Job ID = 1301225 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:40:36 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' 2019-06-03T10:40:36 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/sra17/SRR/001160/SRR1187964' 2019-06-03T10:40:36 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR1187964' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:40:36 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 28,312,405 reads read : 28,312,405 reads written : 28,312,405 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: 00:08:49 28312405 reads; of these: 28312405 (100.00%) were unpaired; of these: 4233253 (14.95%) aligned 0 times 19779501 (69.86%) aligned exactly 1 time 4299651 (15.19%) aligned >1 times 85.05% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 17137313 / 24079152 = 0.7117 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 @ Mon, 03 Jun 2019 20:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 20:25:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:25:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:25:41: 1000000 INFO @ Mon, 03 Jun 2019 20:25:41: 1000000 INFO @ Mon, 03 Jun 2019 20:25:42: 1000000 INFO @ Mon, 03 Jun 2019 20:25:49: 2000000 INFO @ Mon, 03 Jun 2019 20:25:51: 2000000 INFO @ Mon, 03 Jun 2019 20:25:52: 2000000 INFO @ Mon, 03 Jun 2019 20:25:59: 3000000 INFO @ Mon, 03 Jun 2019 20:26:00: 3000000 INFO @ Mon, 03 Jun 2019 20:26:01: 3000000 INFO @ Mon, 03 Jun 2019 20:26:07: 4000000 INFO @ Mon, 03 Jun 2019 20:26:10: 4000000 INFO @ Mon, 03 Jun 2019 20:26:12: 4000000 INFO @ Mon, 03 Jun 2019 20:26:16: 5000000 INFO @ Mon, 03 Jun 2019 20:26:21: 5000000 INFO @ Mon, 03 Jun 2019 20:26:23: 5000000 INFO @ Mon, 03 Jun 2019 20:26:24: 6000000 INFO @ Mon, 03 Jun 2019 20:26:30: 6000000 INFO @ Mon, 03 Jun 2019 20:26:33: 6000000 INFO @ Mon, 03 Jun 2019 20:26:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:26:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:26:33: #1 total tags in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:26:33: #1 tags after filtering in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:33: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:34: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 20:26:34: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:34: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:34: start X-correlation... INFO @ Mon, 03 Jun 2019 20:26:34: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:34: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:34: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 20:26:34: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 20:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10_model.r WARNING @ Mon, 03 Jun 2019 20:26:34: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:34: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 20:26:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:26:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:26:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:26:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:26:40: #1 total tags in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:26:40: #1 tags after filtering in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:40: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:40: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 20:26:40: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:40: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:41: start X-correlation... INFO @ Mon, 03 Jun 2019 20:26:41: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:41: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:41: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 20:26:41: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 20:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05_model.r WARNING @ Mon, 03 Jun 2019 20:26:41: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:41: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 20:26:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:26:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:26:41: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:26:41: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:26:41: #1 total tags in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:26:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 20:26:41: #1 tags after filtering in treatment: 6941839 INFO @ Mon, 03 Jun 2019 20:26:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 20:26:41: #1 finished! INFO @ Mon, 03 Jun 2019 20:26:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:26:42: #2 number of paired peaks: 414 WARNING @ Mon, 03 Jun 2019 20:26:42: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Mon, 03 Jun 2019 20:26:42: start model_add_line... INFO @ Mon, 03 Jun 2019 20:26:42: start X-correlation... INFO @ Mon, 03 Jun 2019 20:26:42: end of X-cor INFO @ Mon, 03 Jun 2019 20:26:42: #2 finished! INFO @ Mon, 03 Jun 2019 20:26:42: #2 predicted fragment length is 60 bps INFO @ Mon, 03 Jun 2019 20:26:42: #2 alternative fragment length(s) may be 60 bps INFO @ Mon, 03 Jun 2019 20:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20_model.r WARNING @ Mon, 03 Jun 2019 20:26:42: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 20:26:42: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Mon, 03 Jun 2019 20:26:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 20:26:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:26:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:02: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:27:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.10_summits.bed INFO @ Mon, 03 Jun 2019 20:27:06: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1047 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:27:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.05_summits.bed INFO @ Mon, 03 Jun 2019 20:27:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1955 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX485206/SRX485206.20_summits.bed INFO @ Mon, 03 Jun 2019 20:27:15: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (456 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。