Job ID = 1293271 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:35:20 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' 2019-06-02T13:35:20 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/era10/ERR/ERR031/ERR031131' 2019-06-02T13:35:20 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR031131' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T13:36:28 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 10461904 of 15692850 2019-06-02T13:36:28 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-06-02T13:36:28 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) spots read : 18,272,772 reads read : 18,272,772 reads written : 18,272,772 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: 00:03:53 18272772 reads; of these: 18272772 (100.00%) were unpaired; of these: 541907 (2.97%) aligned 0 times 15447754 (84.54%) aligned exactly 1 time 2283111 (12.49%) aligned >1 times 97.03% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 4295689 / 17730865 = 0.2423 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 22:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.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 22:51:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.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 22:51:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.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 22:51:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:51:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:51:57: 1000000 INFO @ Sun, 02 Jun 2019 22:51:57: 1000000 INFO @ Sun, 02 Jun 2019 22:51:57: 1000000 INFO @ Sun, 02 Jun 2019 22:52:03: 2000000 INFO @ Sun, 02 Jun 2019 22:52:03: 2000000 INFO @ Sun, 02 Jun 2019 22:52:03: 2000000 INFO @ Sun, 02 Jun 2019 22:52:09: 3000000 INFO @ Sun, 02 Jun 2019 22:52:09: 3000000 INFO @ Sun, 02 Jun 2019 22:52:10: 3000000 INFO @ Sun, 02 Jun 2019 22:52:15: 4000000 INFO @ Sun, 02 Jun 2019 22:52:15: 4000000 INFO @ Sun, 02 Jun 2019 22:52:16: 4000000 INFO @ Sun, 02 Jun 2019 22:52:21: 5000000 INFO @ Sun, 02 Jun 2019 22:52:21: 5000000 INFO @ Sun, 02 Jun 2019 22:52:22: 5000000 INFO @ Sun, 02 Jun 2019 22:52:27: 6000000 INFO @ Sun, 02 Jun 2019 22:52:27: 6000000 INFO @ Sun, 02 Jun 2019 22:52:29: 6000000 INFO @ Sun, 02 Jun 2019 22:52:33: 7000000 INFO @ Sun, 02 Jun 2019 22:52:33: 7000000 INFO @ Sun, 02 Jun 2019 22:52:35: 7000000 INFO @ Sun, 02 Jun 2019 22:52:39: 8000000 INFO @ Sun, 02 Jun 2019 22:52:39: 8000000 INFO @ Sun, 02 Jun 2019 22:52:41: 8000000 INFO @ Sun, 02 Jun 2019 22:52:45: 9000000 INFO @ Sun, 02 Jun 2019 22:52:45: 9000000 INFO @ Sun, 02 Jun 2019 22:52:48: 9000000 INFO @ Sun, 02 Jun 2019 22:52:51: 10000000 INFO @ Sun, 02 Jun 2019 22:52:51: 10000000 INFO @ Sun, 02 Jun 2019 22:52:54: 10000000 INFO @ Sun, 02 Jun 2019 22:52:57: 11000000 INFO @ Sun, 02 Jun 2019 22:52:57: 11000000 INFO @ Sun, 02 Jun 2019 22:53:00: 11000000 INFO @ Sun, 02 Jun 2019 22:53:03: 12000000 INFO @ Sun, 02 Jun 2019 22:53:03: 12000000 INFO @ Sun, 02 Jun 2019 22:53:06: 12000000 INFO @ Sun, 02 Jun 2019 22:53:09: 13000000 INFO @ Sun, 02 Jun 2019 22:53:09: 13000000 INFO @ Sun, 02 Jun 2019 22:53:12: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:12: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:12: #1 total tags in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:12: #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 22:53:12: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:12: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:12: #1 total tags in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:12: #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 22:53:12: #1 tags after filtering in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:12: #1 tags after filtering in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:13: 13000000 INFO @ Sun, 02 Jun 2019 22:53:13: #2 number of paired peaks: 2139 INFO @ Sun, 02 Jun 2019 22:53:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:13: #2 predicted fragment length is 198 bps INFO @ Sun, 02 Jun 2019 22:53:13: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 02 Jun 2019 22:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05_model.r INFO @ Sun, 02 Jun 2019 22:53:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:13: #2 number of paired peaks: 2139 INFO @ Sun, 02 Jun 2019 22:53:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:14: #2 predicted fragment length is 198 bps INFO @ Sun, 02 Jun 2019 22:53:14: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 02 Jun 2019 22:53:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20_model.r INFO @ Sun, 02 Jun 2019 22:53:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:16: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:53:16: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:53:16: #1 total tags in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:53:16: #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 22:53:16: #1 tags after filtering in treatment: 13435176 INFO @ Sun, 02 Jun 2019 22:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:53:16: #1 finished! INFO @ Sun, 02 Jun 2019 22:53:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:53:17: #2 number of paired peaks: 2139 INFO @ Sun, 02 Jun 2019 22:53:17: start model_add_line... INFO @ Sun, 02 Jun 2019 22:53:17: start X-correlation... INFO @ Sun, 02 Jun 2019 22:53:17: end of X-cor INFO @ Sun, 02 Jun 2019 22:53:17: #2 finished! INFO @ Sun, 02 Jun 2019 22:53:17: #2 predicted fragment length is 198 bps INFO @ Sun, 02 Jun 2019 22:53:17: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 02 Jun 2019 22:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10_model.r INFO @ Sun, 02 Jun 2019 22:53:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.05_summits.bed INFO @ Sun, 02 Jun 2019 22:54:14: Done! INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20_peaks.narrowPeak pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8756 records, 4 fields): 17 millis INFO @ Sun, 02 Jun 2019 22:54:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.20_summits.bed INFO @ Sun, 02 Jun 2019 22:54:14: Done! CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4113 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:54:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:54:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:54:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011410/ERX011410.10_summits.bed INFO @ Sun, 02 Jun 2019 22:54:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6213 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。