Job ID = 1293978 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:45:36 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' 2019-06-02T18:45:36 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/sra37/SRR/003057/SRR3130865' 2019-06-02T18:45:46 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3130865' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:45:46 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:51:04 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' 2019-06-02T18:51:04 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/sra37/SRR/003057/SRR3130866' 2019-06-02T18:51:13 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3130866' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:51:13 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:56:37 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' 2019-06-02T18:56:37 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/SRR3130867/SRR3130867.1' 2019-06-02T18:56:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3130867' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:56:48 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 1,726,636 reads read : 1,726,636 reads written : 1,726,636 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: 00:09:56 25726636 reads; of these: 25726636 (100.00%) were unpaired; of these: 2182476 (8.48%) aligned 0 times 17882864 (69.51%) aligned exactly 1 time 5661296 (22.01%) aligned >1 times 91.52% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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 12 files... [bam_rmdupse_core] 3566846 / 23544160 = 0.1515 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 04:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.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 04:17:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:17:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.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 04:17:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:17:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.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 04:17:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:17:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:17:13: 1000000 INFO @ Mon, 03 Jun 2019 04:17:14: 1000000 INFO @ Mon, 03 Jun 2019 04:17:16: 1000000 INFO @ Mon, 03 Jun 2019 04:17:21: 2000000 INFO @ Mon, 03 Jun 2019 04:17:23: 2000000 INFO @ Mon, 03 Jun 2019 04:17:27: 2000000 INFO @ Mon, 03 Jun 2019 04:17:29: 3000000 INFO @ Mon, 03 Jun 2019 04:17:32: 3000000 INFO @ Mon, 03 Jun 2019 04:17:37: 4000000 INFO @ Mon, 03 Jun 2019 04:17:37: 3000000 INFO @ Mon, 03 Jun 2019 04:17:40: 4000000 INFO @ Mon, 03 Jun 2019 04:17:45: 5000000 INFO @ Mon, 03 Jun 2019 04:17:48: 4000000 INFO @ Mon, 03 Jun 2019 04:17:49: 5000000 INFO @ Mon, 03 Jun 2019 04:17:53: 6000000 INFO @ Mon, 03 Jun 2019 04:17:58: 6000000 INFO @ Mon, 03 Jun 2019 04:17:58: 5000000 INFO @ Mon, 03 Jun 2019 04:18:00: 7000000 INFO @ Mon, 03 Jun 2019 04:18:07: 7000000 INFO @ Mon, 03 Jun 2019 04:18:08: 8000000 INFO @ Mon, 03 Jun 2019 04:18:09: 6000000 INFO @ Mon, 03 Jun 2019 04:18:15: 8000000 INFO @ Mon, 03 Jun 2019 04:18:16: 9000000 INFO @ Mon, 03 Jun 2019 04:18:20: 7000000 INFO @ Mon, 03 Jun 2019 04:18:24: 10000000 INFO @ Mon, 03 Jun 2019 04:18:24: 9000000 INFO @ Mon, 03 Jun 2019 04:18:30: 8000000 INFO @ Mon, 03 Jun 2019 04:18:32: 11000000 INFO @ Mon, 03 Jun 2019 04:18:33: 10000000 INFO @ Mon, 03 Jun 2019 04:18:40: 12000000 INFO @ Mon, 03 Jun 2019 04:18:41: 9000000 INFO @ Mon, 03 Jun 2019 04:18:41: 11000000 INFO @ Mon, 03 Jun 2019 04:18:47: 13000000 INFO @ Mon, 03 Jun 2019 04:18:50: 12000000 INFO @ Mon, 03 Jun 2019 04:18:51: 10000000 INFO @ Mon, 03 Jun 2019 04:18:55: 14000000 INFO @ Mon, 03 Jun 2019 04:18:59: 13000000 INFO @ Mon, 03 Jun 2019 04:19:02: 11000000 INFO @ Mon, 03 Jun 2019 04:19:03: 15000000 INFO @ Mon, 03 Jun 2019 04:19:09: 14000000 INFO @ Mon, 03 Jun 2019 04:19:11: 16000000 INFO @ Mon, 03 Jun 2019 04:19:12: 12000000 INFO @ Mon, 03 Jun 2019 04:19:18: 15000000 INFO @ Mon, 03 Jun 2019 04:19:18: 17000000 INFO @ Mon, 03 Jun 2019 04:19:23: 13000000 INFO @ Mon, 03 Jun 2019 04:19:26: 18000000 INFO @ Mon, 03 Jun 2019 04:19:27: 16000000 INFO @ Mon, 03 Jun 2019 04:19:33: 14000000 INFO @ Mon, 03 Jun 2019 04:19:34: 19000000 INFO @ Mon, 03 Jun 2019 04:19:36: 17000000 INFO @ Mon, 03 Jun 2019 04:19:42: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:19:42: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:19:42: #1 total tags in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:19:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:19:42: #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 04:19:43: #1 tags after filtering in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:19:43: #1 finished! INFO @ Mon, 03 Jun 2019 04:19:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:19:44: 15000000 INFO @ Mon, 03 Jun 2019 04:19:44: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 04:19:44: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 04:19:44: start model_add_line... INFO @ Mon, 03 Jun 2019 04:19:45: start X-correlation... INFO @ Mon, 03 Jun 2019 04:19:45: end of X-cor INFO @ Mon, 03 Jun 2019 04:19:45: #2 finished! INFO @ Mon, 03 Jun 2019 04:19:45: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:19:45: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:19:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10_model.r INFO @ Mon, 03 Jun 2019 04:19:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:19:45: 18000000 INFO @ Mon, 03 Jun 2019 04:19:54: 16000000 INFO @ Mon, 03 Jun 2019 04:19:54: 19000000 INFO @ Mon, 03 Jun 2019 04:20:03: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:20:03: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:20:03: #1 total tags in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:20:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:20:03: #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 04:20:04: #1 tags after filtering in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:20:04: #1 finished! INFO @ Mon, 03 Jun 2019 04:20:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:20:04: 17000000 INFO @ Mon, 03 Jun 2019 04:20:05: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 04:20:05: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 04:20:05: start model_add_line... INFO @ Mon, 03 Jun 2019 04:20:05: start X-correlation... INFO @ Mon, 03 Jun 2019 04:20:05: end of X-cor INFO @ Mon, 03 Jun 2019 04:20:05: #2 finished! INFO @ Mon, 03 Jun 2019 04:20:05: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:20:05: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05_model.r INFO @ Mon, 03 Jun 2019 04:20:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:20:14: 18000000 INFO @ Mon, 03 Jun 2019 04:20:23: 19000000 INFO @ Mon, 03 Jun 2019 04:20:33: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:20:33: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:20:33: #1 total tags in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:20:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:20:33: #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 04:20:33: #1 tags after filtering in treatment: 19977314 INFO @ Mon, 03 Jun 2019 04:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:20:33: #1 finished! INFO @ Mon, 03 Jun 2019 04:20:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:20:35: #2 number of paired peaks: 140 WARNING @ Mon, 03 Jun 2019 04:20:35: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Mon, 03 Jun 2019 04:20:35: start model_add_line... INFO @ Mon, 03 Jun 2019 04:20:35: start X-correlation... INFO @ Mon, 03 Jun 2019 04:20:35: end of X-cor INFO @ Mon, 03 Jun 2019 04:20:35: #2 finished! INFO @ Mon, 03 Jun 2019 04:20:35: #2 predicted fragment length is 113 bps INFO @ Mon, 03 Jun 2019 04:20:35: #2 alternative fragment length(s) may be 113 bps INFO @ Mon, 03 Jun 2019 04:20:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20_model.r INFO @ Mon, 03 Jun 2019 04:20:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:20:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:20:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:20:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.10_summits.bed INFO @ Mon, 03 Jun 2019 04:21:02: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2592 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:21:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:21:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.05_summits.bed INFO @ Mon, 03 Jun 2019 04:21:23: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4482 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:21:27: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550612/SRX1550612.20_summits.bed INFO @ Mon, 03 Jun 2019 04:21:53: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1403 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。