Job ID = 1292408 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,561,597 reads read : 11,123,194 reads written : 5,561,597 reads 0-length : 5,561,597 2019-06-02T09:20:27 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' 2019-06-02T09:20:27 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/sra64/SRR/007120/SRR7291459' 2019-06-02T09:20:27 fasterq-dump.2.9.6 err: invalid accession 'SRR7291459' spots read : 5,451,568 reads read : 10,903,136 reads written : 5,451,568 reads 0-length : 5,451,568 spots read : 5,560,025 reads read : 11,120,050 reads written : 5,560,025 reads 0-length : 5,560,025 spots read : 5,386,837 reads read : 10,773,674 reads written : 5,386,837 reads 0-length : 5,386,837 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: 00:10:00 21960027 reads; of these: 21960027 (100.00%) were unpaired; of these: 557619 (2.54%) aligned 0 times 15998065 (72.85%) aligned exactly 1 time 5404343 (24.61%) aligned >1 times 97.46% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 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 12 files... [bam_rmdupse_core] 5348480 / 21402408 = 0.2499 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 18:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.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 18:50:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.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 18:50:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:50:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:50:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.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 18:50:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:50:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:50:16: 1000000 INFO @ Sun, 02 Jun 2019 18:50:18: 1000000 INFO @ Sun, 02 Jun 2019 18:50:19: 1000000 INFO @ Sun, 02 Jun 2019 18:50:26: 2000000 INFO @ Sun, 02 Jun 2019 18:50:30: 2000000 INFO @ Sun, 02 Jun 2019 18:50:31: 2000000 INFO @ Sun, 02 Jun 2019 18:50:35: 3000000 INFO @ Sun, 02 Jun 2019 18:50:41: 3000000 INFO @ Sun, 02 Jun 2019 18:50:44: 3000000 INFO @ Sun, 02 Jun 2019 18:50:45: 4000000 INFO @ Sun, 02 Jun 2019 18:50:53: 4000000 INFO @ Sun, 02 Jun 2019 18:50:55: 5000000 INFO @ Sun, 02 Jun 2019 18:50:56: 4000000 INFO @ Sun, 02 Jun 2019 18:51:04: 5000000 INFO @ Sun, 02 Jun 2019 18:51:05: 6000000 INFO @ Sun, 02 Jun 2019 18:51:08: 5000000 INFO @ Sun, 02 Jun 2019 18:51:15: 7000000 INFO @ Sun, 02 Jun 2019 18:51:16: 6000000 INFO @ Sun, 02 Jun 2019 18:51:21: 6000000 INFO @ Sun, 02 Jun 2019 18:51:25: 8000000 INFO @ Sun, 02 Jun 2019 18:51:28: 7000000 INFO @ Sun, 02 Jun 2019 18:51:34: 7000000 INFO @ Sun, 02 Jun 2019 18:51:35: 9000000 INFO @ Sun, 02 Jun 2019 18:51:39: 8000000 INFO @ Sun, 02 Jun 2019 18:51:45: 10000000 INFO @ Sun, 02 Jun 2019 18:51:46: 8000000 INFO @ Sun, 02 Jun 2019 18:51:51: 9000000 INFO @ Sun, 02 Jun 2019 18:51:55: 11000000 INFO @ Sun, 02 Jun 2019 18:51:59: 9000000 INFO @ Sun, 02 Jun 2019 18:52:03: 10000000 INFO @ Sun, 02 Jun 2019 18:52:04: 12000000 INFO @ Sun, 02 Jun 2019 18:52:12: 10000000 INFO @ Sun, 02 Jun 2019 18:52:14: 13000000 INFO @ Sun, 02 Jun 2019 18:52:15: 11000000 INFO @ Sun, 02 Jun 2019 18:52:24: 11000000 INFO @ Sun, 02 Jun 2019 18:52:24: 14000000 INFO @ Sun, 02 Jun 2019 18:52:26: 12000000 INFO @ Sun, 02 Jun 2019 18:52:33: 15000000 INFO @ Sun, 02 Jun 2019 18:52:36: 12000000 INFO @ Sun, 02 Jun 2019 18:52:38: 13000000 INFO @ Sun, 02 Jun 2019 18:52:43: 16000000 INFO @ Sun, 02 Jun 2019 18:52:44: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 18:52:44: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 18:52:44: #1 total tags in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:52:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:52:44: #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 18:52:44: #1 tags after filtering in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:52:44: #1 finished! INFO @ Sun, 02 Jun 2019 18:52:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:52:46: #2 number of paired peaks: 556 WARNING @ Sun, 02 Jun 2019 18:52:46: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 02 Jun 2019 18:52:46: start model_add_line... INFO @ Sun, 02 Jun 2019 18:52:46: start X-correlation... INFO @ Sun, 02 Jun 2019 18:52:46: end of X-cor INFO @ Sun, 02 Jun 2019 18:52:46: #2 finished! INFO @ Sun, 02 Jun 2019 18:52:46: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:52:46: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Sun, 02 Jun 2019 18:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20_model.r WARNING @ Sun, 02 Jun 2019 18:52:46: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:52:46: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Sun, 02 Jun 2019 18:52:46: #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 18:52:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:52:48: 13000000 INFO @ Sun, 02 Jun 2019 18:52:50: 14000000 INFO @ Sun, 02 Jun 2019 18:52:59: 14000000 INFO @ Sun, 02 Jun 2019 18:53:01: 15000000 INFO @ Sun, 02 Jun 2019 18:53:12: 15000000 INFO @ Sun, 02 Jun 2019 18:53:13: 16000000 INFO @ Sun, 02 Jun 2019 18:53:14: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 18:53:14: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 18:53:14: #1 total tags in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:53:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:53:14: #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 18:53:14: #1 tags after filtering in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:53:14: #1 finished! INFO @ Sun, 02 Jun 2019 18:53:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:53:16: #2 number of paired peaks: 556 WARNING @ Sun, 02 Jun 2019 18:53:16: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 02 Jun 2019 18:53:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:53:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:53:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:53:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:53:16: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:53:16: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Sun, 02 Jun 2019 18:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05_model.r WARNING @ Sun, 02 Jun 2019 18:53:16: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:53:16: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Sun, 02 Jun 2019 18:53:16: #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 18:53:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:53:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:53:24: 16000000 INFO @ Sun, 02 Jun 2019 18:53:24: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 18:53:24: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 18:53:24: #1 total tags in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:53:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:53:24: #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 18:53:25: #1 tags after filtering in treatment: 16053928 INFO @ Sun, 02 Jun 2019 18:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:53:25: #1 finished! INFO @ Sun, 02 Jun 2019 18:53:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:53:26: #2 number of paired peaks: 556 WARNING @ Sun, 02 Jun 2019 18:53:26: Fewer paired peaks (556) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 556 pairs to build model! INFO @ Sun, 02 Jun 2019 18:53:26: start model_add_line... INFO @ Sun, 02 Jun 2019 18:53:26: start X-correlation... INFO @ Sun, 02 Jun 2019 18:53:26: end of X-cor INFO @ Sun, 02 Jun 2019 18:53:26: #2 finished! INFO @ Sun, 02 Jun 2019 18:53:26: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 18:53:26: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Sun, 02 Jun 2019 18:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10_model.r WARNING @ Sun, 02 Jun 2019 18:53:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:53:26: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Sun, 02 Jun 2019 18:53:26: #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 18:53:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.20_summits.bed INFO @ Sun, 02 Jun 2019 18:53:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:53:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:54:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.05_summits.bed INFO @ Sun, 02 Jun 2019 18:54:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194191/SRX4194191.10_summits.bed INFO @ Sun, 02 Jun 2019 18:54:20: 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。