Job ID = 1293011 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:20:28 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' 2019-06-02T12:20:28 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/SRR8201406/SRR8201406.1' 2019-06-02T12:20:28 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' 2019-06-02T12:20:28 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/SRR8201406/SRR8201406.1' 2019-06-02T12:20:33 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' 2019-06-02T12:20:33 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/SRR8201406/SRR8201406.1' 2019-06-02T12:20:33 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8201406' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T12:20:33 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T12:20:39 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR8201406' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T12:20:39 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 6,972,757 reads read : 6,972,757 reads written : 6,972,757 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: 00:01:36 6972757 reads; of these: 6972757 (100.00%) were unpaired; of these: 1541815 (22.11%) aligned 0 times 4454992 (63.89%) aligned exactly 1 time 975950 (14.00%) aligned >1 times 77.89% overall alignment rate Time searching: 00:01:36 Overall time: 00:01:36 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_rmdupse_core] 501651 / 5430942 = 0.0924 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 21:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.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 21:26:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.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 21:26:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.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 21:26:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:19: 1000000 INFO @ Sun, 02 Jun 2019 21:26:20: 1000000 INFO @ Sun, 02 Jun 2019 21:26:21: 1000000 INFO @ Sun, 02 Jun 2019 21:26:26: 2000000 INFO @ Sun, 02 Jun 2019 21:26:27: 2000000 INFO @ Sun, 02 Jun 2019 21:26:29: 2000000 INFO @ Sun, 02 Jun 2019 21:26:33: 3000000 INFO @ Sun, 02 Jun 2019 21:26:35: 3000000 INFO @ Sun, 02 Jun 2019 21:26:38: 3000000 INFO @ Sun, 02 Jun 2019 21:26:39: 4000000 INFO @ Sun, 02 Jun 2019 21:26:43: 4000000 INFO @ Sun, 02 Jun 2019 21:26:46: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:26:46: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:26:46: #1 total tags in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:26:46: #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 21:26:46: #1 tags after filtering in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:26:46: #1 finished! INFO @ Sun, 02 Jun 2019 21:26:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:26:46: 4000000 INFO @ Sun, 02 Jun 2019 21:26:46: #2 number of paired peaks: 519 WARNING @ Sun, 02 Jun 2019 21:26:46: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sun, 02 Jun 2019 21:26:46: start model_add_line... INFO @ Sun, 02 Jun 2019 21:26:46: start X-correlation... INFO @ Sun, 02 Jun 2019 21:26:46: end of X-cor INFO @ Sun, 02 Jun 2019 21:26:46: #2 finished! INFO @ Sun, 02 Jun 2019 21:26:46: #2 predicted fragment length is 62 bps INFO @ Sun, 02 Jun 2019 21:26:46: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 02 Jun 2019 21:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10_model.r WARNING @ Sun, 02 Jun 2019 21:26:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:26:46: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 02 Jun 2019 21:26:46: #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 21:26:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:26:49: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:26:49: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:26:49: #1 total tags in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:26:49: #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 21:26:50: #1 tags after filtering in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:26:50: #1 finished! INFO @ Sun, 02 Jun 2019 21:26:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:26:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:26:50: #2 number of paired peaks: 519 WARNING @ Sun, 02 Jun 2019 21:26:50: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sun, 02 Jun 2019 21:26:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:26:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:26:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:26:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:26:50: #2 predicted fragment length is 62 bps INFO @ Sun, 02 Jun 2019 21:26:50: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 02 Jun 2019 21:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05_model.r WARNING @ Sun, 02 Jun 2019 21:26:50: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:26:50: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 02 Jun 2019 21:26:50: #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 21:26:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:26:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:26:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:26:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:26:53: #1 total tags in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:26:53: #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 21:26:53: #1 tags after filtering in treatment: 4929291 INFO @ Sun, 02 Jun 2019 21:26:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:26:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:26:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:26:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:26:54: #2 number of paired peaks: 519 WARNING @ Sun, 02 Jun 2019 21:26:54: Fewer paired peaks (519) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 519 pairs to build model! INFO @ Sun, 02 Jun 2019 21:26:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:26:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:26:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:26:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:26:54: #2 predicted fragment length is 62 bps INFO @ Sun, 02 Jun 2019 21:26:54: #2 alternative fragment length(s) may be 62 bps INFO @ Sun, 02 Jun 2019 21:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20_model.r WARNING @ Sun, 02 Jun 2019 21:26:54: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:26:54: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sun, 02 Jun 2019 21:26:54: #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 21:26:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:27:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.10_summits.bed INFO @ Sun, 02 Jun 2019 21:27:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:27:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.05_summits.bed INFO @ Sun, 02 Jun 2019 21:27:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (976 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020783/SRX5020783.20_summits.bed INFO @ Sun, 02 Jun 2019 21:27:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。