Job ID = 1294418 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:25:30 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' 2019-06-02T22:25:30 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/sra12/SRR/000849/SRR869732' 2019-06-02T22:25:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869732' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T22:25:40 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T22:47:18 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 ) 2019-06-02T22:49:16 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 : 21,508,050 reads read : 21,508,050 reads written : 21,508,050 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: 00:00:01 Multiseed full-index search: 00:08:29 21508050 reads; of these: 21508050 (100.00%) were unpaired; of these: 1269464 (5.90%) aligned 0 times 14194251 (66.00%) aligned exactly 1 time 6044335 (28.10%) aligned >1 times 94.10% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 3647039 / 20238586 = 0.1802 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 08:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.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 08:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.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 08:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.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 08:06:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:06:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:06:39: 1000000 INFO @ Mon, 03 Jun 2019 08:06:40: 1000000 INFO @ Mon, 03 Jun 2019 08:06:40: 1000000 INFO @ Mon, 03 Jun 2019 08:06:46: 2000000 INFO @ Mon, 03 Jun 2019 08:06:47: 2000000 INFO @ Mon, 03 Jun 2019 08:06:48: 2000000 INFO @ Mon, 03 Jun 2019 08:06:53: 3000000 INFO @ Mon, 03 Jun 2019 08:06:54: 3000000 INFO @ Mon, 03 Jun 2019 08:06:56: 3000000 INFO @ Mon, 03 Jun 2019 08:07:00: 4000000 INFO @ Mon, 03 Jun 2019 08:07:01: 4000000 INFO @ Mon, 03 Jun 2019 08:07:03: 4000000 INFO @ Mon, 03 Jun 2019 08:07:06: 5000000 INFO @ Mon, 03 Jun 2019 08:07:09: 5000000 INFO @ Mon, 03 Jun 2019 08:07:09: 5000000 INFO @ Mon, 03 Jun 2019 08:07:13: 6000000 INFO @ Mon, 03 Jun 2019 08:07:16: 6000000 INFO @ Mon, 03 Jun 2019 08:07:17: 6000000 INFO @ Mon, 03 Jun 2019 08:07:19: 7000000 INFO @ Mon, 03 Jun 2019 08:07:23: 7000000 INFO @ Mon, 03 Jun 2019 08:07:25: 7000000 INFO @ Mon, 03 Jun 2019 08:07:26: 8000000 INFO @ Mon, 03 Jun 2019 08:07:31: 8000000 INFO @ Mon, 03 Jun 2019 08:07:32: 9000000 INFO @ Mon, 03 Jun 2019 08:07:32: 8000000 INFO @ Mon, 03 Jun 2019 08:07:38: 9000000 INFO @ Mon, 03 Jun 2019 08:07:39: 10000000 INFO @ Mon, 03 Jun 2019 08:07:39: 9000000 INFO @ Mon, 03 Jun 2019 08:07:45: 10000000 INFO @ Mon, 03 Jun 2019 08:07:45: 11000000 INFO @ Mon, 03 Jun 2019 08:07:47: 10000000 INFO @ Mon, 03 Jun 2019 08:07:52: 12000000 INFO @ Mon, 03 Jun 2019 08:07:52: 11000000 INFO @ Mon, 03 Jun 2019 08:07:54: 11000000 INFO @ Mon, 03 Jun 2019 08:07:58: 13000000 INFO @ Mon, 03 Jun 2019 08:07:59: 12000000 INFO @ Mon, 03 Jun 2019 08:08:01: 12000000 INFO @ Mon, 03 Jun 2019 08:08:04: 14000000 INFO @ Mon, 03 Jun 2019 08:08:06: 13000000 INFO @ Mon, 03 Jun 2019 08:08:08: 13000000 INFO @ Mon, 03 Jun 2019 08:08:11: 15000000 INFO @ Mon, 03 Jun 2019 08:08:14: 14000000 INFO @ Mon, 03 Jun 2019 08:08:15: 14000000 INFO @ Mon, 03 Jun 2019 08:08:17: 16000000 INFO @ Mon, 03 Jun 2019 08:08:21: 15000000 INFO @ Mon, 03 Jun 2019 08:08:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:08:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:08:21: #1 total tags in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:08:21: #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 08:08:22: #1 tags after filtering in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:08:22: #1 finished! INFO @ Mon, 03 Jun 2019 08:08:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:08:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:08:22: 15000000 INFO @ Mon, 03 Jun 2019 08:08:23: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 08:08:23: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 08:08:23: start model_add_line... INFO @ Mon, 03 Jun 2019 08:08:23: start X-correlation... INFO @ Mon, 03 Jun 2019 08:08:23: end of X-cor INFO @ Mon, 03 Jun 2019 08:08:23: #2 finished! INFO @ Mon, 03 Jun 2019 08:08:23: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 08:08:23: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 08:08:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10_model.r INFO @ Mon, 03 Jun 2019 08:08:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:08:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:08:28: 16000000 INFO @ Mon, 03 Jun 2019 08:08:29: 16000000 INFO @ Mon, 03 Jun 2019 08:08:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:08:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:08:33: #1 total tags in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:08:33: #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 08:08:33: #1 tags after filtering in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:08:33: #1 finished! INFO @ Mon, 03 Jun 2019 08:08:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:08:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:08:34: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:08:34: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:08:34: #1 total tags in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:08:34: #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 08:08:34: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 08:08:34: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 08:08:34: start model_add_line... INFO @ Mon, 03 Jun 2019 08:08:35: start X-correlation... INFO @ Mon, 03 Jun 2019 08:08:35: end of X-cor INFO @ Mon, 03 Jun 2019 08:08:35: #2 finished! INFO @ Mon, 03 Jun 2019 08:08:35: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 08:08:35: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 08:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05_model.r INFO @ Mon, 03 Jun 2019 08:08:35: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:08:35: #1 tags after filtering in treatment: 16591547 INFO @ Mon, 03 Jun 2019 08:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:08:35: #1 finished! INFO @ Mon, 03 Jun 2019 08:08:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:08:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:08:36: #2 number of paired peaks: 237 WARNING @ Mon, 03 Jun 2019 08:08:36: Fewer paired peaks (237) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 237 pairs to build model! INFO @ Mon, 03 Jun 2019 08:08:36: start model_add_line... INFO @ Mon, 03 Jun 2019 08:08:36: start X-correlation... INFO @ Mon, 03 Jun 2019 08:08:36: end of X-cor INFO @ Mon, 03 Jun 2019 08:08:36: #2 finished! INFO @ Mon, 03 Jun 2019 08:08:36: #2 predicted fragment length is 123 bps INFO @ Mon, 03 Jun 2019 08:08:36: #2 alternative fragment length(s) may be 123 bps INFO @ Mon, 03 Jun 2019 08:08:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20_model.r INFO @ Mon, 03 Jun 2019 08:08:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:08:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:09:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:09:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:09:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.10_summits.bed INFO @ Mon, 03 Jun 2019 08:09:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3334 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:09:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:09:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:09:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.05_summits.bed INFO @ Mon, 03 Jun 2019 08:09:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4921 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287589/SRX287589.20_summits.bed INFO @ Mon, 03 Jun 2019 08:09:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1982 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。