Job ID = 1293098 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:45:42 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' 2019-06-02T12:45:42 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/sra36/SRR/001236/SRR1265816' 2019-06-02T12:45:47 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' 2019-06-02T12:45:47 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/sra36/SRR/001236/SRR1265816' 2019-06-02T12:45:47 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1265816' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T12:45:47 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 23,070,060 reads read : 23,070,060 reads written : 23,070,060 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: 00:03:35 23070060 reads; of these: 23070060 (100.00%) were unpaired; of these: 5700678 (24.71%) aligned 0 times 15029303 (65.15%) aligned exactly 1 time 2340079 (10.14%) aligned >1 times 75.29% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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 8 files... [bam_rmdupse_core] 2620509 / 17369382 = 0.1509 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 22:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.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 22:09:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.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 22:09:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.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 22:09:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:09:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:09:47: 1000000 INFO @ Sun, 02 Jun 2019 22:09:48: 1000000 INFO @ Sun, 02 Jun 2019 22:09:49: 1000000 INFO @ Sun, 02 Jun 2019 22:09:54: 2000000 INFO @ Sun, 02 Jun 2019 22:09:55: 2000000 INFO @ Sun, 02 Jun 2019 22:09:59: 2000000 INFO @ Sun, 02 Jun 2019 22:10:01: 3000000 INFO @ Sun, 02 Jun 2019 22:10:03: 3000000 INFO @ Sun, 02 Jun 2019 22:10:08: 4000000 INFO @ Sun, 02 Jun 2019 22:10:09: 3000000 INFO @ Sun, 02 Jun 2019 22:10:10: 4000000 INFO @ Sun, 02 Jun 2019 22:10:16: 5000000 INFO @ Sun, 02 Jun 2019 22:10:18: 5000000 INFO @ Sun, 02 Jun 2019 22:10:18: 4000000 INFO @ Sun, 02 Jun 2019 22:10:23: 6000000 INFO @ Sun, 02 Jun 2019 22:10:26: 6000000 INFO @ Sun, 02 Jun 2019 22:10:28: 5000000 INFO @ Sun, 02 Jun 2019 22:10:30: 7000000 INFO @ Sun, 02 Jun 2019 22:10:34: 7000000 INFO @ Sun, 02 Jun 2019 22:10:37: 8000000 INFO @ Sun, 02 Jun 2019 22:10:37: 6000000 INFO @ Sun, 02 Jun 2019 22:10:41: 8000000 INFO @ Sun, 02 Jun 2019 22:10:44: 9000000 INFO @ Sun, 02 Jun 2019 22:10:46: 7000000 INFO @ Sun, 02 Jun 2019 22:10:49: 9000000 INFO @ Sun, 02 Jun 2019 22:10:51: 10000000 INFO @ Sun, 02 Jun 2019 22:10:55: 8000000 INFO @ Sun, 02 Jun 2019 22:10:56: 10000000 INFO @ Sun, 02 Jun 2019 22:10:58: 11000000 INFO @ Sun, 02 Jun 2019 22:11:04: 11000000 INFO @ Sun, 02 Jun 2019 22:11:04: 9000000 INFO @ Sun, 02 Jun 2019 22:11:05: 12000000 INFO @ Sun, 02 Jun 2019 22:11:12: 12000000 INFO @ Sun, 02 Jun 2019 22:11:12: 13000000 INFO @ Sun, 02 Jun 2019 22:11:13: 10000000 INFO @ Sun, 02 Jun 2019 22:11:19: 14000000 INFO @ Sun, 02 Jun 2019 22:11:19: 13000000 INFO @ Sun, 02 Jun 2019 22:11:22: 11000000 INFO @ Sun, 02 Jun 2019 22:11:24: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:11:24: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:11:24: #1 total tags in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:24: #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 22:11:24: #1 tags after filtering in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:24: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:25: #2 number of paired peaks: 139 WARNING @ Sun, 02 Jun 2019 22:11:25: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 02 Jun 2019 22:11:25: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:25: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:26: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:26: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:26: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 22:11:26: #2 alternative fragment length(s) may be 2,34,487,574 bps INFO @ Sun, 02 Jun 2019 22:11:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10_model.r WARNING @ Sun, 02 Jun 2019 22:11:26: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:11:26: #2 You may need to consider one of the other alternative d(s): 2,34,487,574 WARNING @ Sun, 02 Jun 2019 22:11:26: #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 22:11:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:11:27: 14000000 INFO @ Sun, 02 Jun 2019 22:11:32: 12000000 INFO @ Sun, 02 Jun 2019 22:11:32: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:11:32: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:11:32: #1 total tags in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:32: #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 22:11:33: #1 tags after filtering in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:34: #2 number of paired peaks: 139 WARNING @ Sun, 02 Jun 2019 22:11:34: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 02 Jun 2019 22:11:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:34: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:34: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:34: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:34: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 22:11:34: #2 alternative fragment length(s) may be 2,34,487,574 bps INFO @ Sun, 02 Jun 2019 22:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05_model.r WARNING @ Sun, 02 Jun 2019 22:11:34: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:11:34: #2 You may need to consider one of the other alternative d(s): 2,34,487,574 WARNING @ Sun, 02 Jun 2019 22:11:34: #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 22:11:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:11:41: 13000000 INFO @ Sun, 02 Jun 2019 22:11:49: 14000000 INFO @ Sun, 02 Jun 2019 22:11:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:11:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:11:56: #1 total tags in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:56: #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 22:11:56: #1 tags after filtering in treatment: 14748873 INFO @ Sun, 02 Jun 2019 22:11:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:57: #2 number of paired peaks: 139 WARNING @ Sun, 02 Jun 2019 22:11:57: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Sun, 02 Jun 2019 22:11:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:58: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:58: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:58: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:58: #2 predicted fragment length is 34 bps INFO @ Sun, 02 Jun 2019 22:11:58: #2 alternative fragment length(s) may be 2,34,487,574 bps INFO @ Sun, 02 Jun 2019 22:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20_model.r WARNING @ Sun, 02 Jun 2019 22:11:58: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:11:58: #2 You may need to consider one of the other alternative d(s): 2,34,487,574 WARNING @ Sun, 02 Jun 2019 22:11:58: #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 22:11:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:12:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:12:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.10_summits.bed INFO @ Sun, 02 Jun 2019 22:12:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (298 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.05_summits.bed INFO @ Sun, 02 Jun 2019 22:12:27: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1622 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:12:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529212/SRX529212.20_summits.bed INFO @ Sun, 02 Jun 2019 22:12:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (49 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。