Job ID = 1291861 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T07:40:44 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' 2019-06-02T07:40:44 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/sra35/SRR/000781/SRR800713' 2019-06-02T07:40:44 fasterq-dump.2.9.6 err: invalid accession 'SRR800713' spots read : 13,338,445 reads read : 13,338,445 reads written : 13,338,445 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:41 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88994 (0.67%) aligned 0 times 10992286 (82.41%) aligned exactly 1 time 2257165 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 2113752 / 13249451 = 0.1595 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 16:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.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 16:54:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:54:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.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 16:54:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:54:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:54:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.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 16:54:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:54:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:54:13: 1000000 INFO @ Sun, 02 Jun 2019 16:54:13: 1000000 INFO @ Sun, 02 Jun 2019 16:54:15: 1000000 INFO @ Sun, 02 Jun 2019 16:54:20: 2000000 INFO @ Sun, 02 Jun 2019 16:54:20: 2000000 INFO @ Sun, 02 Jun 2019 16:54:24: 2000000 INFO @ Sun, 02 Jun 2019 16:54:28: 3000000 INFO @ Sun, 02 Jun 2019 16:54:28: 3000000 INFO @ Sun, 02 Jun 2019 16:54:33: 3000000 INFO @ Sun, 02 Jun 2019 16:54:35: 4000000 INFO @ Sun, 02 Jun 2019 16:54:35: 4000000 INFO @ Sun, 02 Jun 2019 16:54:42: 5000000 INFO @ Sun, 02 Jun 2019 16:54:43: 4000000 INFO @ Sun, 02 Jun 2019 16:54:43: 5000000 INFO @ Sun, 02 Jun 2019 16:54:50: 6000000 INFO @ Sun, 02 Jun 2019 16:54:52: 6000000 INFO @ Sun, 02 Jun 2019 16:54:52: 5000000 INFO @ Sun, 02 Jun 2019 16:54:57: 7000000 INFO @ Sun, 02 Jun 2019 16:55:00: 7000000 INFO @ Sun, 02 Jun 2019 16:55:02: 6000000 INFO @ Sun, 02 Jun 2019 16:55:04: 8000000 INFO @ Sun, 02 Jun 2019 16:55:07: 8000000 INFO @ Sun, 02 Jun 2019 16:55:11: 7000000 INFO @ Sun, 02 Jun 2019 16:55:11: 9000000 INFO @ Sun, 02 Jun 2019 16:55:15: 9000000 INFO @ Sun, 02 Jun 2019 16:55:18: 10000000 INFO @ Sun, 02 Jun 2019 16:55:20: 8000000 INFO @ Sun, 02 Jun 2019 16:55:22: 10000000 INFO @ Sun, 02 Jun 2019 16:55:25: 11000000 INFO @ Sun, 02 Jun 2019 16:55:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:55:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:55:26: #1 total tags in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:55:26: #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 16:55:27: #1 tags after filtering in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:55:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:55:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:55:28: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 16:55:28: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 16:55:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:55:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:55:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:55:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:55:28: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 16:55:28: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 16:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20_model.r WARNING @ Sun, 02 Jun 2019 16:55:28: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:55:28: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 16:55:28: #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 16:55:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:55:29: 9000000 INFO @ Sun, 02 Jun 2019 16:55:29: 11000000 INFO @ Sun, 02 Jun 2019 16:55:31: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:55:31: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:55:31: #1 total tags in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:55:31: #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 16:55:31: #1 tags after filtering in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:55:31: #1 finished! INFO @ Sun, 02 Jun 2019 16:55:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:55:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:55:32: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 16:55:32: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 16:55:32: start model_add_line... INFO @ Sun, 02 Jun 2019 16:55:32: start X-correlation... INFO @ Sun, 02 Jun 2019 16:55:32: end of X-cor INFO @ Sun, 02 Jun 2019 16:55:32: #2 finished! INFO @ Sun, 02 Jun 2019 16:55:32: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 16:55:32: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 16:55:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10_model.r WARNING @ Sun, 02 Jun 2019 16:55:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:55:32: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 16:55:32: #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 16:55:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:55:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:55:38: 10000000 INFO @ Sun, 02 Jun 2019 16:55:47: 11000000 INFO @ Sun, 02 Jun 2019 16:55:48: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:55:48: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:55:48: #1 total tags in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:55:48: #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 16:55:48: #1 tags after filtering in treatment: 11135699 INFO @ Sun, 02 Jun 2019 16:55:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:55:48: #1 finished! INFO @ Sun, 02 Jun 2019 16:55:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:55:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:55:49: #2 number of paired peaks: 382 WARNING @ Sun, 02 Jun 2019 16:55:49: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Sun, 02 Jun 2019 16:55:49: start model_add_line... INFO @ Sun, 02 Jun 2019 16:55:49: start X-correlation... INFO @ Sun, 02 Jun 2019 16:55:49: end of X-cor INFO @ Sun, 02 Jun 2019 16:55:49: #2 finished! INFO @ Sun, 02 Jun 2019 16:55:49: #2 predicted fragment length is 41 bps INFO @ Sun, 02 Jun 2019 16:55:49: #2 alternative fragment length(s) may be 2,41 bps INFO @ Sun, 02 Jun 2019 16:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05_model.r WARNING @ Sun, 02 Jun 2019 16:55:49: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:55:49: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Sun, 02 Jun 2019 16:55:49: #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 16:55:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:55:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:56:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.20_summits.bed INFO @ Sun, 02 Jun 2019 16:56:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.10_summits.bed INFO @ Sun, 02 Jun 2019 16:56:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:56:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257696/SRX257696.05_summits.bed INFO @ Sun, 02 Jun 2019 16:56:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (939 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。