Job ID = 1293096 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/sra18/SRR/001236/SRR1265814' 2019-06-02T12:45:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1265814' ) -> 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 : 19,555,555 reads read : 19,555,555 reads written : 19,555,555 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: 00:02:45 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8713207 (44.56%) aligned 0 times 9073493 (46.40%) aligned exactly 1 time 1768855 (9.05%) aligned >1 times 55.44% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 648258 / 10842348 = 0.0598 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 22:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.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 22:06:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:06:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.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 22:06:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:06:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.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 22:06:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:06:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:06:48: 1000000 INFO @ Sun, 02 Jun 2019 22:06:49: 1000000 INFO @ Sun, 02 Jun 2019 22:06:51: 1000000 INFO @ Sun, 02 Jun 2019 22:06:56: 2000000 INFO @ Sun, 02 Jun 2019 22:06:56: 2000000 INFO @ Sun, 02 Jun 2019 22:06:59: 2000000 INFO @ Sun, 02 Jun 2019 22:07:04: 3000000 INFO @ Sun, 02 Jun 2019 22:07:04: 3000000 INFO @ Sun, 02 Jun 2019 22:07:08: 3000000 INFO @ Sun, 02 Jun 2019 22:07:11: 4000000 INFO @ Sun, 02 Jun 2019 22:07:11: 4000000 INFO @ Sun, 02 Jun 2019 22:07:16: 4000000 INFO @ Sun, 02 Jun 2019 22:07:19: 5000000 INFO @ Sun, 02 Jun 2019 22:07:19: 5000000 INFO @ Sun, 02 Jun 2019 22:07:24: 5000000 INFO @ Sun, 02 Jun 2019 22:07:26: 6000000 INFO @ Sun, 02 Jun 2019 22:07:26: 6000000 INFO @ Sun, 02 Jun 2019 22:07:33: 6000000 INFO @ Sun, 02 Jun 2019 22:07:33: 7000000 INFO @ Sun, 02 Jun 2019 22:07:34: 7000000 INFO @ Sun, 02 Jun 2019 22:07:41: 7000000 INFO @ Sun, 02 Jun 2019 22:07:41: 8000000 INFO @ Sun, 02 Jun 2019 22:07:41: 8000000 INFO @ Sun, 02 Jun 2019 22:07:48: 9000000 INFO @ Sun, 02 Jun 2019 22:07:49: 9000000 INFO @ Sun, 02 Jun 2019 22:07:49: 8000000 INFO @ Sun, 02 Jun 2019 22:07:56: 10000000 INFO @ Sun, 02 Jun 2019 22:07:56: 10000000 INFO @ Sun, 02 Jun 2019 22:07:57: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:07:57: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:07:57: #1 total tags in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:07:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:57: #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 22:07:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:07:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:07:58: #1 total tags in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:07:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:58: #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 22:07:58: #1 tags after filtering in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:58: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:58: #1 tags after filtering in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:58: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:58: 9000000 INFO @ Sun, 02 Jun 2019 22:07:59: #2 number of paired peaks: 240 WARNING @ Sun, 02 Jun 2019 22:07:59: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:59: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 22:07:59: #2 alternative fragment length(s) may be 3,31,567,569,592 bps INFO @ Sun, 02 Jun 2019 22:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10_model.r WARNING @ Sun, 02 Jun 2019 22:07:59: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:07:59: #2 You may need to consider one of the other alternative d(s): 3,31,567,569,592 WARNING @ Sun, 02 Jun 2019 22:07:59: #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 22:07:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:59: #2 number of paired peaks: 240 WARNING @ Sun, 02 Jun 2019 22:07:59: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:59: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 22:07:59: #2 alternative fragment length(s) may be 3,31,567,569,592 bps INFO @ Sun, 02 Jun 2019 22:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05_model.r WARNING @ Sun, 02 Jun 2019 22:07:59: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:07:59: #2 You may need to consider one of the other alternative d(s): 3,31,567,569,592 WARNING @ Sun, 02 Jun 2019 22:07:59: #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 22:07:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:08:07: 10000000 INFO @ Sun, 02 Jun 2019 22:08:08: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:08:08: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:08:08: #1 total tags in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:08:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:08:08: #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 22:08:09: #1 tags after filtering in treatment: 10194090 INFO @ Sun, 02 Jun 2019 22:08:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:08:09: #1 finished! INFO @ Sun, 02 Jun 2019 22:08:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:08:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:08:10: #2 number of paired peaks: 240 WARNING @ Sun, 02 Jun 2019 22:08:10: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Sun, 02 Jun 2019 22:08:10: start model_add_line... INFO @ Sun, 02 Jun 2019 22:08:10: start X-correlation... INFO @ Sun, 02 Jun 2019 22:08:10: end of X-cor INFO @ Sun, 02 Jun 2019 22:08:10: #2 finished! INFO @ Sun, 02 Jun 2019 22:08:10: #2 predicted fragment length is 31 bps INFO @ Sun, 02 Jun 2019 22:08:10: #2 alternative fragment length(s) may be 3,31,567,569,592 bps INFO @ Sun, 02 Jun 2019 22:08:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20_model.r WARNING @ Sun, 02 Jun 2019 22:08:10: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:08:10: #2 You may need to consider one of the other alternative d(s): 3,31,567,569,592 WARNING @ Sun, 02 Jun 2019 22:08:10: #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 22:08:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:08:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:08:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.10_summits.bed INFO @ Sun, 02 Jun 2019 22:08:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.05_summits.bed INFO @ Sun, 02 Jun 2019 22:08:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529210/SRX529210.20_summits.bed INFO @ Sun, 02 Jun 2019 22:08:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (59 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。