Job ID = 1299145 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T08:55:24 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' 2019-06-03T08:55:24 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/sra18/SRR/001146/SRR1174368' 2019-06-03T08:55:24 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR1174368' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T08:55:24 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 0 of 19525308 2019-06-03T08:55:24 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-06-03T08:55:24 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-06-03T09:00:16 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 19,525,308 reads read : 19,525,308 reads written : 19,525,308 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: 00:07:59 19525308 reads; of these: 19525308 (100.00%) were unpaired; of these: 297005 (1.52%) aligned 0 times 12534962 (64.20%) aligned exactly 1 time 6693341 (34.28%) aligned >1 times 98.48% overall alignment rate Time searching: 00:07:59 Overall time: 00:07:59 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] 668135 / 19228303 = 0.0347 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 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.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 18:20:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:20:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.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 18:20:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:20:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.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 18:20:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:20:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:20:11: 1000000 INFO @ Mon, 03 Jun 2019 18:20:14: 1000000 INFO @ Mon, 03 Jun 2019 18:20:14: 1000000 INFO @ Mon, 03 Jun 2019 18:20:19: 2000000 INFO @ Mon, 03 Jun 2019 18:20:24: 2000000 INFO @ Mon, 03 Jun 2019 18:20:25: 2000000 INFO @ Mon, 03 Jun 2019 18:20:26: 3000000 INFO @ Mon, 03 Jun 2019 18:20:34: 3000000 INFO @ Mon, 03 Jun 2019 18:20:34: 4000000 INFO @ Mon, 03 Jun 2019 18:20:35: 3000000 INFO @ Mon, 03 Jun 2019 18:20:42: 5000000 INFO @ Mon, 03 Jun 2019 18:20:44: 4000000 INFO @ Mon, 03 Jun 2019 18:20:45: 4000000 INFO @ Mon, 03 Jun 2019 18:20:49: 6000000 INFO @ Mon, 03 Jun 2019 18:20:54: 5000000 INFO @ Mon, 03 Jun 2019 18:20:55: 5000000 INFO @ Mon, 03 Jun 2019 18:20:57: 7000000 INFO @ Mon, 03 Jun 2019 18:21:03: 6000000 INFO @ Mon, 03 Jun 2019 18:21:04: 8000000 INFO @ Mon, 03 Jun 2019 18:21:05: 6000000 INFO @ Mon, 03 Jun 2019 18:21:12: 9000000 INFO @ Mon, 03 Jun 2019 18:21:13: 7000000 INFO @ Mon, 03 Jun 2019 18:21:15: 7000000 INFO @ Mon, 03 Jun 2019 18:21:19: 10000000 INFO @ Mon, 03 Jun 2019 18:21:22: 8000000 INFO @ Mon, 03 Jun 2019 18:21:25: 8000000 INFO @ Mon, 03 Jun 2019 18:21:27: 11000000 INFO @ Mon, 03 Jun 2019 18:21:32: 9000000 INFO @ Mon, 03 Jun 2019 18:21:34: 9000000 INFO @ Mon, 03 Jun 2019 18:21:35: 12000000 INFO @ Mon, 03 Jun 2019 18:21:41: 10000000 INFO @ Mon, 03 Jun 2019 18:21:42: 13000000 INFO @ Mon, 03 Jun 2019 18:21:44: 10000000 INFO @ Mon, 03 Jun 2019 18:21:50: 14000000 INFO @ Mon, 03 Jun 2019 18:21:51: 11000000 INFO @ Mon, 03 Jun 2019 18:21:54: 11000000 INFO @ Mon, 03 Jun 2019 18:21:58: 15000000 INFO @ Mon, 03 Jun 2019 18:22:01: 12000000 INFO @ Mon, 03 Jun 2019 18:22:04: 12000000 INFO @ Mon, 03 Jun 2019 18:22:05: 16000000 INFO @ Mon, 03 Jun 2019 18:22:11: 13000000 INFO @ Mon, 03 Jun 2019 18:22:13: 17000000 INFO @ Mon, 03 Jun 2019 18:22:14: 13000000 INFO @ Mon, 03 Jun 2019 18:22:21: 18000000 INFO @ Mon, 03 Jun 2019 18:22:21: 14000000 INFO @ Mon, 03 Jun 2019 18:22:24: 14000000 INFO @ Mon, 03 Jun 2019 18:22:25: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:22:25: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:22:25: #1 total tags in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:22:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:22:25: #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 18:22:25: #1 tags after filtering in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:22:25: #1 finished! INFO @ Mon, 03 Jun 2019 18:22:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:22:27: #2 number of paired peaks: 162 WARNING @ Mon, 03 Jun 2019 18:22:27: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 03 Jun 2019 18:22:27: start model_add_line... INFO @ Mon, 03 Jun 2019 18:22:27: start X-correlation... INFO @ Mon, 03 Jun 2019 18:22:27: end of X-cor INFO @ Mon, 03 Jun 2019 18:22:27: #2 finished! INFO @ Mon, 03 Jun 2019 18:22:27: #2 predicted fragment length is 173 bps INFO @ Mon, 03 Jun 2019 18:22:27: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 03 Jun 2019 18:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10_model.r INFO @ Mon, 03 Jun 2019 18:22:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:22:30: 15000000 INFO @ Mon, 03 Jun 2019 18:22:33: 15000000 INFO @ Mon, 03 Jun 2019 18:22:40: 16000000 INFO @ Mon, 03 Jun 2019 18:22:43: 16000000 INFO @ Mon, 03 Jun 2019 18:22:49: 17000000 INFO @ Mon, 03 Jun 2019 18:22:53: 17000000 INFO @ Mon, 03 Jun 2019 18:22:59: 18000000 INFO @ Mon, 03 Jun 2019 18:23:02: 18000000 INFO @ Mon, 03 Jun 2019 18:23:04: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:23:04: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:23:04: #1 total tags in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:23:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:04: #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 18:23:05: #1 tags after filtering in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:05: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:06: #2 number of paired peaks: 162 WARNING @ Mon, 03 Jun 2019 18:23:06: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 03 Jun 2019 18:23:06: start model_add_line... INFO @ Mon, 03 Jun 2019 18:23:06: start X-correlation... INFO @ Mon, 03 Jun 2019 18:23:06: end of X-cor INFO @ Mon, 03 Jun 2019 18:23:06: #2 finished! INFO @ Mon, 03 Jun 2019 18:23:06: #2 predicted fragment length is 173 bps INFO @ Mon, 03 Jun 2019 18:23:06: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 03 Jun 2019 18:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05_model.r INFO @ Mon, 03 Jun 2019 18:23:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:23:08: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 18:23:08: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 18:23:08: #1 total tags in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:23:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:23:08: #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 18:23:08: #1 tags after filtering in treatment: 18560168 INFO @ Mon, 03 Jun 2019 18:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 18:23:08: #1 finished! INFO @ Mon, 03 Jun 2019 18:23:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:23:10: #2 number of paired peaks: 162 WARNING @ Mon, 03 Jun 2019 18:23:10: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 03 Jun 2019 18:23:10: start model_add_line... INFO @ Mon, 03 Jun 2019 18:23:10: start X-correlation... INFO @ Mon, 03 Jun 2019 18:23:10: end of X-cor INFO @ Mon, 03 Jun 2019 18:23:10: #2 finished! INFO @ Mon, 03 Jun 2019 18:23:10: #2 predicted fragment length is 173 bps INFO @ Mon, 03 Jun 2019 18:23:10: #2 alternative fragment length(s) may be 173 bps INFO @ Mon, 03 Jun 2019 18:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20_model.r INFO @ Mon, 03 Jun 2019 18:23:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:23:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.10_summits.bed INFO @ Mon, 03 Jun 2019 18:23:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2583 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:24:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:24:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:24:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:24:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:24:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.05_summits.bed INFO @ Mon, 03 Jun 2019 18:24:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4411 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474521/SRX474521.20_summits.bed INFO @ Mon, 03 Jun 2019 18:24:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1197 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。