Job ID = 1294967 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T01:55:47 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' 2019-06-03T01:55:47 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/sra11/SRR/000849/SRR870216' 2019-06-03T01:55:57 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR870216', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 17,570,684 reads read : 17,570,684 reads written : 17,570,684 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: 00:08:48 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 850058 (4.84%) aligned 0 times 11024830 (62.75%) aligned exactly 1 time 5695796 (32.42%) aligned >1 times 95.16% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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 8 files... [bam_rmdupse_core] 2897704 / 16720626 = 0.1733 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 11:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.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 11:19:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.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 11:19:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.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 11:19:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:32: 1000000 INFO @ Mon, 03 Jun 2019 11:19:32: 1000000 INFO @ Mon, 03 Jun 2019 11:19:32: 1000000 INFO @ Mon, 03 Jun 2019 11:19:40: 2000000 INFO @ Mon, 03 Jun 2019 11:19:40: 2000000 INFO @ Mon, 03 Jun 2019 11:19:40: 2000000 INFO @ Mon, 03 Jun 2019 11:19:48: 3000000 INFO @ Mon, 03 Jun 2019 11:19:49: 3000000 INFO @ Mon, 03 Jun 2019 11:19:49: 3000000 INFO @ Mon, 03 Jun 2019 11:19:56: 4000000 INFO @ Mon, 03 Jun 2019 11:19:57: 4000000 INFO @ Mon, 03 Jun 2019 11:19:58: 4000000 INFO @ Mon, 03 Jun 2019 11:20:04: 5000000 INFO @ Mon, 03 Jun 2019 11:20:05: 5000000 INFO @ Mon, 03 Jun 2019 11:20:07: 5000000 INFO @ Mon, 03 Jun 2019 11:20:12: 6000000 INFO @ Mon, 03 Jun 2019 11:20:14: 6000000 INFO @ Mon, 03 Jun 2019 11:20:15: 6000000 INFO @ Mon, 03 Jun 2019 11:20:21: 7000000 INFO @ Mon, 03 Jun 2019 11:20:24: 7000000 INFO @ Mon, 03 Jun 2019 11:20:24: 7000000 INFO @ Mon, 03 Jun 2019 11:20:29: 8000000 INFO @ Mon, 03 Jun 2019 11:20:33: 8000000 INFO @ Mon, 03 Jun 2019 11:20:33: 8000000 INFO @ Mon, 03 Jun 2019 11:20:37: 9000000 INFO @ Mon, 03 Jun 2019 11:20:41: 9000000 INFO @ Mon, 03 Jun 2019 11:20:41: 9000000 INFO @ Mon, 03 Jun 2019 11:20:45: 10000000 INFO @ Mon, 03 Jun 2019 11:20:49: 10000000 INFO @ Mon, 03 Jun 2019 11:20:49: 10000000 INFO @ Mon, 03 Jun 2019 11:20:53: 11000000 INFO @ Mon, 03 Jun 2019 11:20:57: 11000000 INFO @ Mon, 03 Jun 2019 11:20:58: 11000000 INFO @ Mon, 03 Jun 2019 11:21:01: 12000000 INFO @ Mon, 03 Jun 2019 11:21:06: 12000000 INFO @ Mon, 03 Jun 2019 11:21:07: 12000000 INFO @ Mon, 03 Jun 2019 11:21:09: 13000000 INFO @ Mon, 03 Jun 2019 11:21:14: 13000000 INFO @ Mon, 03 Jun 2019 11:21:15: 13000000 INFO @ Mon, 03 Jun 2019 11:21:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:21:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:21:16: #1 total tags in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:21:16: #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 11:21:16: #1 tags after filtering in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:21:16: #1 finished! INFO @ Mon, 03 Jun 2019 11:21:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:21:18: #2 number of paired peaks: 471 WARNING @ Mon, 03 Jun 2019 11:21:18: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Mon, 03 Jun 2019 11:21:18: start model_add_line... INFO @ Mon, 03 Jun 2019 11:21:18: start X-correlation... INFO @ Mon, 03 Jun 2019 11:21:18: end of X-cor INFO @ Mon, 03 Jun 2019 11:21:18: #2 finished! INFO @ Mon, 03 Jun 2019 11:21:18: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:21:18: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20_model.r WARNING @ Mon, 03 Jun 2019 11:21:18: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:21:18: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:21:18: #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 11:21:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:21:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:21:20: #1 total tags in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:21:20: #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 11:21:21: #1 tags after filtering in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:21:21: #1 finished! INFO @ Mon, 03 Jun 2019 11:21:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:21:22: #2 number of paired peaks: 471 WARNING @ Mon, 03 Jun 2019 11:21:22: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Mon, 03 Jun 2019 11:21:22: start model_add_line... INFO @ Mon, 03 Jun 2019 11:21:22: start X-correlation... INFO @ Mon, 03 Jun 2019 11:21:22: end of X-cor INFO @ Mon, 03 Jun 2019 11:21:22: #2 finished! INFO @ Mon, 03 Jun 2019 11:21:22: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:21:22: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10_model.r WARNING @ Mon, 03 Jun 2019 11:21:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:21:22: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:21:22: #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 11:21:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:21:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:21:22: #1 total tags in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:21:22: #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 11:21:22: #1 tags after filtering in treatment: 13822922 INFO @ Mon, 03 Jun 2019 11:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:21:22: #1 finished! INFO @ Mon, 03 Jun 2019 11:21:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:21:24: #2 number of paired peaks: 471 WARNING @ Mon, 03 Jun 2019 11:21:24: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Mon, 03 Jun 2019 11:21:24: start model_add_line... INFO @ Mon, 03 Jun 2019 11:21:24: start X-correlation... INFO @ Mon, 03 Jun 2019 11:21:24: end of X-cor INFO @ Mon, 03 Jun 2019 11:21:24: #2 finished! INFO @ Mon, 03 Jun 2019 11:21:24: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 11:21:24: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 11:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05_model.r WARNING @ Mon, 03 Jun 2019 11:21:24: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:21:24: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 11:21:24: #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 11:21:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:22:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.20_summits.bed INFO @ Mon, 03 Jun 2019 11:22:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1512 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.10_summits.bed INFO @ Mon, 03 Jun 2019 11:22:17: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1900 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288027/SRX288027.05_summits.bed INFO @ Mon, 03 Jun 2019 11:22:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2171 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。