Job ID = 1292872 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,747,489 reads read : 31,494,978 reads written : 31,494,978 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: 00:19:34 15747489 reads; of these: 15747489 (100.00%) were paired; of these: 927391 (5.89%) aligned concordantly 0 times 12053027 (76.54%) aligned concordantly exactly 1 time 2767071 (17.57%) aligned concordantly >1 times ---- 927391 pairs aligned concordantly 0 times; of these: 373213 (40.24%) aligned discordantly 1 time ---- 554178 pairs aligned 0 times concordantly or discordantly; of these: 1108356 mates make up the pairs; of these: 778285 (70.22%) aligned 0 times 184286 (16.63%) aligned exactly 1 time 145785 (13.15%) aligned >1 times 97.53% overall alignment rate Time searching: 00:19:34 Overall time: 00:19:34 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 16 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] 2720489 / 15186077 = 0.1791 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 21:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.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 21:31:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:31:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.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 21:31:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:31:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:31:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.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 21:31:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:31:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:31:11: 1000000 INFO @ Sun, 02 Jun 2019 21:31:12: 1000000 INFO @ Sun, 02 Jun 2019 21:31:12: 1000000 INFO @ Sun, 02 Jun 2019 21:31:17: 2000000 INFO @ Sun, 02 Jun 2019 21:31:21: 2000000 INFO @ Sun, 02 Jun 2019 21:31:22: 2000000 INFO @ Sun, 02 Jun 2019 21:31:24: 3000000 INFO @ Sun, 02 Jun 2019 21:31:30: 4000000 INFO @ Sun, 02 Jun 2019 21:31:31: 3000000 INFO @ Sun, 02 Jun 2019 21:31:31: 3000000 INFO @ Sun, 02 Jun 2019 21:31:37: 5000000 INFO @ Sun, 02 Jun 2019 21:31:40: 4000000 INFO @ Sun, 02 Jun 2019 21:31:41: 4000000 INFO @ Sun, 02 Jun 2019 21:31:43: 6000000 INFO @ Sun, 02 Jun 2019 21:31:50: 5000000 INFO @ Sun, 02 Jun 2019 21:31:50: 7000000 INFO @ Sun, 02 Jun 2019 21:31:50: 5000000 INFO @ Sun, 02 Jun 2019 21:31:56: 8000000 INFO @ Sun, 02 Jun 2019 21:31:59: 6000000 INFO @ Sun, 02 Jun 2019 21:31:59: 6000000 INFO @ Sun, 02 Jun 2019 21:32:03: 9000000 INFO @ Sun, 02 Jun 2019 21:32:08: 7000000 INFO @ Sun, 02 Jun 2019 21:32:09: 7000000 INFO @ Sun, 02 Jun 2019 21:32:09: 10000000 INFO @ Sun, 02 Jun 2019 21:32:16: 11000000 INFO @ Sun, 02 Jun 2019 21:32:16: 8000000 INFO @ Sun, 02 Jun 2019 21:32:18: 8000000 INFO @ Sun, 02 Jun 2019 21:32:22: 12000000 INFO @ Sun, 02 Jun 2019 21:32:25: 9000000 INFO @ Sun, 02 Jun 2019 21:32:27: 9000000 INFO @ Sun, 02 Jun 2019 21:32:29: 13000000 INFO @ Sun, 02 Jun 2019 21:32:34: 10000000 INFO @ Sun, 02 Jun 2019 21:32:36: 10000000 INFO @ Sun, 02 Jun 2019 21:32:36: 14000000 INFO @ Sun, 02 Jun 2019 21:32:43: 15000000 INFO @ Sun, 02 Jun 2019 21:32:43: 11000000 INFO @ Sun, 02 Jun 2019 21:32:45: 11000000 INFO @ Sun, 02 Jun 2019 21:32:49: 16000000 INFO @ Sun, 02 Jun 2019 21:32:52: 12000000 INFO @ Sun, 02 Jun 2019 21:32:54: 12000000 INFO @ Sun, 02 Jun 2019 21:32:56: 17000000 INFO @ Sun, 02 Jun 2019 21:33:01: 13000000 INFO @ Sun, 02 Jun 2019 21:33:03: 18000000 INFO @ Sun, 02 Jun 2019 21:33:03: 13000000 INFO @ Sun, 02 Jun 2019 21:33:09: 19000000 INFO @ Sun, 02 Jun 2019 21:33:10: 14000000 INFO @ Sun, 02 Jun 2019 21:33:12: 14000000 INFO @ Sun, 02 Jun 2019 21:33:16: 20000000 INFO @ Sun, 02 Jun 2019 21:33:19: 15000000 INFO @ Sun, 02 Jun 2019 21:33:21: 15000000 INFO @ Sun, 02 Jun 2019 21:33:22: 21000000 INFO @ Sun, 02 Jun 2019 21:33:28: 16000000 INFO @ Sun, 02 Jun 2019 21:33:29: 22000000 INFO @ Sun, 02 Jun 2019 21:33:30: 16000000 INFO @ Sun, 02 Jun 2019 21:33:35: 23000000 INFO @ Sun, 02 Jun 2019 21:33:37: 17000000 INFO @ Sun, 02 Jun 2019 21:33:39: 17000000 INFO @ Sun, 02 Jun 2019 21:33:41: 24000000 INFO @ Sun, 02 Jun 2019 21:33:46: 18000000 INFO @ Sun, 02 Jun 2019 21:33:48: 18000000 INFO @ Sun, 02 Jun 2019 21:33:48: 25000000 INFO @ Sun, 02 Jun 2019 21:33:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:33:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:33:50: #1 total tags in treatment: 12126411 INFO @ Sun, 02 Jun 2019 21:33:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:33:50: #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 21:33:50: #1 tags after filtering in treatment: 10991939 INFO @ Sun, 02 Jun 2019 21:33:50: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:33:50: #1 finished! INFO @ Sun, 02 Jun 2019 21:33:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:33:51: #2 number of paired peaks: 527 WARNING @ Sun, 02 Jun 2019 21:33:51: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 02 Jun 2019 21:33:51: start model_add_line... INFO @ Sun, 02 Jun 2019 21:33:51: start X-correlation... INFO @ Sun, 02 Jun 2019 21:33:51: end of X-cor INFO @ Sun, 02 Jun 2019 21:33:51: #2 finished! INFO @ Sun, 02 Jun 2019 21:33:51: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 21:33:51: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 02 Jun 2019 21:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05_model.r INFO @ Sun, 02 Jun 2019 21:33:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:33:54: 19000000 INFO @ Sun, 02 Jun 2019 21:33:56: 19000000 INFO @ Sun, 02 Jun 2019 21:34:03: 20000000 INFO @ Sun, 02 Jun 2019 21:34:05: 20000000 INFO @ Sun, 02 Jun 2019 21:34:12: 21000000 INFO @ Sun, 02 Jun 2019 21:34:13: 21000000 INFO @ Sun, 02 Jun 2019 21:34:20: 22000000 INFO @ Sun, 02 Jun 2019 21:34:22: 22000000 INFO @ Sun, 02 Jun 2019 21:34:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:34:29: 23000000 INFO @ Sun, 02 Jun 2019 21:34:30: 23000000 INFO @ Sun, 02 Jun 2019 21:34:37: 24000000 INFO @ Sun, 02 Jun 2019 21:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.05_summits.bed INFO @ Sun, 02 Jun 2019 21:34:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:34:38: 24000000 INFO @ Sun, 02 Jun 2019 21:34:45: 25000000 INFO @ Sun, 02 Jun 2019 21:34:46: 25000000 INFO @ Sun, 02 Jun 2019 21:34:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:34:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:34:48: #1 total tags in treatment: 12126411 INFO @ Sun, 02 Jun 2019 21:34:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:34:48: #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 21:34:48: #1 tags after filtering in treatment: 10991939 INFO @ Sun, 02 Jun 2019 21:34:48: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:34:48: #1 finished! INFO @ Sun, 02 Jun 2019 21:34:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:34:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 21:34:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 21:34:48: #1 total tags in treatment: 12126411 INFO @ Sun, 02 Jun 2019 21:34:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:34:48: #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 21:34:49: #1 tags after filtering in treatment: 10991939 INFO @ Sun, 02 Jun 2019 21:34:49: #1 Redundant rate of treatment: 0.09 INFO @ Sun, 02 Jun 2019 21:34:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:34:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:34:49: #2 number of paired peaks: 527 WARNING @ Sun, 02 Jun 2019 21:34:49: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 02 Jun 2019 21:34:49: start model_add_line... INFO @ Sun, 02 Jun 2019 21:34:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:34:49: end of X-cor INFO @ Sun, 02 Jun 2019 21:34:49: #2 finished! INFO @ Sun, 02 Jun 2019 21:34:49: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 21:34:49: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 02 Jun 2019 21:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20_model.r INFO @ Sun, 02 Jun 2019 21:34:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:34:50: #2 number of paired peaks: 527 WARNING @ Sun, 02 Jun 2019 21:34:50: Fewer paired peaks (527) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 527 pairs to build model! INFO @ Sun, 02 Jun 2019 21:34:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:34:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:34:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:34:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:34:50: #2 predicted fragment length is 136 bps INFO @ Sun, 02 Jun 2019 21:34:50: #2 alternative fragment length(s) may be 4,136 bps INFO @ Sun, 02 Jun 2019 21:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10_model.r INFO @ Sun, 02 Jun 2019 21:34:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:35:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:35:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.20_summits.bed INFO @ Sun, 02 Jun 2019 21:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4996804/SRX4996804.10_summits.bed INFO @ Sun, 02 Jun 2019 21:35:36: Done! INFO @ Sun, 02 Jun 2019 21:35:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (238 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (350 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。