Job ID = 1292549 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T10:25:21 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' 2019-06-02T10:25:21 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/SRR1163628/SRR1163628.1' 2019-06-02T10:25:21 fasterq-dump.2.9.6 err: invalid accession 'SRR1163628' spots read : 15,485,332 reads read : 15,485,332 reads written : 15,485,332 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: 00:03:09 15485332 reads; of these: 15485332 (100.00%) were unpaired; of these: 1060796 (6.85%) aligned 0 times 11552848 (74.61%) aligned exactly 1 time 2871688 (18.54%) aligned >1 times 93.15% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 2634743 / 14424536 = 0.1827 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 19:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.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 19:34:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.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 19:34:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.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 19:34:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:34:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:34:31: 1000000 INFO @ Sun, 02 Jun 2019 19:34:32: 1000000 INFO @ Sun, 02 Jun 2019 19:34:32: 1000000 INFO @ Sun, 02 Jun 2019 19:34:38: 2000000 INFO @ Sun, 02 Jun 2019 19:34:40: 2000000 INFO @ Sun, 02 Jun 2019 19:34:40: 2000000 INFO @ Sun, 02 Jun 2019 19:34:46: 3000000 INFO @ Sun, 02 Jun 2019 19:34:48: 3000000 INFO @ Sun, 02 Jun 2019 19:34:49: 3000000 INFO @ Sun, 02 Jun 2019 19:34:53: 4000000 INFO @ Sun, 02 Jun 2019 19:34:57: 4000000 INFO @ Sun, 02 Jun 2019 19:34:57: 4000000 INFO @ Sun, 02 Jun 2019 19:35:01: 5000000 INFO @ Sun, 02 Jun 2019 19:35:05: 5000000 INFO @ Sun, 02 Jun 2019 19:35:05: 5000000 INFO @ Sun, 02 Jun 2019 19:35:08: 6000000 INFO @ Sun, 02 Jun 2019 19:35:13: 6000000 INFO @ Sun, 02 Jun 2019 19:35:14: 6000000 INFO @ Sun, 02 Jun 2019 19:35:16: 7000000 INFO @ Sun, 02 Jun 2019 19:35:21: 7000000 INFO @ Sun, 02 Jun 2019 19:35:22: 7000000 INFO @ Sun, 02 Jun 2019 19:35:23: 8000000 INFO @ Sun, 02 Jun 2019 19:35:30: 8000000 INFO @ Sun, 02 Jun 2019 19:35:30: 8000000 INFO @ Sun, 02 Jun 2019 19:35:30: 9000000 INFO @ Sun, 02 Jun 2019 19:35:38: 9000000 INFO @ Sun, 02 Jun 2019 19:35:38: 10000000 INFO @ Sun, 02 Jun 2019 19:35:40: 9000000 INFO @ Sun, 02 Jun 2019 19:35:46: 11000000 INFO @ Sun, 02 Jun 2019 19:35:46: 10000000 INFO @ Sun, 02 Jun 2019 19:35:48: 10000000 INFO @ Sun, 02 Jun 2019 19:35:52: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:35:52: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:35:52: #1 total tags in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:35:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:35:52: #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 19:35:52: #1 tags after filtering in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:35:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:35:52: #1 finished! INFO @ Sun, 02 Jun 2019 19:35:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:35:53: #2 number of paired peaks: 354 WARNING @ Sun, 02 Jun 2019 19:35:53: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sun, 02 Jun 2019 19:35:53: start model_add_line... INFO @ Sun, 02 Jun 2019 19:35:53: start X-correlation... INFO @ Sun, 02 Jun 2019 19:35:53: end of X-cor INFO @ Sun, 02 Jun 2019 19:35:53: #2 finished! INFO @ Sun, 02 Jun 2019 19:35:53: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 19:35:53: #2 alternative fragment length(s) may be 2,38 bps INFO @ Sun, 02 Jun 2019 19:35:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10_model.r WARNING @ Sun, 02 Jun 2019 19:35:53: #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 19:35:53: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Sun, 02 Jun 2019 19:35:53: #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 19:35:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:35:54: 11000000 INFO @ Sun, 02 Jun 2019 19:35:57: 11000000 INFO @ Sun, 02 Jun 2019 19:36:00: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:36:00: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:36:00: #1 total tags in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:36:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:00: #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 19:36:01: #1 tags after filtering in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:36:01: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:02: #2 number of paired peaks: 354 WARNING @ Sun, 02 Jun 2019 19:36:02: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:02: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:02: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:02: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:02: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:02: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 19:36:02: #2 alternative fragment length(s) may be 2,38 bps INFO @ Sun, 02 Jun 2019 19:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05_model.r WARNING @ Sun, 02 Jun 2019 19:36:02: #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 19:36:02: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Sun, 02 Jun 2019 19:36:02: #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 19:36:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:36:03: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:36:03: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:36:03: #1 total tags in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:36:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:36:03: #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 19:36:04: #1 tags after filtering in treatment: 11789793 INFO @ Sun, 02 Jun 2019 19:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:36:04: #1 finished! INFO @ Sun, 02 Jun 2019 19:36:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:36:05: #2 number of paired peaks: 354 WARNING @ Sun, 02 Jun 2019 19:36:05: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Sun, 02 Jun 2019 19:36:05: start model_add_line... INFO @ Sun, 02 Jun 2019 19:36:05: start X-correlation... INFO @ Sun, 02 Jun 2019 19:36:05: end of X-cor INFO @ Sun, 02 Jun 2019 19:36:05: #2 finished! INFO @ Sun, 02 Jun 2019 19:36:05: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 19:36:05: #2 alternative fragment length(s) may be 2,38 bps INFO @ Sun, 02 Jun 2019 19:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20_model.r WARNING @ Sun, 02 Jun 2019 19:36:05: #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 19:36:05: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Sun, 02 Jun 2019 19:36:05: #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 19:36:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:36:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:36:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:36:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.10_summits.bed INFO @ Sun, 02 Jun 2019 19:36:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:36:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:36:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:36:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.05_summits.bed INFO @ Sun, 02 Jun 2019 19:36:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466562/SRX466562.20_summits.bed INFO @ Sun, 02 Jun 2019 19:36:47: 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。