Job ID = 4178392 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-05T03:18:30 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 14,686,336 reads read : 14,686,336 reads written : 14,686,336 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:15 14686336 reads; of these: 14686336 (100.00%) were unpaired; of these: 1233658 (8.40%) aligned 0 times 11590310 (78.92%) aligned exactly 1 time 1862368 (12.68%) aligned >1 times 91.60% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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 8 files... [bam_rmdupse_core] 2166979 / 13452678 = 0.1611 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.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 @ Thu, 05 Dec 2019 12:33:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:16: 1000000 INFO @ Thu, 05 Dec 2019 12:33:24: 2000000 INFO @ Thu, 05 Dec 2019 12:33:33: 3000000 INFO @ Thu, 05 Dec 2019 12:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.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 @ Thu, 05 Dec 2019 12:33:36: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:33:36: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:33:41: 4000000 INFO @ Thu, 05 Dec 2019 12:33:45: 1000000 INFO @ Thu, 05 Dec 2019 12:33:49: 5000000 INFO @ Thu, 05 Dec 2019 12:33:54: 2000000 INFO @ Thu, 05 Dec 2019 12:33:58: 6000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:34:03: 3000000 INFO @ Thu, 05 Dec 2019 12:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.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 @ Thu, 05 Dec 2019 12:34:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:34:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:34:07: 7000000 INFO @ Thu, 05 Dec 2019 12:34:12: 4000000 INFO @ Thu, 05 Dec 2019 12:34:16: 1000000 INFO @ Thu, 05 Dec 2019 12:34:17: 8000000 INFO @ Thu, 05 Dec 2019 12:34:20: 5000000 INFO @ Thu, 05 Dec 2019 12:34:27: 9000000 INFO @ Thu, 05 Dec 2019 12:34:27: 2000000 INFO @ Thu, 05 Dec 2019 12:34:29: 6000000 INFO @ Thu, 05 Dec 2019 12:34:35: 3000000 INFO @ Thu, 05 Dec 2019 12:34:36: 10000000 INFO @ Thu, 05 Dec 2019 12:34:39: 7000000 INFO @ Thu, 05 Dec 2019 12:34:43: 4000000 INFO @ Thu, 05 Dec 2019 12:34:44: 11000000 INFO @ Thu, 05 Dec 2019 12:34:46: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:34:46: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:34:46: #1 total tags in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:34:46: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:34:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:34:46: #1 tags after filtering in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:34:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:34:46: #1 finished! INFO @ Thu, 05 Dec 2019 12:34:46: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:34:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:34:47: #2 number of paired peaks: 389 WARNING @ Thu, 05 Dec 2019 12:34:47: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 05 Dec 2019 12:34:47: start model_add_line... INFO @ Thu, 05 Dec 2019 12:34:47: start X-correlation... INFO @ Thu, 05 Dec 2019 12:34:48: end of X-cor INFO @ Thu, 05 Dec 2019 12:34:48: #2 finished! INFO @ Thu, 05 Dec 2019 12:34:48: #2 predicted fragment length is 109 bps INFO @ Thu, 05 Dec 2019 12:34:48: #2 alternative fragment length(s) may be 109 bps INFO @ Thu, 05 Dec 2019 12:34:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05_model.r INFO @ Thu, 05 Dec 2019 12:34:48: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:34:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:34:48: 8000000 INFO @ Thu, 05 Dec 2019 12:34:52: 5000000 INFO @ Thu, 05 Dec 2019 12:34:58: 9000000 INFO @ Thu, 05 Dec 2019 12:35:01: 6000000 INFO @ Thu, 05 Dec 2019 12:35:08: 10000000 INFO @ Thu, 05 Dec 2019 12:35:08: 7000000 INFO @ Thu, 05 Dec 2019 12:35:16: 8000000 INFO @ Thu, 05 Dec 2019 12:35:18: 11000000 INFO @ Thu, 05 Dec 2019 12:35:20: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:20: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:20: #1 total tags in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:35:20: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:21: #1 tags after filtering in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:21: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:21: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:22: #2 number of paired peaks: 389 WARNING @ Thu, 05 Dec 2019 12:35:22: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 05 Dec 2019 12:35:22: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:22: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:22: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:22: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:22: #2 predicted fragment length is 109 bps INFO @ Thu, 05 Dec 2019 12:35:22: #2 alternative fragment length(s) may be 109 bps INFO @ Thu, 05 Dec 2019 12:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10_model.r INFO @ Thu, 05 Dec 2019 12:35:22: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:35:24: 9000000 INFO @ Thu, 05 Dec 2019 12:35:32: 10000000 INFO @ Thu, 05 Dec 2019 12:35:41: 11000000 INFO @ Thu, 05 Dec 2019 12:35:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:35:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:35:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.05_summits.bed INFO @ Thu, 05 Dec 2019 12:35:42: Done! pass1 - making usageList (7 chroms): 9 millis pass2 - checking and writing primary data (4006 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:35:43: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:35:43: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:35:43: #1 total tags in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:35:43: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:35:43: #1 tags after filtering in treatment: 11285699 INFO @ Thu, 05 Dec 2019 12:35:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:35:43: #1 finished! INFO @ Thu, 05 Dec 2019 12:35:43: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:35:44: #2 number of paired peaks: 389 WARNING @ Thu, 05 Dec 2019 12:35:44: Fewer paired peaks (389) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 389 pairs to build model! INFO @ Thu, 05 Dec 2019 12:35:44: start model_add_line... INFO @ Thu, 05 Dec 2019 12:35:44: start X-correlation... INFO @ Thu, 05 Dec 2019 12:35:44: end of X-cor INFO @ Thu, 05 Dec 2019 12:35:44: #2 finished! INFO @ Thu, 05 Dec 2019 12:35:44: #2 predicted fragment length is 109 bps INFO @ Thu, 05 Dec 2019 12:35:44: #2 alternative fragment length(s) may be 109 bps INFO @ Thu, 05 Dec 2019 12:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20_model.r INFO @ Thu, 05 Dec 2019 12:35:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:35:54: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.10_summits.bed INFO @ Thu, 05 Dec 2019 12:36:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2540 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:36:17: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:36:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:36:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:36:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107870/SRX4107870.20_summits.bed INFO @ Thu, 05 Dec 2019 12:36:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1097 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。