Job ID = 1293097 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:45:27 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-02T12:45:27 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra36/SRR/001236/SRR1265815' 2019-06-02T12:45:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1265815' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T12:45:36 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 19,263,987 reads read : 19,263,987 reads written : 19,263,987 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: 00:04:30 19263987 reads; of these: 19263987 (100.00%) were unpaired; of these: 287249 (1.49%) aligned 0 times 15656650 (81.27%) aligned exactly 1 time 3320088 (17.23%) aligned >1 times 98.51% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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] 1890330 / 18976738 = 0.0996 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 22:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.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 22:13:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.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 22:13:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.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 22:13:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:14:01: 1000000 INFO @ Sun, 02 Jun 2019 22:14:01: 1000000 INFO @ Sun, 02 Jun 2019 22:14:02: 1000000 INFO @ Sun, 02 Jun 2019 22:14:08: 2000000 INFO @ Sun, 02 Jun 2019 22:14:08: 2000000 INFO @ Sun, 02 Jun 2019 22:14:10: 2000000 INFO @ Sun, 02 Jun 2019 22:14:16: 3000000 INFO @ Sun, 02 Jun 2019 22:14:16: 3000000 INFO @ Sun, 02 Jun 2019 22:14:19: 3000000 INFO @ Sun, 02 Jun 2019 22:14:23: 4000000 INFO @ Sun, 02 Jun 2019 22:14:23: 4000000 INFO @ Sun, 02 Jun 2019 22:14:27: 4000000 INFO @ Sun, 02 Jun 2019 22:14:31: 5000000 INFO @ Sun, 02 Jun 2019 22:14:31: 5000000 INFO @ Sun, 02 Jun 2019 22:14:36: 5000000 INFO @ Sun, 02 Jun 2019 22:14:38: 6000000 INFO @ Sun, 02 Jun 2019 22:14:38: 6000000 INFO @ Sun, 02 Jun 2019 22:14:44: 6000000 INFO @ Sun, 02 Jun 2019 22:14:45: 7000000 INFO @ Sun, 02 Jun 2019 22:14:46: 7000000 INFO @ Sun, 02 Jun 2019 22:14:52: 7000000 INFO @ Sun, 02 Jun 2019 22:14:53: 8000000 INFO @ Sun, 02 Jun 2019 22:14:53: 8000000 INFO @ Sun, 02 Jun 2019 22:15:00: 8000000 INFO @ Sun, 02 Jun 2019 22:15:00: 9000000 INFO @ Sun, 02 Jun 2019 22:15:00: 9000000 INFO @ Sun, 02 Jun 2019 22:15:08: 10000000 INFO @ Sun, 02 Jun 2019 22:15:08: 10000000 INFO @ Sun, 02 Jun 2019 22:15:08: 9000000 INFO @ Sun, 02 Jun 2019 22:15:15: 11000000 INFO @ Sun, 02 Jun 2019 22:15:15: 11000000 INFO @ Sun, 02 Jun 2019 22:15:16: 10000000 INFO @ Sun, 02 Jun 2019 22:15:22: 12000000 INFO @ Sun, 02 Jun 2019 22:15:23: 12000000 INFO @ Sun, 02 Jun 2019 22:15:25: 11000000 INFO @ Sun, 02 Jun 2019 22:15:30: 13000000 INFO @ Sun, 02 Jun 2019 22:15:30: 13000000 INFO @ Sun, 02 Jun 2019 22:15:33: 12000000 INFO @ Sun, 02 Jun 2019 22:15:37: 14000000 INFO @ Sun, 02 Jun 2019 22:15:37: 14000000 INFO @ Sun, 02 Jun 2019 22:15:41: 13000000 INFO @ Sun, 02 Jun 2019 22:15:44: 15000000 INFO @ Sun, 02 Jun 2019 22:15:44: 15000000 INFO @ Sun, 02 Jun 2019 22:15:49: 14000000 INFO @ Sun, 02 Jun 2019 22:15:51: 16000000 INFO @ Sun, 02 Jun 2019 22:15:51: 16000000 INFO @ Sun, 02 Jun 2019 22:15:57: 15000000 INFO @ Sun, 02 Jun 2019 22:15:58: 17000000 INFO @ Sun, 02 Jun 2019 22:15:58: 17000000 INFO @ Sun, 02 Jun 2019 22:15:59: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:15:59: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:15:59: #1 total tags in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:15:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:15:59: #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 22:15:59: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:15:59: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:15:59: #1 total tags in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:15:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:15:59: #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 22:15:59: #1 tags after filtering in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:15:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:15:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:15:59: #1 tags after filtering in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:15:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:15:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:15:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:15:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:16:01: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 22:16:01: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 22:16:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:16:01: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 22:16:01: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 22:16:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:16:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:16:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:16:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:16:01: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:16:01: #2 alternative fragment length(s) may be 1,32,546,554 bps INFO @ Sun, 02 Jun 2019 22:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05_model.r WARNING @ Sun, 02 Jun 2019 22:16:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:16:01: #2 You may need to consider one of the other alternative d(s): 1,32,546,554 WARNING @ Sun, 02 Jun 2019 22:16:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:16:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:16:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:16:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:16:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:16:01: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:16:01: #2 alternative fragment length(s) may be 1,32,546,554 bps INFO @ Sun, 02 Jun 2019 22:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10_model.r WARNING @ Sun, 02 Jun 2019 22:16:01: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:16:01: #2 You may need to consider one of the other alternative d(s): 1,32,546,554 WARNING @ Sun, 02 Jun 2019 22:16:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:16:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:16:05: 16000000 INFO @ Sun, 02 Jun 2019 22:16:13: 17000000 INFO @ Sun, 02 Jun 2019 22:16:14: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 22:16:14: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 22:16:14: #1 total tags in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:16:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:16:14: #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 22:16:15: #1 tags after filtering in treatment: 17086408 INFO @ Sun, 02 Jun 2019 22:16:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:16:15: #1 finished! INFO @ Sun, 02 Jun 2019 22:16:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:16:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:16:16: #2 number of paired peaks: 186 WARNING @ Sun, 02 Jun 2019 22:16:16: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Sun, 02 Jun 2019 22:16:16: start model_add_line... INFO @ Sun, 02 Jun 2019 22:16:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:16:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:16:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:16:16: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:16:16: #2 alternative fragment length(s) may be 1,32,546,554 bps INFO @ Sun, 02 Jun 2019 22:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20_model.r WARNING @ Sun, 02 Jun 2019 22:16:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:16:16: #2 You may need to consider one of the other alternative d(s): 1,32,546,554 WARNING @ Sun, 02 Jun 2019 22:16:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 22:16:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:16:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:16:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:16:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.10_summits.bed INFO @ Sun, 02 Jun 2019 22:16:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:16:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:16:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:16:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.05_summits.bed INFO @ Sun, 02 Jun 2019 22:16:58: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529211/SRX529211.20_summits.bed INFO @ Sun, 02 Jun 2019 22:17:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。