Job ID = 1293293 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:41:02 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' 2019-06-02T13:41:02 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/era1/ERR/ERR111/ERR111424' 2019-06-02T13:41:12 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'ERR111424' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T13:41:12 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 35,727,074 reads read : 35,727,074 reads written : 35,727,074 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: 00:10:04 35727074 reads; of these: 35727074 (100.00%) were unpaired; of these: 1491713 (4.18%) aligned 0 times 26831053 (75.10%) aligned exactly 1 time 7404308 (20.72%) aligned >1 times 95.82% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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] 10504023 / 34235361 = 0.3068 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 23:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.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 23:41:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:41:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.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 23:41:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:41:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.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 23:41:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:41:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:41:38: 1000000 INFO @ Sun, 02 Jun 2019 23:41:39: 1000000 INFO @ Sun, 02 Jun 2019 23:41:39: 1000000 INFO @ Sun, 02 Jun 2019 23:41:47: 2000000 INFO @ Sun, 02 Jun 2019 23:41:47: 2000000 INFO @ Sun, 02 Jun 2019 23:41:48: 2000000 INFO @ Sun, 02 Jun 2019 23:41:56: 3000000 INFO @ Sun, 02 Jun 2019 23:41:56: 3000000 INFO @ Sun, 02 Jun 2019 23:41:57: 3000000 INFO @ Sun, 02 Jun 2019 23:42:05: 4000000 INFO @ Sun, 02 Jun 2019 23:42:05: 4000000 INFO @ Sun, 02 Jun 2019 23:42:06: 4000000 INFO @ Sun, 02 Jun 2019 23:42:13: 5000000 INFO @ Sun, 02 Jun 2019 23:42:14: 5000000 INFO @ Sun, 02 Jun 2019 23:42:15: 5000000 INFO @ Sun, 02 Jun 2019 23:42:21: 6000000 INFO @ Sun, 02 Jun 2019 23:42:23: 6000000 INFO @ Sun, 02 Jun 2019 23:42:24: 6000000 INFO @ Sun, 02 Jun 2019 23:42:30: 7000000 INFO @ Sun, 02 Jun 2019 23:42:32: 7000000 INFO @ Sun, 02 Jun 2019 23:42:33: 7000000 INFO @ Sun, 02 Jun 2019 23:42:38: 8000000 INFO @ Sun, 02 Jun 2019 23:42:41: 8000000 INFO @ Sun, 02 Jun 2019 23:42:42: 8000000 INFO @ Sun, 02 Jun 2019 23:42:46: 9000000 INFO @ Sun, 02 Jun 2019 23:42:50: 9000000 INFO @ Sun, 02 Jun 2019 23:42:51: 9000000 INFO @ Sun, 02 Jun 2019 23:42:54: 10000000 INFO @ Sun, 02 Jun 2019 23:42:59: 10000000 INFO @ Sun, 02 Jun 2019 23:43:01: 10000000 INFO @ Sun, 02 Jun 2019 23:43:03: 11000000 INFO @ Sun, 02 Jun 2019 23:43:09: 11000000 INFO @ Sun, 02 Jun 2019 23:43:10: 11000000 INFO @ Sun, 02 Jun 2019 23:43:11: 12000000 INFO @ Sun, 02 Jun 2019 23:43:18: 12000000 INFO @ Sun, 02 Jun 2019 23:43:19: 12000000 INFO @ Sun, 02 Jun 2019 23:43:19: 13000000 INFO @ Sun, 02 Jun 2019 23:43:27: 13000000 INFO @ Sun, 02 Jun 2019 23:43:28: 14000000 INFO @ Sun, 02 Jun 2019 23:43:28: 13000000 INFO @ Sun, 02 Jun 2019 23:43:36: 15000000 INFO @ Sun, 02 Jun 2019 23:43:36: 14000000 INFO @ Sun, 02 Jun 2019 23:43:37: 14000000 INFO @ Sun, 02 Jun 2019 23:43:44: 16000000 INFO @ Sun, 02 Jun 2019 23:43:46: 15000000 INFO @ Sun, 02 Jun 2019 23:43:47: 15000000 INFO @ Sun, 02 Jun 2019 23:43:52: 17000000 INFO @ Sun, 02 Jun 2019 23:43:55: 16000000 INFO @ Sun, 02 Jun 2019 23:43:56: 16000000 INFO @ Sun, 02 Jun 2019 23:44:01: 18000000 INFO @ Sun, 02 Jun 2019 23:44:05: 17000000 INFO @ Sun, 02 Jun 2019 23:44:06: 17000000 INFO @ Sun, 02 Jun 2019 23:44:09: 19000000 INFO @ Sun, 02 Jun 2019 23:44:14: 18000000 INFO @ Sun, 02 Jun 2019 23:44:15: 18000000 INFO @ Sun, 02 Jun 2019 23:44:17: 20000000 INFO @ Sun, 02 Jun 2019 23:44:23: 19000000 INFO @ Sun, 02 Jun 2019 23:44:24: 19000000 INFO @ Sun, 02 Jun 2019 23:44:25: 21000000 INFO @ Sun, 02 Jun 2019 23:44:33: 20000000 INFO @ Sun, 02 Jun 2019 23:44:33: 20000000 INFO @ Sun, 02 Jun 2019 23:44:34: 22000000 INFO @ Sun, 02 Jun 2019 23:44:42: 23000000 INFO @ Sun, 02 Jun 2019 23:44:43: 21000000 INFO @ Sun, 02 Jun 2019 23:44:43: 21000000 INFO @ Sun, 02 Jun 2019 23:44:48: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:44:48: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:44:48: #1 total tags in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:44:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:44:48: #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 23:44:49: #1 tags after filtering in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:44:49: #1 finished! INFO @ Sun, 02 Jun 2019 23:44:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:44:51: #2 number of paired peaks: 2650 INFO @ Sun, 02 Jun 2019 23:44:51: start model_add_line... INFO @ Sun, 02 Jun 2019 23:44:51: 22000000 INFO @ Sun, 02 Jun 2019 23:44:52: start X-correlation... INFO @ Sun, 02 Jun 2019 23:44:52: end of X-cor INFO @ Sun, 02 Jun 2019 23:44:52: #2 finished! INFO @ Sun, 02 Jun 2019 23:44:52: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 23:44:52: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 23:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10_model.r INFO @ Sun, 02 Jun 2019 23:44:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:44:52: 22000000 INFO @ Sun, 02 Jun 2019 23:45:01: 23000000 INFO @ Sun, 02 Jun 2019 23:45:01: 23000000 INFO @ Sun, 02 Jun 2019 23:45:07: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:45:07: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:45:07: #1 total tags in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:45:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:45:07: #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 23:45:08: #1 tags after filtering in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:45:08: #1 finished! INFO @ Sun, 02 Jun 2019 23:45:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:45:08: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 23:45:08: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 23:45:08: #1 total tags in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:45:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:45:08: #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 23:45:09: #1 tags after filtering in treatment: 23731338 INFO @ Sun, 02 Jun 2019 23:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:45:09: #1 finished! INFO @ Sun, 02 Jun 2019 23:45:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:45:10: #2 number of paired peaks: 2650 INFO @ Sun, 02 Jun 2019 23:45:10: start model_add_line... INFO @ Sun, 02 Jun 2019 23:45:11: start X-correlation... INFO @ Sun, 02 Jun 2019 23:45:11: end of X-cor INFO @ Sun, 02 Jun 2019 23:45:11: #2 finished! INFO @ Sun, 02 Jun 2019 23:45:11: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 23:45:11: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 23:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20_model.r INFO @ Sun, 02 Jun 2019 23:45:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:45:11: #2 number of paired peaks: 2650 INFO @ Sun, 02 Jun 2019 23:45:11: start model_add_line... INFO @ Sun, 02 Jun 2019 23:45:11: start X-correlation... INFO @ Sun, 02 Jun 2019 23:45:11: end of X-cor INFO @ Sun, 02 Jun 2019 23:45:11: #2 finished! INFO @ Sun, 02 Jun 2019 23:45:11: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 23:45:11: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 23:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05_model.r INFO @ Sun, 02 Jun 2019 23:45:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:46:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:46:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:46:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:46:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:46:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.10_summits.bed INFO @ Sun, 02 Jun 2019 23:46:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9881 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.20_summits.bed INFO @ Sun, 02 Jun 2019 23:46:49: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7256 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX088858/ERX088858.05_summits.bed INFO @ Sun, 02 Jun 2019 23:46:51: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12487 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。