Job ID = 1293944 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T18:25:43 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' 2019-06-02T18:25:43 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-2/SRR503391/SRR503391.1' 2019-06-02T18:25:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR503391' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:25:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 23,498,093 reads read : 46,996,186 reads written : 46,996,186 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: 00:17:11 23498093 reads; of these: 23498093 (100.00%) were paired; of these: 19601028 (83.42%) aligned concordantly 0 times 2213261 (9.42%) aligned concordantly exactly 1 time 1683804 (7.17%) aligned concordantly >1 times ---- 19601028 pairs aligned concordantly 0 times; of these: 46003 (0.23%) aligned discordantly 1 time ---- 19555025 pairs aligned 0 times concordantly or discordantly; of these: 39110050 mates make up the pairs; of these: 38091647 (97.40%) aligned 0 times 639212 (1.63%) aligned exactly 1 time 379191 (0.97%) aligned >1 times 18.95% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2005686 / 3917477 = 0.5120 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 03:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.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 03:51:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:51:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.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 03:51:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:51:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:51:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.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 03:51:24: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:51:24: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:51:31: 1000000 INFO @ Mon, 03 Jun 2019 03:51:31: 1000000 INFO @ Mon, 03 Jun 2019 03:51:32: 1000000 INFO @ Mon, 03 Jun 2019 03:51:37: 2000000 INFO @ Mon, 03 Jun 2019 03:51:38: 2000000 INFO @ Mon, 03 Jun 2019 03:51:41: 2000000 INFO @ Mon, 03 Jun 2019 03:51:44: 3000000 INFO @ Mon, 03 Jun 2019 03:51:45: 3000000 INFO @ Mon, 03 Jun 2019 03:51:49: 3000000 INFO @ Mon, 03 Jun 2019 03:51:50: 4000000 INFO @ Mon, 03 Jun 2019 03:51:52: 4000000 INFO @ Mon, 03 Jun 2019 03:51:56: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 03:51:56: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 03:51:56: #1 total tags in treatment: 1913776 INFO @ Mon, 03 Jun 2019 03:51:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:51:56: #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 03:51:56: #1 tags after filtering in treatment: 1369096 INFO @ Mon, 03 Jun 2019 03:51:56: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 03:51:56: #1 finished! INFO @ Mon, 03 Jun 2019 03:51:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:51:56: #2 number of paired peaks: 1729 INFO @ Mon, 03 Jun 2019 03:51:56: start model_add_line... INFO @ Mon, 03 Jun 2019 03:51:56: start X-correlation... INFO @ Mon, 03 Jun 2019 03:51:56: end of X-cor INFO @ Mon, 03 Jun 2019 03:51:56: #2 finished! INFO @ Mon, 03 Jun 2019 03:51:56: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 03:51:56: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 03:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20_model.r WARNING @ Mon, 03 Jun 2019 03:51:56: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:51:56: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 03:51:56: #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 03:51:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:51:58: 4000000 INFO @ Mon, 03 Jun 2019 03:51:59: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 03:51:59: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 03:51:59: #1 total tags in treatment: 1913776 INFO @ Mon, 03 Jun 2019 03:51:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:51:59: #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 03:51:59: #1 tags after filtering in treatment: 1369096 INFO @ Mon, 03 Jun 2019 03:51:59: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 03:51:59: #1 finished! INFO @ Mon, 03 Jun 2019 03:51:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:51:59: #2 number of paired peaks: 1729 INFO @ Mon, 03 Jun 2019 03:51:59: start model_add_line... INFO @ Mon, 03 Jun 2019 03:51:59: start X-correlation... INFO @ Mon, 03 Jun 2019 03:51:59: end of X-cor INFO @ Mon, 03 Jun 2019 03:51:59: #2 finished! INFO @ Mon, 03 Jun 2019 03:51:59: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 03:51:59: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 03:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05_model.r WARNING @ Mon, 03 Jun 2019 03:51:59: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:51:59: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 03:51:59: #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 03:51:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:52:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.20_summits.bed INFO @ Mon, 03 Jun 2019 03:52:03: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (821 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:52:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:05: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 03:52:05: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 03:52:05: #1 total tags in treatment: 1913776 INFO @ Mon, 03 Jun 2019 03:52:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:52:05: #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 03:52:05: #1 tags after filtering in treatment: 1369096 INFO @ Mon, 03 Jun 2019 03:52:05: #1 Redundant rate of treatment: 0.28 INFO @ Mon, 03 Jun 2019 03:52:05: #1 finished! INFO @ Mon, 03 Jun 2019 03:52:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:52:05: #2 number of paired peaks: 1729 INFO @ Mon, 03 Jun 2019 03:52:05: start model_add_line... INFO @ Mon, 03 Jun 2019 03:52:05: start X-correlation... INFO @ Mon, 03 Jun 2019 03:52:05: end of X-cor INFO @ Mon, 03 Jun 2019 03:52:05: #2 finished! INFO @ Mon, 03 Jun 2019 03:52:05: #2 predicted fragment length is 86 bps INFO @ Mon, 03 Jun 2019 03:52:05: #2 alternative fragment length(s) may be 86 bps INFO @ Mon, 03 Jun 2019 03:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10_model.r WARNING @ Mon, 03 Jun 2019 03:52:05: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 03:52:05: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Mon, 03 Jun 2019 03:52:05: #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 03:52:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.05_summits.bed INFO @ Mon, 03 Jun 2019 03:52:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1447 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:52:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX151219/SRX151219.10_summits.bed INFO @ Mon, 03 Jun 2019 03:52:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1023 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。