Job ID = 1293288 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:40:54 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' 2019-06-02T13:40:54 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/ERR031145/ERR031145.3' 2019-06-02T13:40:54 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR031145' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T13:40:54 fasterq-dump.2.9.6 err: perform_fastq_split_3_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 25,592,798 reads read : 25,592,798 reads written : 25,592,798 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: 00:08:37 25592798 reads; of these: 25592798 (100.00%) were unpaired; of these: 813881 (3.18%) aligned 0 times 17725176 (69.26%) aligned exactly 1 time 7053741 (27.56%) aligned >1 times 96.82% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 7209939 / 24778917 = 0.2910 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 @ Sun, 02 Jun 2019 23:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.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 @ Sun, 02 Jun 2019 23:08:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.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 @ Sun, 02 Jun 2019 23:08:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.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 @ Sun, 02 Jun 2019 23:08:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:08:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:09:05: 1000000 INFO @ Sun, 02 Jun 2019 23:09:05: 1000000 INFO @ Sun, 02 Jun 2019 23:09:06: 1000000 INFO @ Sun, 02 Jun 2019 23:09:12: 2000000 INFO @ Sun, 02 Jun 2019 23:09:12: 2000000 INFO @ Sun, 02 Jun 2019 23:09:14: 2000000 INFO @ Sun, 02 Jun 2019 23:09:19: 3000000 INFO @ Sun, 02 Jun 2019 23:09:19: 3000000 INFO @ Sun, 02 Jun 2019 23:09:22: 3000000 INFO @ Sun, 02 Jun 2019 23:09:26: 4000000 INFO @ Sun, 02 Jun 2019 23:09:27: 4000000 INFO @ Sun, 02 Jun 2019 23:09:30: 4000000 INFO @ Sun, 02 Jun 2019 23:09:33: 5000000 INFO @ Sun, 02 Jun 2019 23:09:34: 5000000 INFO @ Sun, 02 Jun 2019 23:09:39: 5000000 INFO @ Sun, 02 Jun 2019 23:09:40: 6000000 INFO @ Sun, 02 Jun 2019 23:09:41: 6000000 INFO @ Sun, 02 Jun 2019 23:09:47: 7000000 INFO @ Sun, 02 Jun 2019 23:09:48: 6000000 INFO @ Sun, 02 Jun 2019 23:09:48: 7000000 INFO @ Sun, 02 Jun 2019 23:09:54: 8000000 INFO @ Sun, 02 Jun 2019 23:09:55: 8000000 INFO @ Sun, 02 Jun 2019 23:09:55: 7000000 INFO @ Sun, 02 Jun 2019 23:10:01: 9000000 INFO @ Sun, 02 Jun 2019 23:10:02: 9000000 INFO @ Sun, 02 Jun 2019 23:10:04: 8000000 INFO @ Sun, 02 Jun 2019 23:10:07: 10000000 INFO @ Sun, 02 Jun 2019 23:10:08: 10000000 INFO @ Sun, 02 Jun 2019 23:10:12: 9000000 INFO @ Sun, 02 Jun 2019 23:10:14: 11000000 INFO @ Sun, 02 Jun 2019 23:10:15: 11000000 INFO @ Sun, 02 Jun 2019 23:10:20: 10000000 INFO @ Sun, 02 Jun 2019 23:10:21: 12000000 INFO @ Sun, 02 Jun 2019 23:10:22: 12000000 INFO @ Sun, 02 Jun 2019 23:10:27: 11000000 INFO @ Sun, 02 Jun 2019 23:10:27: 13000000 INFO @ Sun, 02 Jun 2019 23:10:29: 13000000 INFO @ Sun, 02 Jun 2019 23:10:34: 14000000 INFO @ Sun, 02 Jun 2019 23:10:35: 12000000 INFO @ Sun, 02 Jun 2019 23:10:36: 14000000 INFO @ Sun, 02 Jun 2019 23:10:41: 15000000 INFO @ Sun, 02 Jun 2019 23:10:42: 15000000 INFO @ Sun, 02 Jun 2019 23:10:43: 13000000 INFO @ Sun, 02 Jun 2019 23:10:48: 16000000 INFO @ Sun, 02 Jun 2019 23:10:49: 16000000 INFO @ Sun, 02 Jun 2019 23:10:51: 14000000 INFO @ Sun, 02 Jun 2019 23:10:54: 17000000 INFO @ Sun, 02 Jun 2019 23:10:56: 17000000 INFO @ Sun, 02 Jun 2019 23:10:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:10:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:10:58: #1 total tags in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:10:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:10:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:10:59: #1 tags after filtering in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:10:59: #1 finished! INFO @ Sun, 02 Jun 2019 23:10:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:10:59: 15000000 INFO @ Sun, 02 Jun 2019 23:11:00: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:11:00: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:11:00: #1 total tags in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:11:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:11:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:11:00: #1 tags after filtering in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:11:00: #1 finished! INFO @ Sun, 02 Jun 2019 23:11:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:11:00: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 23:11:00: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 23:11:00: start model_add_line... INFO @ Sun, 02 Jun 2019 23:11:00: start X-correlation... INFO @ Sun, 02 Jun 2019 23:11:00: end of X-cor INFO @ Sun, 02 Jun 2019 23:11:00: #2 finished! INFO @ Sun, 02 Jun 2019 23:11:00: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:11:00: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05_model.r INFO @ Sun, 02 Jun 2019 23:11:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:11:02: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 23:11:02: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 23:11:02: start model_add_line... INFO @ Sun, 02 Jun 2019 23:11:02: start X-correlation... INFO @ Sun, 02 Jun 2019 23:11:02: end of X-cor INFO @ Sun, 02 Jun 2019 23:11:02: #2 finished! INFO @ Sun, 02 Jun 2019 23:11:02: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:11:02: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10_model.r INFO @ Sun, 02 Jun 2019 23:11:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:11:07: 16000000 INFO @ Sun, 02 Jun 2019 23:11:14: 17000000 INFO @ Sun, 02 Jun 2019 23:11:19: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:11:19: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:11:19: #1 total tags in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:11:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:11:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 23:11:19: #1 tags after filtering in treatment: 17568978 INFO @ Sun, 02 Jun 2019 23:11:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:11:19: #1 finished! INFO @ Sun, 02 Jun 2019 23:11:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:11:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:11:20: #2 number of paired peaks: 207 WARNING @ Sun, 02 Jun 2019 23:11:20: Fewer paired peaks (207) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 207 pairs to build model! INFO @ Sun, 02 Jun 2019 23:11:20: start model_add_line... INFO @ Sun, 02 Jun 2019 23:11:21: start X-correlation... INFO @ Sun, 02 Jun 2019 23:11:21: end of X-cor INFO @ Sun, 02 Jun 2019 23:11:21: #2 finished! INFO @ Sun, 02 Jun 2019 23:11:21: #2 predicted fragment length is 105 bps INFO @ Sun, 02 Jun 2019 23:11:21: #2 alternative fragment length(s) may be 105 bps INFO @ Sun, 02 Jun 2019 23:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20_model.r INFO @ Sun, 02 Jun 2019 23:11:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:11:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:11:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:12:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.05_summits.bed INFO @ Sun, 02 Jun 2019 23:12:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4465 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.10_summits.bed INFO @ Sun, 02 Jun 2019 23:12:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2755 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011424/ERX011424.20_summits.bed INFO @ Sun, 02 Jun 2019 23:12:30: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1499 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。