Job ID = 1293099 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:45:33 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' 2019-06-02T12:45:33 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/sra27/SRR/001236/SRR1265817' 2019-06-02T12:45:42 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR1265817', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 19,253,374 reads read : 19,253,374 reads written : 19,253,374 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: 00:03:53 19253374 reads; of these: 19253374 (100.00%) were unpaired; of these: 168382 (0.87%) aligned 0 times 16238793 (84.34%) aligned exactly 1 time 2846199 (14.78%) aligned >1 times 99.13% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1844563 / 19084992 = 0.0966 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 22:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.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 22:01:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.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 22:01:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.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 22:01:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:01:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:01:52: 1000000 INFO @ Sun, 02 Jun 2019 22:01:53: 1000000 INFO @ Sun, 02 Jun 2019 22:01:53: 1000000 INFO @ Sun, 02 Jun 2019 22:02:02: 2000000 INFO @ Sun, 02 Jun 2019 22:02:02: 2000000 INFO @ Sun, 02 Jun 2019 22:02:03: 2000000 INFO @ Sun, 02 Jun 2019 22:02:11: 3000000 INFO @ Sun, 02 Jun 2019 22:02:12: 3000000 INFO @ Sun, 02 Jun 2019 22:02:13: 3000000 INFO @ Sun, 02 Jun 2019 22:02:21: 4000000 INFO @ Sun, 02 Jun 2019 22:02:21: 4000000 INFO @ Sun, 02 Jun 2019 22:02:23: 4000000 INFO @ Sun, 02 Jun 2019 22:02:30: 5000000 INFO @ Sun, 02 Jun 2019 22:02:31: 5000000 INFO @ Sun, 02 Jun 2019 22:02:33: 5000000 INFO @ Sun, 02 Jun 2019 22:02:41: 6000000 INFO @ Sun, 02 Jun 2019 22:02:41: 6000000 INFO @ Sun, 02 Jun 2019 22:02:43: 6000000 INFO @ Sun, 02 Jun 2019 22:02:51: 7000000 INFO @ Sun, 02 Jun 2019 22:02:51: 7000000 INFO @ Sun, 02 Jun 2019 22:02:53: 7000000 INFO @ Sun, 02 Jun 2019 22:03:00: 8000000 INFO @ Sun, 02 Jun 2019 22:03:01: 8000000 INFO @ Sun, 02 Jun 2019 22:03:03: 8000000 INFO @ Sun, 02 Jun 2019 22:03:10: 9000000 INFO @ Sun, 02 Jun 2019 22:03:11: 9000000 INFO @ Sun, 02 Jun 2019 22:03:12: 9000000 INFO @ Sun, 02 Jun 2019 22:03:19: 10000000 INFO @ Sun, 02 Jun 2019 22:03:20: 10000000 INFO @ Sun, 02 Jun 2019 22:03:22: 10000000 INFO @ Sun, 02 Jun 2019 22:03:28: 11000000 INFO @ Sun, 02 Jun 2019 22:03:30: 11000000 INFO @ Sun, 02 Jun 2019 22:03:32: 11000000 INFO @ Sun, 02 Jun 2019 22:03:37: 12000000 INFO @ Sun, 02 Jun 2019 22:03:40: 12000000 INFO @ Sun, 02 Jun 2019 22:03:42: 12000000 INFO @ Sun, 02 Jun 2019 22:03:46: 13000000 INFO @ Sun, 02 Jun 2019 22:03:50: 13000000 INFO @ Sun, 02 Jun 2019 22:03:52: 13000000 INFO @ Sun, 02 Jun 2019 22:03:56: 14000000 INFO @ Sun, 02 Jun 2019 22:04:01: 14000000 INFO @ Sun, 02 Jun 2019 22:04:03: 14000000 INFO @ Sun, 02 Jun 2019 22:04:06: 15000000 INFO @ Sun, 02 Jun 2019 22:04:12: 15000000 INFO @ Sun, 02 Jun 2019 22:04:14: 15000000 INFO @ Sun, 02 Jun 2019 22:04:16: 16000000 INFO @ Sun, 02 Jun 2019 22:04:23: 16000000 INFO @ Sun, 02 Jun 2019 22:04:24: 16000000 INFO @ Sun, 02 Jun 2019 22:04:26: 17000000 INFO @ Sun, 02 Jun 2019 22:04:28: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:04:28: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:04:28: #1 total tags in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:28: #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 22:04:28: #1 tags after filtering in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:28: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:30: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 22:04:30: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:30: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:30: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:30: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:30: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:30: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:30: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 02 Jun 2019 22:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20_model.r WARNING @ Sun, 02 Jun 2019 22:04:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:30: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 02 Jun 2019 22:04:30: #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 22:04:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:33: 17000000 INFO @ Sun, 02 Jun 2019 22:04:35: 17000000 INFO @ Sun, 02 Jun 2019 22:04:35: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:04:35: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:04:35: #1 total tags in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:35: #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 22:04:36: #1 tags after filtering in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:37: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:04:37: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:04:37: #1 total tags in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:04:37: #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 22:04:37: #1 tags after filtering in treatment: 17240429 INFO @ Sun, 02 Jun 2019 22:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:04:37: #1 finished! INFO @ Sun, 02 Jun 2019 22:04:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:04:37: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 22:04:37: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:37: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:37: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 02 Jun 2019 22:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10_model.r WARNING @ Sun, 02 Jun 2019 22:04:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:37: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 02 Jun 2019 22:04:37: #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 22:04:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:04:39: #2 number of paired peaks: 203 WARNING @ Sun, 02 Jun 2019 22:04:39: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sun, 02 Jun 2019 22:04:39: start model_add_line... INFO @ Sun, 02 Jun 2019 22:04:39: start X-correlation... INFO @ Sun, 02 Jun 2019 22:04:39: end of X-cor INFO @ Sun, 02 Jun 2019 22:04:39: #2 finished! INFO @ Sun, 02 Jun 2019 22:04:39: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:04:39: #2 alternative fragment length(s) may be 1,31 bps INFO @ Sun, 02 Jun 2019 22:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05_model.r WARNING @ Sun, 02 Jun 2019 22:04:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:04:39: #2 You may need to consider one of the other alternative d(s): 1,31 WARNING @ Sun, 02 Jun 2019 22:04:39: #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 22:04:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.10_summits.bed INFO @ Sun, 02 Jun 2019 22:05:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529213/SRX529213.05_summits.bed INFO @ Sun, 02 Jun 2019 22:05:35: 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。