Job ID = 1300455 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:10:43 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' 2019-06-03T10:10:43 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/traces/sra17/SRR/001155/SRR1182752' 2019-06-03T10:10:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR1182752' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-03T10:10:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 16,333,147 reads read : 16,333,147 reads written : 16,333,147 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: 00:05:02 16333147 reads; of these: 16333147 (100.00%) were unpaired; of these: 669041 (4.10%) aligned 0 times 13812837 (84.57%) aligned exactly 1 time 1851269 (11.33%) aligned >1 times 95.90% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 1534295 / 15664106 = 0.0979 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 19:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.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 19:37:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.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 19:37:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.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 19:37:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:37:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:37:16: 1000000 INFO @ Mon, 03 Jun 2019 19:37:17: 1000000 INFO @ Mon, 03 Jun 2019 19:37:17: 1000000 INFO @ Mon, 03 Jun 2019 19:37:24: 2000000 INFO @ Mon, 03 Jun 2019 19:37:26: 2000000 INFO @ Mon, 03 Jun 2019 19:37:26: 2000000 INFO @ Mon, 03 Jun 2019 19:37:34: 3000000 INFO @ Mon, 03 Jun 2019 19:37:35: 3000000 INFO @ Mon, 03 Jun 2019 19:37:35: 3000000 INFO @ Mon, 03 Jun 2019 19:37:42: 4000000 INFO @ Mon, 03 Jun 2019 19:37:43: 4000000 INFO @ Mon, 03 Jun 2019 19:37:44: 4000000 INFO @ Mon, 03 Jun 2019 19:37:50: 5000000 INFO @ Mon, 03 Jun 2019 19:37:51: 5000000 INFO @ Mon, 03 Jun 2019 19:37:53: 5000000 INFO @ Mon, 03 Jun 2019 19:37:58: 6000000 INFO @ Mon, 03 Jun 2019 19:38:00: 6000000 INFO @ Mon, 03 Jun 2019 19:38:01: 6000000 INFO @ Mon, 03 Jun 2019 19:38:06: 7000000 INFO @ Mon, 03 Jun 2019 19:38:08: 7000000 INFO @ Mon, 03 Jun 2019 19:38:10: 7000000 INFO @ Mon, 03 Jun 2019 19:38:14: 8000000 INFO @ Mon, 03 Jun 2019 19:38:17: 8000000 INFO @ Mon, 03 Jun 2019 19:38:19: 8000000 INFO @ Mon, 03 Jun 2019 19:38:22: 9000000 INFO @ Mon, 03 Jun 2019 19:38:25: 9000000 INFO @ Mon, 03 Jun 2019 19:38:27: 9000000 INFO @ Mon, 03 Jun 2019 19:38:30: 10000000 INFO @ Mon, 03 Jun 2019 19:38:33: 10000000 INFO @ Mon, 03 Jun 2019 19:38:36: 10000000 INFO @ Mon, 03 Jun 2019 19:38:38: 11000000 INFO @ Mon, 03 Jun 2019 19:38:42: 11000000 INFO @ Mon, 03 Jun 2019 19:38:45: 11000000 INFO @ Mon, 03 Jun 2019 19:38:48: 12000000 INFO @ Mon, 03 Jun 2019 19:38:51: 12000000 INFO @ Mon, 03 Jun 2019 19:38:54: 12000000 INFO @ Mon, 03 Jun 2019 19:38:56: 13000000 INFO @ Mon, 03 Jun 2019 19:38:59: 13000000 INFO @ Mon, 03 Jun 2019 19:39:02: 13000000 INFO @ Mon, 03 Jun 2019 19:39:04: 14000000 INFO @ Mon, 03 Jun 2019 19:39:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:05: #1 total tags in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:05: #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 19:39:05: #1 tags after filtering in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:05: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:06: #2 number of paired peaks: 602 WARNING @ Mon, 03 Jun 2019 19:39:06: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:06: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:07: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:07: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:07: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:07: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 19:39:07: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 19:39:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10_model.r INFO @ Mon, 03 Jun 2019 19:39:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:07: 14000000 INFO @ Mon, 03 Jun 2019 19:39:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:09: #1 total tags in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:09: #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 19:39:09: #1 tags after filtering in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:09: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:10: #2 number of paired peaks: 602 WARNING @ Mon, 03 Jun 2019 19:39:10: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:10: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:10: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:10: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:10: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:10: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 19:39:10: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 19:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05_model.r INFO @ Mon, 03 Jun 2019 19:39:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:11: 14000000 INFO @ Mon, 03 Jun 2019 19:39:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:39:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:39:12: #1 total tags in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:39:12: #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 19:39:12: #1 tags after filtering in treatment: 14129811 INFO @ Mon, 03 Jun 2019 19:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:39:12: #1 finished! INFO @ Mon, 03 Jun 2019 19:39:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:39:14: #2 number of paired peaks: 602 WARNING @ Mon, 03 Jun 2019 19:39:14: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Mon, 03 Jun 2019 19:39:14: start model_add_line... INFO @ Mon, 03 Jun 2019 19:39:14: start X-correlation... INFO @ Mon, 03 Jun 2019 19:39:14: end of X-cor INFO @ Mon, 03 Jun 2019 19:39:14: #2 finished! INFO @ Mon, 03 Jun 2019 19:39:14: #2 predicted fragment length is 211 bps INFO @ Mon, 03 Jun 2019 19:39:14: #2 alternative fragment length(s) may be 211 bps INFO @ Mon, 03 Jun 2019 19:39:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20_model.r INFO @ Mon, 03 Jun 2019 19:39:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:39:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:39:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:39:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:40:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:40:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:40:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.10_summits.bed INFO @ Mon, 03 Jun 2019 19:40:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4735 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:40:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:40:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:40:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.05_summits.bed INFO @ Mon, 03 Jun 2019 19:40:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6619 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:40:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:40:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:40:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481129/SRX481129.20_summits.bed INFO @ Mon, 03 Jun 2019 19:40:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2896 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。