Job ID = 1292440 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,723,173 reads read : 21,446,346 reads written : 21,446,346 spots read : 3,562,823 reads read : 7,125,646 reads written : 7,125,646 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: 00:14:40 14285996 reads; of these: 14285996 (100.00%) were paired; of these: 1488065 (10.42%) aligned concordantly 0 times 10880080 (76.16%) aligned concordantly exactly 1 time 1917851 (13.42%) aligned concordantly >1 times ---- 1488065 pairs aligned concordantly 0 times; of these: 323485 (21.74%) aligned discordantly 1 time ---- 1164580 pairs aligned 0 times concordantly or discordantly; of these: 2329160 mates make up the pairs; of these: 1818451 (78.07%) aligned 0 times 338328 (14.53%) aligned exactly 1 time 172381 (7.40%) aligned >1 times 93.64% overall alignment rate Time searching: 00:14:40 Overall time: 00:14:40 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 12 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] 435412 / 13027853 = 0.0334 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 19:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.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 19:07:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:07:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.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 19:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.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 19:07:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:07:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:07:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:07:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:07:26: 1000000 INFO @ Sun, 02 Jun 2019 19:07:29: 1000000 INFO @ Sun, 02 Jun 2019 19:07:29: 1000000 INFO @ Sun, 02 Jun 2019 19:07:33: 2000000 INFO @ Sun, 02 Jun 2019 19:07:38: 2000000 INFO @ Sun, 02 Jun 2019 19:07:38: 2000000 INFO @ Sun, 02 Jun 2019 19:07:40: 3000000 INFO @ Sun, 02 Jun 2019 19:07:46: 3000000 INFO @ Sun, 02 Jun 2019 19:07:46: 3000000 INFO @ Sun, 02 Jun 2019 19:07:47: 4000000 INFO @ Sun, 02 Jun 2019 19:07:54: 5000000 INFO @ Sun, 02 Jun 2019 19:07:55: 4000000 INFO @ Sun, 02 Jun 2019 19:07:55: 4000000 INFO @ Sun, 02 Jun 2019 19:08:01: 6000000 INFO @ Sun, 02 Jun 2019 19:08:04: 5000000 INFO @ Sun, 02 Jun 2019 19:08:04: 5000000 INFO @ Sun, 02 Jun 2019 19:08:07: 7000000 INFO @ Sun, 02 Jun 2019 19:08:13: 6000000 INFO @ Sun, 02 Jun 2019 19:08:13: 6000000 INFO @ Sun, 02 Jun 2019 19:08:14: 8000000 INFO @ Sun, 02 Jun 2019 19:08:21: 9000000 INFO @ Sun, 02 Jun 2019 19:08:21: 7000000 INFO @ Sun, 02 Jun 2019 19:08:21: 7000000 INFO @ Sun, 02 Jun 2019 19:08:28: 10000000 INFO @ Sun, 02 Jun 2019 19:08:30: 8000000 INFO @ Sun, 02 Jun 2019 19:08:30: 8000000 INFO @ Sun, 02 Jun 2019 19:08:34: 11000000 INFO @ Sun, 02 Jun 2019 19:08:39: 9000000 INFO @ Sun, 02 Jun 2019 19:08:39: 9000000 INFO @ Sun, 02 Jun 2019 19:08:41: 12000000 INFO @ Sun, 02 Jun 2019 19:08:47: 10000000 INFO @ Sun, 02 Jun 2019 19:08:47: 10000000 INFO @ Sun, 02 Jun 2019 19:08:48: 13000000 INFO @ Sun, 02 Jun 2019 19:08:54: 14000000 INFO @ Sun, 02 Jun 2019 19:08:56: 11000000 INFO @ Sun, 02 Jun 2019 19:08:56: 11000000 INFO @ Sun, 02 Jun 2019 19:09:01: 15000000 INFO @ Sun, 02 Jun 2019 19:09:04: 12000000 INFO @ Sun, 02 Jun 2019 19:09:05: 12000000 INFO @ Sun, 02 Jun 2019 19:09:08: 16000000 INFO @ Sun, 02 Jun 2019 19:09:13: 13000000 INFO @ Sun, 02 Jun 2019 19:09:13: 13000000 INFO @ Sun, 02 Jun 2019 19:09:15: 17000000 INFO @ Sun, 02 Jun 2019 19:09:21: 14000000 INFO @ Sun, 02 Jun 2019 19:09:21: 18000000 INFO @ Sun, 02 Jun 2019 19:09:21: 14000000 INFO @ Sun, 02 Jun 2019 19:09:28: 19000000 INFO @ Sun, 02 Jun 2019 19:09:30: 15000000 INFO @ Sun, 02 Jun 2019 19:09:30: 15000000 INFO @ Sun, 02 Jun 2019 19:09:35: 20000000 INFO @ Sun, 02 Jun 2019 19:09:38: 16000000 INFO @ Sun, 02 Jun 2019 19:09:38: 16000000 INFO @ Sun, 02 Jun 2019 19:09:41: 21000000 INFO @ Sun, 02 Jun 2019 19:09:46: 17000000 INFO @ Sun, 02 Jun 2019 19:09:47: 17000000 INFO @ Sun, 02 Jun 2019 19:09:48: 22000000 INFO @ Sun, 02 Jun 2019 19:09:54: 23000000 INFO @ Sun, 02 Jun 2019 19:09:55: 18000000 INFO @ Sun, 02 Jun 2019 19:09:55: 18000000 INFO @ Sun, 02 Jun 2019 19:10:01: 24000000 INFO @ Sun, 02 Jun 2019 19:10:03: 19000000 INFO @ Sun, 02 Jun 2019 19:10:03: 19000000 INFO @ Sun, 02 Jun 2019 19:10:08: 25000000 INFO @ Sun, 02 Jun 2019 19:10:11: 20000000 INFO @ Sun, 02 Jun 2019 19:10:11: 20000000 INFO @ Sun, 02 Jun 2019 19:10:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:10:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:10:14: #1 total tags in treatment: 12365746 INFO @ Sun, 02 Jun 2019 19:10:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:10:14: #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 19:10:14: #1 tags after filtering in treatment: 10735794 INFO @ Sun, 02 Jun 2019 19:10:14: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:10:14: #1 finished! INFO @ Sun, 02 Jun 2019 19:10:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:10:15: #2 number of paired peaks: 216 WARNING @ Sun, 02 Jun 2019 19:10:15: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 02 Jun 2019 19:10:15: start model_add_line... INFO @ Sun, 02 Jun 2019 19:10:15: start X-correlation... INFO @ Sun, 02 Jun 2019 19:10:15: end of X-cor INFO @ Sun, 02 Jun 2019 19:10:15: #2 finished! INFO @ Sun, 02 Jun 2019 19:10:15: #2 predicted fragment length is 162 bps INFO @ Sun, 02 Jun 2019 19:10:15: #2 alternative fragment length(s) may be 4,68,162 bps INFO @ Sun, 02 Jun 2019 19:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05_model.r INFO @ Sun, 02 Jun 2019 19:10:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:10:20: 21000000 INFO @ Sun, 02 Jun 2019 19:10:20: 21000000 INFO @ Sun, 02 Jun 2019 19:10:28: 22000000 INFO @ Sun, 02 Jun 2019 19:10:28: 22000000 INFO @ Sun, 02 Jun 2019 19:10:37: 23000000 INFO @ Sun, 02 Jun 2019 19:10:37: 23000000 INFO @ Sun, 02 Jun 2019 19:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:46: 24000000 INFO @ Sun, 02 Jun 2019 19:10:46: 24000000 INFO @ Sun, 02 Jun 2019 19:10:54: 25000000 INFO @ Sun, 02 Jun 2019 19:10:55: 25000000 INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.05_summits.bed INFO @ Sun, 02 Jun 2019 19:10:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:11:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:11:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:11:02: #1 total tags in treatment: 12365746 INFO @ Sun, 02 Jun 2019 19:11:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:11:02: #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 19:11:02: #1 tags after filtering in treatment: 10735794 INFO @ Sun, 02 Jun 2019 19:11:02: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:11:02: #1 finished! INFO @ Sun, 02 Jun 2019 19:11:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:11:02: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:11:02: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:11:02: #1 total tags in treatment: 12365746 INFO @ Sun, 02 Jun 2019 19:11:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:11:02: #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 19:11:03: #1 tags after filtering in treatment: 10735794 INFO @ Sun, 02 Jun 2019 19:11:03: #1 Redundant rate of treatment: 0.13 INFO @ Sun, 02 Jun 2019 19:11:03: #1 finished! INFO @ Sun, 02 Jun 2019 19:11:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:11:03: #2 number of paired peaks: 216 WARNING @ Sun, 02 Jun 2019 19:11:03: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 02 Jun 2019 19:11:03: start model_add_line... INFO @ Sun, 02 Jun 2019 19:11:03: start X-correlation... INFO @ Sun, 02 Jun 2019 19:11:03: end of X-cor INFO @ Sun, 02 Jun 2019 19:11:03: #2 finished! INFO @ Sun, 02 Jun 2019 19:11:03: #2 predicted fragment length is 162 bps INFO @ Sun, 02 Jun 2019 19:11:03: #2 alternative fragment length(s) may be 4,68,162 bps INFO @ Sun, 02 Jun 2019 19:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10_model.r INFO @ Sun, 02 Jun 2019 19:11:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:11:04: #2 number of paired peaks: 216 WARNING @ Sun, 02 Jun 2019 19:11:04: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Sun, 02 Jun 2019 19:11:04: start model_add_line... INFO @ Sun, 02 Jun 2019 19:11:04: start X-correlation... INFO @ Sun, 02 Jun 2019 19:11:04: end of X-cor INFO @ Sun, 02 Jun 2019 19:11:04: #2 finished! INFO @ Sun, 02 Jun 2019 19:11:04: #2 predicted fragment length is 162 bps INFO @ Sun, 02 Jun 2019 19:11:04: #2 alternative fragment length(s) may be 4,68,162 bps INFO @ Sun, 02 Jun 2019 19:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20_model.r INFO @ Sun, 02 Jun 2019 19:11:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:11:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:11:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:11:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:11:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:11:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.10_summits.bed INFO @ Sun, 02 Jun 2019 19:11:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:11:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:11:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:11:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4419819/SRX4419819.20_summits.bed INFO @ Sun, 02 Jun 2019 19:11:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。