Job ID = 1293052 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:30:42 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' 2019-06-02T12:30:42 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/sos/sra-pub-run-1/SRR8201439/SRR8201439.1' 2019-06-02T12:30:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8201439' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T12:30:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 14,097,384 reads read : 14,097,384 reads written : 14,097,384 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: 00:03:39 14097384 reads; of these: 14097384 (100.00%) were unpaired; of these: 258920 (1.84%) aligned 0 times 11500479 (81.58%) aligned exactly 1 time 2337985 (16.58%) aligned >1 times 98.16% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 1083408 / 13838464 = 0.0783 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 21:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.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 21:42:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.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 21:42:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.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 21:42:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:42:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:42:32: 1000000 INFO @ Sun, 02 Jun 2019 21:42:33: 1000000 INFO @ Sun, 02 Jun 2019 21:42:33: 1000000 INFO @ Sun, 02 Jun 2019 21:42:41: 2000000 INFO @ Sun, 02 Jun 2019 21:42:43: 2000000 INFO @ Sun, 02 Jun 2019 21:42:43: 2000000 INFO @ Sun, 02 Jun 2019 21:42:50: 3000000 INFO @ Sun, 02 Jun 2019 21:42:53: 3000000 INFO @ Sun, 02 Jun 2019 21:42:53: 3000000 INFO @ Sun, 02 Jun 2019 21:42:59: 4000000 INFO @ Sun, 02 Jun 2019 21:43:03: 4000000 INFO @ Sun, 02 Jun 2019 21:43:03: 4000000 INFO @ Sun, 02 Jun 2019 21:43:07: 5000000 INFO @ Sun, 02 Jun 2019 21:43:12: 5000000 INFO @ Sun, 02 Jun 2019 21:43:13: 5000000 INFO @ Sun, 02 Jun 2019 21:43:16: 6000000 INFO @ Sun, 02 Jun 2019 21:43:22: 6000000 INFO @ Sun, 02 Jun 2019 21:43:23: 6000000 INFO @ Sun, 02 Jun 2019 21:43:25: 7000000 INFO @ Sun, 02 Jun 2019 21:43:31: 7000000 INFO @ Sun, 02 Jun 2019 21:43:32: 7000000 INFO @ Sun, 02 Jun 2019 21:43:33: 8000000 INFO @ Sun, 02 Jun 2019 21:43:40: 8000000 INFO @ Sun, 02 Jun 2019 21:43:42: 9000000 INFO @ Sun, 02 Jun 2019 21:43:42: 8000000 INFO @ Sun, 02 Jun 2019 21:43:50: 9000000 INFO @ Sun, 02 Jun 2019 21:43:50: 10000000 INFO @ Sun, 02 Jun 2019 21:43:52: 9000000 INFO @ Sun, 02 Jun 2019 21:43:59: 10000000 INFO @ Sun, 02 Jun 2019 21:43:59: 11000000 INFO @ Sun, 02 Jun 2019 21:44:01: 10000000 INFO @ Sun, 02 Jun 2019 21:44:08: 12000000 INFO @ Sun, 02 Jun 2019 21:44:08: 11000000 INFO @ Sun, 02 Jun 2019 21:44:11: 11000000 INFO @ Sun, 02 Jun 2019 21:44:15: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:44:15: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:44:15: #1 total tags in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:15: #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 21:44:15: #1 tags after filtering in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:15: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:16: #2 number of paired peaks: 281 WARNING @ Sun, 02 Jun 2019 21:44:16: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:16: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:16: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:16: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:16: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:16: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:44:16: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 21:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20_model.r WARNING @ Sun, 02 Jun 2019 21:44:16: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:16: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 21:44:16: #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 21:44:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:17: 12000000 INFO @ Sun, 02 Jun 2019 21:44:21: 12000000 INFO @ Sun, 02 Jun 2019 21:44:24: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:44:24: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:44:24: #1 total tags in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:24: #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 21:44:25: #1 tags after filtering in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:25: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:26: #2 number of paired peaks: 281 WARNING @ Sun, 02 Jun 2019 21:44:26: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:26: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:26: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:26: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:26: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:26: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:44:26: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 21:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05_model.r WARNING @ Sun, 02 Jun 2019 21:44:26: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:26: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 21:44:26: #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 21:44:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:28: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:44:28: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:44:28: #1 total tags in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:44:28: #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 21:44:29: #1 tags after filtering in treatment: 12755056 INFO @ Sun, 02 Jun 2019 21:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:44:29: #1 finished! INFO @ Sun, 02 Jun 2019 21:44:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:44:30: #2 number of paired peaks: 281 WARNING @ Sun, 02 Jun 2019 21:44:30: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 02 Jun 2019 21:44:30: start model_add_line... INFO @ Sun, 02 Jun 2019 21:44:30: start X-correlation... INFO @ Sun, 02 Jun 2019 21:44:30: end of X-cor INFO @ Sun, 02 Jun 2019 21:44:30: #2 finished! INFO @ Sun, 02 Jun 2019 21:44:30: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:44:30: #2 alternative fragment length(s) may be 2,49 bps INFO @ Sun, 02 Jun 2019 21:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10_model.r WARNING @ Sun, 02 Jun 2019 21:44:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:44:30: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Sun, 02 Jun 2019 21:44:30: #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 21:44:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:44:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:44:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:45:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.20_summits.bed INFO @ Sun, 02 Jun 2019 21:45:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.05_summits.bed INFO @ Sun, 02 Jun 2019 21:45:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020816/SRX5020816.10_summits.bed INFO @ Sun, 02 Jun 2019 21:45:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。