Job ID = 1294412 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:20:40 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' 2019-06-02T22:20:40 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/SRR869727' 2019-06-02T22:20:49 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869727' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T22:26:38 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 ) 2019-06-02T22:26:39 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 ) 2019-06-02T22:32:01 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 ) 2019-06-02T22:33:13 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 ) 2019-06-02T22:34:31 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 : 27,852,683 reads read : 27,852,683 reads written : 27,852,683 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: 00:08:43 27852683 reads; of these: 27852683 (100.00%) were unpaired; of these: 2307026 (8.28%) aligned 0 times 20461590 (73.46%) aligned exactly 1 time 5084067 (18.25%) aligned >1 times 91.72% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 7009651 / 25545657 = 0.2744 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 07:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.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 07:53:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:53:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.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 07:53:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:53:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.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 07:53:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:53:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:53:45: 1000000 INFO @ Mon, 03 Jun 2019 07:53:46: 1000000 INFO @ Mon, 03 Jun 2019 07:53:47: 1000000 INFO @ Mon, 03 Jun 2019 07:53:52: 2000000 INFO @ Mon, 03 Jun 2019 07:53:54: 2000000 INFO @ Mon, 03 Jun 2019 07:53:55: 2000000 INFO @ Mon, 03 Jun 2019 07:53:58: 3000000 INFO @ Mon, 03 Jun 2019 07:54:02: 3000000 INFO @ Mon, 03 Jun 2019 07:54:04: 3000000 INFO @ Mon, 03 Jun 2019 07:54:07: 4000000 INFO @ Mon, 03 Jun 2019 07:54:10: 4000000 INFO @ Mon, 03 Jun 2019 07:54:12: 4000000 INFO @ Mon, 03 Jun 2019 07:54:14: 5000000 INFO @ Mon, 03 Jun 2019 07:54:17: 5000000 INFO @ Mon, 03 Jun 2019 07:54:20: 5000000 INFO @ Mon, 03 Jun 2019 07:54:21: 6000000 INFO @ Mon, 03 Jun 2019 07:54:25: 6000000 INFO @ Mon, 03 Jun 2019 07:54:28: 7000000 INFO @ Mon, 03 Jun 2019 07:54:28: 6000000 INFO @ Mon, 03 Jun 2019 07:54:32: 7000000 INFO @ Mon, 03 Jun 2019 07:54:34: 8000000 INFO @ Mon, 03 Jun 2019 07:54:37: 7000000 INFO @ Mon, 03 Jun 2019 07:54:40: 8000000 INFO @ Mon, 03 Jun 2019 07:54:41: 9000000 INFO @ Mon, 03 Jun 2019 07:54:45: 8000000 INFO @ Mon, 03 Jun 2019 07:54:48: 9000000 INFO @ Mon, 03 Jun 2019 07:54:48: 10000000 INFO @ Mon, 03 Jun 2019 07:54:53: 9000000 INFO @ Mon, 03 Jun 2019 07:54:55: 11000000 INFO @ Mon, 03 Jun 2019 07:54:55: 10000000 INFO @ Mon, 03 Jun 2019 07:55:01: 10000000 INFO @ Mon, 03 Jun 2019 07:55:02: 12000000 INFO @ Mon, 03 Jun 2019 07:55:03: 11000000 INFO @ Mon, 03 Jun 2019 07:55:08: 11000000 INFO @ Mon, 03 Jun 2019 07:55:09: 13000000 INFO @ Mon, 03 Jun 2019 07:55:10: 12000000 INFO @ Mon, 03 Jun 2019 07:55:16: 12000000 INFO @ Mon, 03 Jun 2019 07:55:17: 14000000 INFO @ Mon, 03 Jun 2019 07:55:19: 13000000 INFO @ Mon, 03 Jun 2019 07:55:23: 13000000 INFO @ Mon, 03 Jun 2019 07:55:25: 15000000 INFO @ Mon, 03 Jun 2019 07:55:26: 14000000 INFO @ Mon, 03 Jun 2019 07:55:30: 14000000 INFO @ Mon, 03 Jun 2019 07:55:32: 16000000 INFO @ Mon, 03 Jun 2019 07:55:34: 15000000 INFO @ Mon, 03 Jun 2019 07:55:37: 15000000 INFO @ Mon, 03 Jun 2019 07:55:38: 17000000 INFO @ Mon, 03 Jun 2019 07:55:41: 16000000 INFO @ Mon, 03 Jun 2019 07:55:44: 16000000 INFO @ Mon, 03 Jun 2019 07:55:45: 18000000 INFO @ Mon, 03 Jun 2019 07:55:48: 17000000 INFO @ Mon, 03 Jun 2019 07:55:49: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:55:49: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:55:49: #1 total tags in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:55:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:55:49: #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 07:55:49: #1 tags after filtering in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:55:49: #1 finished! INFO @ Mon, 03 Jun 2019 07:55:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:55:51: #2 number of paired peaks: 1359 INFO @ Mon, 03 Jun 2019 07:55:51: start model_add_line... INFO @ Mon, 03 Jun 2019 07:55:51: 17000000 INFO @ Mon, 03 Jun 2019 07:55:51: start X-correlation... INFO @ Mon, 03 Jun 2019 07:55:51: end of X-cor INFO @ Mon, 03 Jun 2019 07:55:51: #2 finished! INFO @ Mon, 03 Jun 2019 07:55:51: #2 predicted fragment length is 257 bps INFO @ Mon, 03 Jun 2019 07:55:51: #2 alternative fragment length(s) may be 257 bps INFO @ Mon, 03 Jun 2019 07:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20_model.r INFO @ Mon, 03 Jun 2019 07:55:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:55:55: 18000000 INFO @ Mon, 03 Jun 2019 07:55:59: 18000000 INFO @ Mon, 03 Jun 2019 07:55:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:55:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:55:59: #1 total tags in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:55:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:55:59: #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 07:55:59: #1 tags after filtering in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:55:59: #1 finished! INFO @ Mon, 03 Jun 2019 07:55:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:01: #2 number of paired peaks: 1359 INFO @ Mon, 03 Jun 2019 07:56:01: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:01: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:01: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:01: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:01: #2 predicted fragment length is 257 bps INFO @ Mon, 03 Jun 2019 07:56:01: #2 alternative fragment length(s) may be 257 bps INFO @ Mon, 03 Jun 2019 07:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10_model.r INFO @ Mon, 03 Jun 2019 07:56:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:56:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:56:03: #1 total tags in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:56:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:56:03: #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 07:56:03: #1 tags after filtering in treatment: 18536006 INFO @ Mon, 03 Jun 2019 07:56:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:56:03: #1 finished! INFO @ Mon, 03 Jun 2019 07:56:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:56:05: #2 number of paired peaks: 1359 INFO @ Mon, 03 Jun 2019 07:56:05: start model_add_line... INFO @ Mon, 03 Jun 2019 07:56:05: start X-correlation... INFO @ Mon, 03 Jun 2019 07:56:05: end of X-cor INFO @ Mon, 03 Jun 2019 07:56:05: #2 finished! INFO @ Mon, 03 Jun 2019 07:56:05: #2 predicted fragment length is 257 bps INFO @ Mon, 03 Jun 2019 07:56:05: #2 alternative fragment length(s) may be 257 bps INFO @ Mon, 03 Jun 2019 07:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05_model.r INFO @ Mon, 03 Jun 2019 07:56:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:56:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:56:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:57:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.20_summits.bed INFO @ Mon, 03 Jun 2019 07:57:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3971 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.10_summits.bed INFO @ Mon, 03 Jun 2019 07:57:20: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4937 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:57:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:57:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:57:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287584/SRX287584.05_summits.bed INFO @ Mon, 03 Jun 2019 07:57:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6365 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。