Job ID = 1295825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T06:40:53 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' 2019-06-03T06:40:53 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/SRR1153275/SRR1153275.1' 2019-06-03T06:41:04 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1153275' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T06:41:20 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' 2019-06-03T06:41:20 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/SRR1153275/SRR1153275.1' 2019-06-03T06:41:30 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1153275' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 7,500,488 reads read : 7,500,488 reads written : 7,500,488 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: 00:03:21 7500488 reads; of these: 7500488 (100.00%) were unpaired; of these: 183509 (2.45%) aligned 0 times 5466407 (72.88%) aligned exactly 1 time 1850572 (24.67%) aligned >1 times 97.55% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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_rmdupse_core] 316933 / 7316979 = 0.0433 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 15:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.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 15:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.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 15:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.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 15:49:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:49:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:49:17: 1000000 INFO @ Mon, 03 Jun 2019 15:49:18: 1000000 INFO @ Mon, 03 Jun 2019 15:49:18: 1000000 INFO @ Mon, 03 Jun 2019 15:49:26: 2000000 INFO @ Mon, 03 Jun 2019 15:49:27: 2000000 INFO @ Mon, 03 Jun 2019 15:49:27: 2000000 INFO @ Mon, 03 Jun 2019 15:49:34: 3000000 INFO @ Mon, 03 Jun 2019 15:49:35: 3000000 INFO @ Mon, 03 Jun 2019 15:49:36: 3000000 INFO @ Mon, 03 Jun 2019 15:49:41: 4000000 INFO @ Mon, 03 Jun 2019 15:49:45: 4000000 INFO @ Mon, 03 Jun 2019 15:49:45: 4000000 INFO @ Mon, 03 Jun 2019 15:49:48: 5000000 INFO @ Mon, 03 Jun 2019 15:49:53: 5000000 INFO @ Mon, 03 Jun 2019 15:49:53: 5000000 INFO @ Mon, 03 Jun 2019 15:49:56: 6000000 INFO @ Mon, 03 Jun 2019 15:50:02: 6000000 INFO @ Mon, 03 Jun 2019 15:50:02: 6000000 INFO @ Mon, 03 Jun 2019 15:50:03: 7000000 INFO @ Mon, 03 Jun 2019 15:50:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:50:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:50:03: #1 total tags in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:50:03: #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 15:50:03: #1 tags after filtering in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:50:03: #1 finished! INFO @ Mon, 03 Jun 2019 15:50:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:50:04: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 15:50:04: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 15:50:04: start model_add_line... INFO @ Mon, 03 Jun 2019 15:50:04: start X-correlation... INFO @ Mon, 03 Jun 2019 15:50:04: end of X-cor INFO @ Mon, 03 Jun 2019 15:50:04: #2 finished! INFO @ Mon, 03 Jun 2019 15:50:04: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:50:04: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05_model.r WARNING @ Mon, 03 Jun 2019 15:50:04: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:50:04: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:50:04: #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 15:50:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:50:10: 7000000 INFO @ Mon, 03 Jun 2019 15:50:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:50:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:50:10: #1 total tags in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:50:10: #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 15:50:10: #1 tags after filtering in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:50:10: #1 finished! INFO @ Mon, 03 Jun 2019 15:50:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:50:11: 7000000 INFO @ Mon, 03 Jun 2019 15:50:11: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 15:50:11: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 15:50:11: #1 total tags in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:50:11: #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 15:50:11: #1 tags after filtering in treatment: 7000046 INFO @ Mon, 03 Jun 2019 15:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:50:11: #1 finished! INFO @ Mon, 03 Jun 2019 15:50:11: #2 number of paired peaks: 116 INFO @ Mon, 03 Jun 2019 15:50:11: #2 Build Peak Model... WARNING @ Mon, 03 Jun 2019 15:50:11: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 15:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:50:11: start model_add_line... INFO @ Mon, 03 Jun 2019 15:50:11: start X-correlation... INFO @ Mon, 03 Jun 2019 15:50:11: end of X-cor INFO @ Mon, 03 Jun 2019 15:50:11: #2 finished! INFO @ Mon, 03 Jun 2019 15:50:11: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:50:11: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20_model.r WARNING @ Mon, 03 Jun 2019 15:50:11: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:50:11: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:50:11: #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 15:50:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:50:12: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 15:50:12: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 15:50:12: start model_add_line... INFO @ Mon, 03 Jun 2019 15:50:12: start X-correlation... INFO @ Mon, 03 Jun 2019 15:50:12: end of X-cor INFO @ Mon, 03 Jun 2019 15:50:12: #2 finished! INFO @ Mon, 03 Jun 2019 15:50:12: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 15:50:12: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 15:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10_model.r WARNING @ Mon, 03 Jun 2019 15:50:12: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:50:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 15:50:12: #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 15:50:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:50:24: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:50:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:50:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.05_summits.bed INFO @ Mon, 03 Jun 2019 15:50:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.20_summits.bed INFO @ Mon, 03 Jun 2019 15:50:42: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX457599/SRX457599.10_summits.bed INFO @ Mon, 03 Jun 2019 15:50:43: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。