Job ID = 1292439 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,373,894 reads read : 22,747,788 reads written : 22,747,788 spots read : 12,959,611 reads read : 25,919,222 reads written : 25,919,222 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: 00:26:18 24333505 reads; of these: 24333505 (100.00%) were paired; of these: 3159405 (12.98%) aligned concordantly 0 times 17711258 (72.79%) aligned concordantly exactly 1 time 3462842 (14.23%) aligned concordantly >1 times ---- 3159405 pairs aligned concordantly 0 times; of these: 868345 (27.48%) aligned discordantly 1 time ---- 2291060 pairs aligned 0 times concordantly or discordantly; of these: 4582120 mates make up the pairs; of these: 3515790 (76.73%) aligned 0 times 650990 (14.21%) aligned exactly 1 time 415340 (9.06%) aligned >1 times 92.78% overall alignment rate Time searching: 00:26:18 Overall time: 00:26:18 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] 770205 / 21974145 = 0.0351 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 19:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.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 19:29:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:29:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.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 19:29:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:29:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.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 19:29:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:29:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:29:48: 1000000 INFO @ Sun, 02 Jun 2019 19:29:49: 1000000 INFO @ Sun, 02 Jun 2019 19:29:49: 1000000 INFO @ Sun, 02 Jun 2019 19:29:55: 2000000 INFO @ Sun, 02 Jun 2019 19:29:57: 2000000 INFO @ Sun, 02 Jun 2019 19:29:57: 2000000 INFO @ Sun, 02 Jun 2019 19:30:02: 3000000 INFO @ Sun, 02 Jun 2019 19:30:04: 3000000 INFO @ Sun, 02 Jun 2019 19:30:05: 3000000 INFO @ Sun, 02 Jun 2019 19:30:10: 4000000 INFO @ Sun, 02 Jun 2019 19:30:11: 4000000 INFO @ Sun, 02 Jun 2019 19:30:12: 4000000 INFO @ Sun, 02 Jun 2019 19:30:18: 5000000 INFO @ Sun, 02 Jun 2019 19:30:18: 5000000 INFO @ Sun, 02 Jun 2019 19:30:20: 5000000 INFO @ Sun, 02 Jun 2019 19:30:25: 6000000 INFO @ Sun, 02 Jun 2019 19:30:26: 6000000 INFO @ Sun, 02 Jun 2019 19:30:28: 6000000 INFO @ Sun, 02 Jun 2019 19:30:32: 7000000 INFO @ Sun, 02 Jun 2019 19:30:34: 7000000 INFO @ Sun, 02 Jun 2019 19:30:37: 7000000 INFO @ Sun, 02 Jun 2019 19:30:39: 8000000 INFO @ Sun, 02 Jun 2019 19:30:41: 8000000 INFO @ Sun, 02 Jun 2019 19:30:46: 9000000 INFO @ Sun, 02 Jun 2019 19:30:46: 8000000 INFO @ Sun, 02 Jun 2019 19:30:47: 9000000 INFO @ Sun, 02 Jun 2019 19:30:53: 10000000 INFO @ Sun, 02 Jun 2019 19:30:54: 10000000 INFO @ Sun, 02 Jun 2019 19:30:56: 9000000 INFO @ Sun, 02 Jun 2019 19:31:00: 11000000 INFO @ Sun, 02 Jun 2019 19:31:01: 11000000 INFO @ Sun, 02 Jun 2019 19:31:05: 10000000 INFO @ Sun, 02 Jun 2019 19:31:07: 12000000 INFO @ Sun, 02 Jun 2019 19:31:08: 12000000 INFO @ Sun, 02 Jun 2019 19:31:14: 13000000 INFO @ Sun, 02 Jun 2019 19:31:15: 11000000 INFO @ Sun, 02 Jun 2019 19:31:15: 13000000 INFO @ Sun, 02 Jun 2019 19:31:21: 14000000 INFO @ Sun, 02 Jun 2019 19:31:22: 14000000 INFO @ Sun, 02 Jun 2019 19:31:24: 12000000 INFO @ Sun, 02 Jun 2019 19:31:28: 15000000 INFO @ Sun, 02 Jun 2019 19:31:29: 15000000 INFO @ Sun, 02 Jun 2019 19:31:33: 13000000 INFO @ Sun, 02 Jun 2019 19:31:35: 16000000 INFO @ Sun, 02 Jun 2019 19:31:36: 16000000 INFO @ Sun, 02 Jun 2019 19:31:41: 17000000 INFO @ Sun, 02 Jun 2019 19:31:43: 17000000 INFO @ Sun, 02 Jun 2019 19:31:43: 14000000 INFO @ Sun, 02 Jun 2019 19:31:48: 18000000 INFO @ Sun, 02 Jun 2019 19:31:50: 18000000 INFO @ Sun, 02 Jun 2019 19:31:53: 15000000 INFO @ Sun, 02 Jun 2019 19:31:55: 19000000 INFO @ Sun, 02 Jun 2019 19:31:57: 19000000 INFO @ Sun, 02 Jun 2019 19:32:02: 20000000 INFO @ Sun, 02 Jun 2019 19:32:02: 16000000 INFO @ Sun, 02 Jun 2019 19:32:04: 20000000 INFO @ Sun, 02 Jun 2019 19:32:09: 21000000 INFO @ Sun, 02 Jun 2019 19:32:11: 21000000 INFO @ Sun, 02 Jun 2019 19:32:12: 17000000 INFO @ Sun, 02 Jun 2019 19:32:16: 22000000 INFO @ Sun, 02 Jun 2019 19:32:18: 22000000 INFO @ Sun, 02 Jun 2019 19:32:21: 18000000 INFO @ Sun, 02 Jun 2019 19:32:23: 23000000 INFO @ Sun, 02 Jun 2019 19:32:24: 23000000 INFO @ Sun, 02 Jun 2019 19:32:30: 24000000 INFO @ Sun, 02 Jun 2019 19:32:31: 19000000 INFO @ Sun, 02 Jun 2019 19:32:31: 24000000 INFO @ Sun, 02 Jun 2019 19:32:37: 25000000 INFO @ Sun, 02 Jun 2019 19:32:38: 25000000 INFO @ Sun, 02 Jun 2019 19:32:40: 20000000 INFO @ Sun, 02 Jun 2019 19:32:44: 26000000 INFO @ Sun, 02 Jun 2019 19:32:45: 26000000 INFO @ Sun, 02 Jun 2019 19:32:50: 21000000 INFO @ Sun, 02 Jun 2019 19:32:51: 27000000 INFO @ Sun, 02 Jun 2019 19:32:52: 27000000 INFO @ Sun, 02 Jun 2019 19:32:58: 28000000 INFO @ Sun, 02 Jun 2019 19:32:59: 28000000 INFO @ Sun, 02 Jun 2019 19:32:59: 22000000 INFO @ Sun, 02 Jun 2019 19:33:05: 29000000 INFO @ Sun, 02 Jun 2019 19:33:06: 29000000 INFO @ Sun, 02 Jun 2019 19:33:09: 23000000 INFO @ Sun, 02 Jun 2019 19:33:12: 30000000 INFO @ Sun, 02 Jun 2019 19:33:13: 30000000 INFO @ Sun, 02 Jun 2019 19:33:18: 31000000 INFO @ Sun, 02 Jun 2019 19:33:18: 24000000 INFO @ Sun, 02 Jun 2019 19:33:20: 31000000 INFO @ Sun, 02 Jun 2019 19:33:25: 32000000 INFO @ Sun, 02 Jun 2019 19:33:27: 32000000 INFO @ Sun, 02 Jun 2019 19:33:28: 25000000 INFO @ Sun, 02 Jun 2019 19:33:32: 33000000 INFO @ Sun, 02 Jun 2019 19:33:34: 33000000 INFO @ Sun, 02 Jun 2019 19:33:37: 26000000 INFO @ Sun, 02 Jun 2019 19:33:39: 34000000 INFO @ Sun, 02 Jun 2019 19:33:41: 34000000 INFO @ Sun, 02 Jun 2019 19:33:46: 35000000 INFO @ Sun, 02 Jun 2019 19:33:47: 27000000 INFO @ Sun, 02 Jun 2019 19:33:47: 35000000 INFO @ Sun, 02 Jun 2019 19:33:53: 36000000 INFO @ Sun, 02 Jun 2019 19:33:54: 36000000 INFO @ Sun, 02 Jun 2019 19:33:56: 28000000 INFO @ Sun, 02 Jun 2019 19:34:00: 37000000 INFO @ Sun, 02 Jun 2019 19:34:01: 37000000 INFO @ Sun, 02 Jun 2019 19:34:06: 29000000 INFO @ Sun, 02 Jun 2019 19:34:07: 38000000 INFO @ Sun, 02 Jun 2019 19:34:08: 38000000 INFO @ Sun, 02 Jun 2019 19:34:13: 39000000 INFO @ Sun, 02 Jun 2019 19:34:15: 39000000 INFO @ Sun, 02 Jun 2019 19:34:15: 30000000 INFO @ Sun, 02 Jun 2019 19:34:20: 40000000 INFO @ Sun, 02 Jun 2019 19:34:22: 40000000 INFO @ Sun, 02 Jun 2019 19:34:24: 31000000 INFO @ Sun, 02 Jun 2019 19:34:27: 41000000 INFO @ Sun, 02 Jun 2019 19:34:29: 41000000 INFO @ Sun, 02 Jun 2019 19:34:34: 32000000 INFO @ Sun, 02 Jun 2019 19:34:34: 42000000 INFO @ Sun, 02 Jun 2019 19:34:36: 42000000 INFO @ Sun, 02 Jun 2019 19:34:41: 43000000 INFO @ Sun, 02 Jun 2019 19:34:42: 43000000 INFO @ Sun, 02 Jun 2019 19:34:43: 33000000 INFO @ Sun, 02 Jun 2019 19:34:45: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:34:45: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:34:45: #1 total tags in treatment: 20408617 INFO @ Sun, 02 Jun 2019 19:34:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:34:45: #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 19:34:46: #1 tags after filtering in treatment: 16514443 INFO @ Sun, 02 Jun 2019 19:34:46: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 02 Jun 2019 19:34:46: #1 finished! INFO @ Sun, 02 Jun 2019 19:34:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:34:47: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:34:47: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:34:47: #1 total tags in treatment: 20408617 INFO @ Sun, 02 Jun 2019 19:34:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:34:47: #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 19:34:47: #1 tags after filtering in treatment: 16514443 INFO @ Sun, 02 Jun 2019 19:34:47: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 02 Jun 2019 19:34:47: #1 finished! INFO @ Sun, 02 Jun 2019 19:34:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:34:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:34:47: #2 number of paired peaks: 191 WARNING @ Sun, 02 Jun 2019 19:34:47: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sun, 02 Jun 2019 19:34:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:34:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:34:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:34:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:34:47: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 19:34:47: #2 alternative fragment length(s) may be 3,77,105,109,157,172 bps INFO @ Sun, 02 Jun 2019 19:34:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05_model.r INFO @ Sun, 02 Jun 2019 19:34:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:34:49: #2 number of paired peaks: 191 WARNING @ Sun, 02 Jun 2019 19:34:49: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sun, 02 Jun 2019 19:34:49: start model_add_line... INFO @ Sun, 02 Jun 2019 19:34:49: start X-correlation... INFO @ Sun, 02 Jun 2019 19:34:49: end of X-cor INFO @ Sun, 02 Jun 2019 19:34:49: #2 finished! INFO @ Sun, 02 Jun 2019 19:34:49: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 19:34:49: #2 alternative fragment length(s) may be 3,77,105,109,157,172 bps INFO @ Sun, 02 Jun 2019 19:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20_model.r INFO @ Sun, 02 Jun 2019 19:34:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:34:52: 34000000 INFO @ Sun, 02 Jun 2019 19:35:01: 35000000 INFO @ Sun, 02 Jun 2019 19:35:09: 36000000 INFO @ Sun, 02 Jun 2019 19:35:18: 37000000 INFO @ Sun, 02 Jun 2019 19:35:27: 38000000 INFO @ Sun, 02 Jun 2019 19:35:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:35:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:35:36: 39000000 INFO @ Sun, 02 Jun 2019 19:35:44: 40000000 INFO @ Sun, 02 Jun 2019 19:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.05_summits.bed INFO @ Sun, 02 Jun 2019 19:35:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:35:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:35:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:35:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.20_summits.bed INFO @ Sun, 02 Jun 2019 19:35:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:35:54: 41000000 INFO @ Sun, 02 Jun 2019 19:36:02: 42000000 INFO @ Sun, 02 Jun 2019 19:36:11: 43000000 INFO @ Sun, 02 Jun 2019 19:36:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:36:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:36:17: #1 total tags in treatment: 20408617 INFO @ Sun, 02 Jun 2019 19:36:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:17: #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 19:36:17: #1 tags after filtering in treatment: 16514443 INFO @ Sun, 02 Jun 2019 19:36:17: #1 Redundant rate of treatment: 0.19 INFO @ Sun, 02 Jun 2019 19:36:17: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:19: #2 number of paired peaks: 191 WARNING @ Sun, 02 Jun 2019 19:36:19: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:19: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:19: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:19: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:19: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:19: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 19:36:19: #2 alternative fragment length(s) may be 3,77,105,109,157,172 bps INFO @ Sun, 02 Jun 2019 19:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10_model.r INFO @ Sun, 02 Jun 2019 19:36:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:37:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419818/SRX4419818.10_summits.bed INFO @ Sun, 02 Jun 2019 19:37:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 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。