Job ID = 1294459 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:00:44 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' 2019-06-02T23:00:44 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/sra12/SRR/000849/SRR869848' 2019-06-02T23:00:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869848' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:00:54 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 12,830,446 reads read : 12,830,446 reads written : 12,830,446 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: 00:08:00 12830446 reads; of these: 12830446 (100.00%) were unpaired; of these: 566991 (4.42%) aligned 0 times 6016593 (46.89%) aligned exactly 1 time 6246862 (48.69%) aligned >1 times 95.58% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 1897178 / 12263455 = 0.1547 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 08:26:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.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 08:26:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.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 08:26:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.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 08:26:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:26:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:26:09: 1000000 INFO @ Mon, 03 Jun 2019 08:26:09: 1000000 INFO @ Mon, 03 Jun 2019 08:26:10: 1000000 INFO @ Mon, 03 Jun 2019 08:26:16: 2000000 INFO @ Mon, 03 Jun 2019 08:26:16: 2000000 INFO @ Mon, 03 Jun 2019 08:26:18: 2000000 INFO @ Mon, 03 Jun 2019 08:26:23: 3000000 INFO @ Mon, 03 Jun 2019 08:26:24: 3000000 INFO @ Mon, 03 Jun 2019 08:26:26: 3000000 INFO @ Mon, 03 Jun 2019 08:26:30: 4000000 INFO @ Mon, 03 Jun 2019 08:26:32: 4000000 INFO @ Mon, 03 Jun 2019 08:26:33: 4000000 INFO @ Mon, 03 Jun 2019 08:26:37: 5000000 INFO @ Mon, 03 Jun 2019 08:26:39: 5000000 INFO @ Mon, 03 Jun 2019 08:26:41: 5000000 INFO @ Mon, 03 Jun 2019 08:26:44: 6000000 INFO @ Mon, 03 Jun 2019 08:26:46: 6000000 INFO @ Mon, 03 Jun 2019 08:26:48: 6000000 INFO @ Mon, 03 Jun 2019 08:26:51: 7000000 INFO @ Mon, 03 Jun 2019 08:26:53: 7000000 INFO @ Mon, 03 Jun 2019 08:26:56: 7000000 INFO @ Mon, 03 Jun 2019 08:26:59: 8000000 INFO @ Mon, 03 Jun 2019 08:27:00: 8000000 INFO @ Mon, 03 Jun 2019 08:27:03: 8000000 INFO @ Mon, 03 Jun 2019 08:27:05: 9000000 INFO @ Mon, 03 Jun 2019 08:27:07: 9000000 INFO @ Mon, 03 Jun 2019 08:27:11: 9000000 INFO @ Mon, 03 Jun 2019 08:27:12: 10000000 INFO @ Mon, 03 Jun 2019 08:27:14: 10000000 INFO @ Mon, 03 Jun 2019 08:27:15: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:15: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:15: #1 total tags in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:15: #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 08:27:15: #1 tags after filtering in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:15: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:16: #2 number of paired peaks: 924 WARNING @ Mon, 03 Jun 2019 08:27:16: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:16: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:16: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:16: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:16: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:16: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 08:27:16: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 08:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10_model.r WARNING @ Mon, 03 Jun 2019 08:27:16: #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 08:27:16: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 08:27:16: #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 08:27:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:17: #1 total tags in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:17: #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 08:27:17: #1 tags after filtering in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:17: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:18: 10000000 INFO @ Mon, 03 Jun 2019 08:27:18: #2 number of paired peaks: 924 WARNING @ Mon, 03 Jun 2019 08:27:18: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:18: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:18: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:18: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:18: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:18: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 08:27:18: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 08:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05_model.r WARNING @ Mon, 03 Jun 2019 08:27:18: #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 08:27:18: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 08:27:18: #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 08:27:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:21: #1 total tags in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:21: #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 08:27:21: #1 tags after filtering in treatment: 10366277 INFO @ Mon, 03 Jun 2019 08:27:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:27:21: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:22: #2 number of paired peaks: 924 WARNING @ Mon, 03 Jun 2019 08:27:22: Fewer paired peaks (924) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 924 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:22: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:22: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:22: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:22: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:22: #2 predicted fragment length is 53 bps INFO @ Mon, 03 Jun 2019 08:27:22: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 03 Jun 2019 08:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20_model.r WARNING @ Mon, 03 Jun 2019 08:27:22: #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 08:27:22: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 03 Jun 2019 08:27:22: #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 08:27:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:27:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:27:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:28:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.10_summits.bed INFO @ Mon, 03 Jun 2019 08:28:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1854 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:28:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.05_summits.bed INFO @ Mon, 03 Jun 2019 08:28:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2990 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287660/SRX287660.20_summits.bed INFO @ Mon, 03 Jun 2019 08:28:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1219 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。