000 INFO @ Sun, 02 Jun 2019 21:56:36: 2000000 INFO @ Sun, 02 Jun 2019 21:56:38: 2000000 INFO @ Sun, 02 Jun 2019 21:56:41: 3000000 INFO @ Sun, 02 Jun 2019 21:56:43: 3000000 INFO @ Sun, 02 Jun 2019 21:56:46: 3000000 INFO @ Sun, 02 Jun 2019 21:56:48: 4000000 INFO @ Sun, 02 Jun 2019 21:56:50: 4000000 INFO @ Sun, 02 Jun 2019 21:56:55: 4000000 INFO @ Sun, 02 Jun 2019 21:56:55: 5000000 INFO @ Sun, 02 Jun 2019 21:56:57: 5000000 INFO @ Sun, 02 Jun 2019 21:57:02: 6000000 INFO @ Sun, 02 Jun 2019 21:57:03: 5000000 INFO @ Sun, 02 Jun 2019 21:57:04: 6000000 INFO @ Sun, 02 Jun 2019 21:57:08: 7000000 INFO @ Sun, 02 Jun 2019 21:57:10: 7000000 INFO @ Sun, 02 Jun 2019 21:57:11: 6000000 INFO @ Sun, 02 Jun 2019 21:57:14: 8000000 INFO @ Sun, 02 Jun 2019 21:57:17: 8000000 INFO @ Sun, 02 Jun 2019 21:57:18: 7000000 INFO @ Sun, 02 Jun 2019 21:57:20: 9000000 INFO @ Sun, 02 Jun 2019 21:57:24: 9000000 INFO @ Sun, 02 Jun 2019 21:57:26: 10000000 INFO @ Sun, 02 Jun 2019 21:57:27: 8000000 INFO @ Sun, 02 Jun 2019 21:57:31: 10000000 INFO @ Sun, 02 Jun 2019 21:57:32: 11000000 INFO @ Sun, 02 Jun 2019 21:57:34: 9000000 INFO @ Sun, 02 Jun 2019 21:57:37: 11000000 INFO @ Sun, 02 Jun 2019 21:57:38: 12000000 INFO @ Sun, 02 Jun 2019 21:57:42: 10000000 INFO @ Sun, 02 Jun 2019 21:57:44: 12000000 INFO @ Sun, 02 Jun 2019 21:57:44: 13000000 INFO @ Sun, 02 Jun 2019 21:57:50: 14000000 INFO @ Sun, 02 Jun 2019 21:57:50: 11000000 INFO @ Sun, 02 Jun 2019 21:57:51: 13000000 INFO @ Sun, 02 Jun 2019 21:57:56: 15000000 INFO @ Sun, 02 Jun 2019 21:57:58: 14000000 INFO @ Sun, 02 Jun 2019 21:57:58: 12000000 INFO @ Sun, 02 Jun 2019 21:58:02: 16000000 INFO @ Sun, 02 Jun 2019 21:58:04: 15000000 INFO @ Sun, 02 Jun 2019 21:58:06: 13000000 INFO @ Sun, 02 Jun 2019 21:58:09: 17000000 INFO @ Sun, 02 Jun 2019 21:58:11: 16000000 INFO @ Sun, 02 Jun 2019 21:58:14: 14000000 INFO @ Sun, 02 Jun 2019 21:58:15: 18000000 INFO @ Sun, 02 Jun 2019 21:58:18: 17000000 INFO @ Sun, 02 Jun 2019 21:58:21: 19000000 INFO @ Sun, 02 Jun 2019 21:58:22: 15000000 INFO @ Sun, 02 Jun 2019 21:58:25: 18000000 INFO @ Sun, 02 Jun 2019 21:58:27: 20000000 INFO @ Sun, 02 Jun 2019 21:58:30: 16000000 INFO @ Sun, 02 Jun 2019 21:58:31: 19000000 INFO @ Sun, 02 Jun 2019 21:58:34: 21000000 INFO @ Sun, 02 Jun 2019 21:58:37: 17000000 INFO @ Sun, 02 Jun 2019 21:58:38: 20000000 INFO @ Sun, 02 Jun 2019 21:58:40: 22000000 INFO @ Sun, 02 Jun 2019 21:58:45: 21000000 INFO @ Sun, 02 Jun 2019 21:58:45: 18000000 INFO @ Sun, 02 Jun 2019 21:58:46: 23000000 INFO @ Sun, 02 Jun 2019 21:58:51: 22000000 INFO @ Sun, 02 Jun 2019 21:58:52: 24000000 INFO @ Sun, 02 Jun 2019 21:58:53: 19000000 INFO @ Sun, 02 Jun 2019 21:58:58: 25000000 INFO @ Sun, 02 Jun 2019 21:58:58: 23000000 INFO @ Sun, 02 Jun 2019 21:59:01: 20000000 INFO @ Sun, 02 Jun 2019 21:59:04: 26000000 INFO @ Sun, 02 Jun 2019 21:59:05: 24000000 INFO @ Sun, 02 Jun 2019 21:59:09: 21000000 INFO @ Sun, 02 Jun 2019 21:59:10: 27000000 INFO @ Sun, 02 Jun 2019 21:59:12: 25000000 INFO @ Sun, 02 Jun 2019 21:59:17: 28000000 INFO @ Sun, 02 Jun 2019 21:59:17: 22000000 INFO @ Sun, 02 Jun 2019 21:59:18: 26000000 INFO @ Sun, 02 Jun 2019 21:59:23: 29000000 INFO @ Sun, 02 Jun 2019 21:59:25: 23000000 INFO @ Sun, 02 Jun 2019 21:59:25: 27000000 INFO @ Sun, 02 Jun 2019 21:59:29: 30000000 INFO @ Sun, 02 Jun 2019 21:59:32: 28000000 INFO @ Sun, 02 Jun 2019 21:59:33: 24000000 INFO @ Sun, 02 Jun 2019 21:59:35: 31000000 INFO @ Sun, 02 Jun 2019 21:59:39: 29000000 INFO @ Sun, 02 Jun 2019 21:59:40: 25000000 INFO @ Sun, 02 Jun 2019 21:59:41: 32000000 INFO @ Sun, 02 Jun 2019 21:59:45: 30000000 INFO @ Sun, 02 Jun 2019 21:59:47: 33000000 INFO @ Sun, 02 Jun 2019 21:59:48: 26000000 INFO @ Sun, 02 Jun 2019 21:59:52: 31000000 INFO @ Sun, 02 Jun 2019 21:59:53: 34000000 INFO @ Sun, 02 Jun 2019 21:59:56: 27000000 INFO @ Sun, 02 Jun 2019 21:59:59: 32000000 INFO @ Sun, 02 Jun 2019 21:59:59: 35000000 INFO @ Sun, 02 Jun 2019 22:00:04: 28000000 INFO @ Sun, 02 Jun 2019 22:00:05: 33000000 INFO @ Sun, 02 Jun 2019 22:00:05: 36000000 INFO @ Sun, 02 Jun 2019 22:00:11: 37000000 INFO @ Sun, 02 Jun 2019 22:00:12: 29000000 INFO @ Sun, 02 Jun 2019 22:00:12: 34000000 INFO @ Sun, 02 Jun 2019 22:00:18: 38000000 INFO @ Sun, 02 Jun 2019 22:00:19: 35000000 INFO @ Sun, 02 Jun 2019 22:00:19: 30000000 INFO @ Sun, 02 Jun 2019 22:00:24: 39000000 INFO @ Sun, 02 Jun 2019 22:00:25: 36000000 INFO @ Sun, 02 Jun 2019 22:00:27: 31000000 INFO @ Sun, 02 Jun 2019 22:00:30: 40000000 INFO @ Sun, 02 Jun 2019 22:00:32: 37000000 INFO @ Sun, 02 Jun 2019 22:00:35: 32000000 INFO @ Sun, 02 Jun 2019 22:00:36: 41000000 INFO @ Sun, 02 Jun 2019 22:00:39: 38000000 INFO @ Sun, 02 Jun 2019 22:00:42: 42000000 INFO @ Sun, 02 Jun 2019 22:00:43: 33000000 INFO @ Sun, 02 Jun 2019 22:00:46: 39000000 INFO @ Sun, 02 Jun 2019 22:00:48: 43000000 INFO @ Sun, 02 Jun 2019 22:00:51: 34000000 INFO @ Sun, 02 Jun 2019 22:00:52: 40000000 INFO @ Sun, 02 Jun 2019 22:00:54: 44000000 INFO @ Sun, 02 Jun 2019 22:00:58: 35000000 INFO @ Sun, 02 Jun 2019 22:00:59: 41000000 INFO @ Sun, 02 Jun 2019 22:01:00: 45000000 INFO @ Sun, 02 Jun 2019 22:01:06: 46000000 INFO @ Sun, 02 Jun 2019 22:01:06: 42000000 INFO @ Sun, 02 Jun 2019 22:01:06: 36000000 INFO @ Sun, 02 Jun 2019 22:01:12: 47000000 INFO @ Sun, 02 Jun 2019 22:01:13: 43000000 INFO @ Sun, 02 Jun 2019 22:01:14: 37000000 INFO @ Sun, 02 Jun 2019 22:01:18: 48000000 INFO @ Sun, 02 Jun 2019 22:01:19: 44000000 INFO @ Sun, 02 Jun 2019 22:01:22: 38000000 INFO @ Sun, 02 Jun 2019 22:01:22: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:01:22: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:01:22: #1 total tags in treatment: 23535472 INFO @ Sun, 02 Jun 2019 22:01:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:01:22: #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 22:01:23: #1 tags after filtering in treatment: 21000993 INFO @ Sun, 02 Jun 2019 22:01:23: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 02 Jun 2019 22:01:23: #1 finished! INFO @ Sun, 02 Jun 2019 22:01:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:01:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:01:25: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 22:01:25: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 22:01:25: start model_add_line... INFO @ Sun, 02 Jun 2019 22:01:25: start X-correlation... INFO @ Sun, 02 Jun 2019 22:01:25: end of X-cor INFO @ Sun, 02 Jun 2019 22:01:25: #2 finished! INFO @ Sun, 02 Jun 2019 22:01:25: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 22:01:25: #2 alternative fragment length(s) may be 3,97,117 bps INFO @ Sun, 02 Jun 2019 22:01:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10_model.r INFO @ Sun, 02 Jun 2019 22:01:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:01:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:01:26: 45000000 INFO @ Sun, 02 Jun 2019 22:01:30: 39000000 INFO @ Sun, 02 Jun 2019 22:01:33: 46000000 INFO @ Sun, 02 Jun 2019 22:01:37: 40000000 INFO @ Sun, 02 Jun 2019 22:01:39: 47000000 INFO @ Sun, 02 Jun 2019 22:01:45: 41000000 INFO @ Sun, 02 Jun 2019 22:01:46: 48000000 INFO @ Sun, 02 Jun 2019 22:01:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:01:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:01:51: #1 total tags in treatment: 23535472 INFO @ Sun, 02 Jun 2019 22:01:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:01:51: #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 22:01:51: #1 tags after filtering in treatment: 21000993 INFO @ Sun, 02 Jun 2019 22:01:51: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 02 Jun 2019 22:01:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:01:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:01:53: 42000000 INFO @ Sun, 02 Jun 2019 22:01:53: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 22:01:53: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 22:01:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:01:53: start X-correlation... INFO @ Sun, 02 Jun 2019 22:01:53: end of X-cor INFO @ Sun, 02 Jun 2019 22:01:53: #2 finished! INFO @ Sun, 02 Jun 2019 22:01:53: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 22:01:53: #2 alternative fragment length(s) may be 3,97,117 bps INFO @ Sun, 02 Jun 2019 22:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20_model.r INFO @ Sun, 02 Jun 2019 22:01:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:02:00: 43000000 INFO @ Sun, 02 Jun 2019 22:02:08: 44000000 INFO @ Sun, 02 Jun 2019 22:02:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:02:15: 45000000 INFO @ Sun, 02 Jun 2019 22:02:23: 46000000 INFO @ Sun, 02 Jun 2019 22:02:30: 47000000 INFO @ Sun, 02 Jun 2019 22:02:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:02:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:02:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.10_summits.bed INFO @ Sun, 02 Jun 2019 22:02:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:02:38: 48000000 INFO @ Sun, 02 Jun 2019 22:02:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:02:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:02:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:02:44: #1 total tags in treatment: 23535472 INFO @ Sun, 02 Jun 2019 22:02:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:02:44: #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 22:02:44: #1 tags after filtering in treatment: 21000993 INFO @ Sun, 02 Jun 2019 22:02:44: #1 Redundant rate of treatment: 0.11 INFO @ Sun, 02 Jun 2019 22:02:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:02:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:02:46: #2 number of paired peaks: 269 WARNING @ Sun, 02 Jun 2019 22:02:46: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sun, 02 Jun 2019 22:02:46: start model_add_line... INFO @ Sun, 02 Jun 2019 22:02:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:02:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:02:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:02:46: #2 predicted fragment length is 117 bps INFO @ Sun, 02 Jun 2019 22:02:46: #2 alternative fragment length(s) may be 3,97,117 bps INFO @ Sun, 02 Jun 2019 22:02:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05_model.r INFO @ Sun, 02 Jun 2019 22:02:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:02:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:03:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:03:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:03:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.20_summits.bed INFO @ Sun, 02 Jun 2019 22:03:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:03:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996820/SRX4996820.05_summits.bed INFO @ Sun, 02 Jun 2019 22:03:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (517 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。