Job ID = 2001629 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T21:27:42 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T21:27:47 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T21:27:47 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era9/ERR/ERR125/ERR125830' 2019-07-04T21:27:47 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR125830' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-04T21:27:47 fasterq-dump.2.9.6 err: sorter.c run_producer_pool(): row_count == 0! 2019-07-04T21:27:47 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcParam,rcInvalid) 2019-07-04T21:27:47 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcParam,rcInvalid) 2019-07-04T21:27:51 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T21:27:51 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era9/ERR/ERR125/ERR125830' 2019-07-04T21:27:51 fasterq-dump.2.9.6 err: invalid accession 'ERR125830' 2019-07-04T21:28:07 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T21:28:07 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era9/ERR/ERR125/ERR125830' 2019-07-04T21:28:07 fasterq-dump.2.9.6 err: invalid accession 'ERR125830' 2019-07-04T21:28:21 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-04T21:28:21 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/era9/ERR/ERR125/ERR125830' 2019-07-04T21:28:21 fasterq-dump.2.9.6 err: invalid accession 'ERR125830' 2019-07-04T21:36:31 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 : 14,478,117 reads read : 14,478,117 reads written : 14,478,117 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:28 14478117 reads; of these: 14478117 (100.00%) were unpaired; of these: 662161 (4.57%) aligned 0 times 10596909 (73.19%) aligned exactly 1 time 3219047 (22.23%) aligned >1 times 95.43% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 546769 / 13815956 = 0.0396 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 @ Fri, 05 Jul 2019 06:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:48:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:48:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:48:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:48:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 06:48:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 06:48:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 06:48:25: 1000000 INFO @ Fri, 05 Jul 2019 06:48:25: 1000000 INFO @ Fri, 05 Jul 2019 06:48:26: 1000000 INFO @ Fri, 05 Jul 2019 06:48:33: 2000000 INFO @ Fri, 05 Jul 2019 06:48:33: 2000000 INFO @ Fri, 05 Jul 2019 06:48:34: 2000000 INFO @ Fri, 05 Jul 2019 06:48:40: 3000000 INFO @ Fri, 05 Jul 2019 06:48:41: 3000000 INFO @ Fri, 05 Jul 2019 06:48:41: 3000000 INFO @ Fri, 05 Jul 2019 06:48:47: 4000000 INFO @ Fri, 05 Jul 2019 06:48:48: 4000000 INFO @ Fri, 05 Jul 2019 06:48:48: 4000000 INFO @ Fri, 05 Jul 2019 06:48:54: 5000000 INFO @ Fri, 05 Jul 2019 06:48:55: 5000000 INFO @ Fri, 05 Jul 2019 06:48:55: 5000000 INFO @ Fri, 05 Jul 2019 06:49:01: 6000000 INFO @ Fri, 05 Jul 2019 06:49:02: 6000000 INFO @ Fri, 05 Jul 2019 06:49:03: 6000000 INFO @ Fri, 05 Jul 2019 06:49:09: 7000000 INFO @ Fri, 05 Jul 2019 06:49:09: 7000000 INFO @ Fri, 05 Jul 2019 06:49:10: 7000000 INFO @ Fri, 05 Jul 2019 06:49:16: 8000000 INFO @ Fri, 05 Jul 2019 06:49:17: 8000000 INFO @ Fri, 05 Jul 2019 06:49:17: 8000000 INFO @ Fri, 05 Jul 2019 06:49:23: 9000000 INFO @ Fri, 05 Jul 2019 06:49:24: 9000000 INFO @ Fri, 05 Jul 2019 06:49:25: 9000000 INFO @ Fri, 05 Jul 2019 06:49:30: 10000000 INFO @ Fri, 05 Jul 2019 06:49:31: 10000000 INFO @ Fri, 05 Jul 2019 06:49:32: 10000000 INFO @ Fri, 05 Jul 2019 06:49:37: 11000000 INFO @ Fri, 05 Jul 2019 06:49:38: 11000000 INFO @ Fri, 05 Jul 2019 06:49:39: 11000000 INFO @ Fri, 05 Jul 2019 06:49:45: 12000000 INFO @ Fri, 05 Jul 2019 06:49:45: 12000000 INFO @ Fri, 05 Jul 2019 06:49:46: 12000000 INFO @ Fri, 05 Jul 2019 06:49:52: 13000000 INFO @ Fri, 05 Jul 2019 06:49:53: 13000000 INFO @ Fri, 05 Jul 2019 06:49:54: 13000000 INFO @ Fri, 05 Jul 2019 06:49:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:49:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:49:54: #1 total tags in treatment: 13269187 INFO @ Fri, 05 Jul 2019 06:49:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:49:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:49:54: #1 tags after filtering in treatment: 13268977 INFO @ Fri, 05 Jul 2019 06:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:49:54: #1 finished! INFO @ Fri, 05 Jul 2019 06:49:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:49:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:49:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:49:55: #1 total tags in treatment: 13269187 INFO @ Fri, 05 Jul 2019 06:49:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:49:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:49:55: #1 tags after filtering in treatment: 13268977 INFO @ Fri, 05 Jul 2019 06:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:49:55: #1 finished! INFO @ Fri, 05 Jul 2019 06:49:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:49:56: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 06:49:56: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 06:49:56: #1 total tags in treatment: 13269187 INFO @ Fri, 05 Jul 2019 06:49:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 06:49:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 06:49:56: #1 tags after filtering in treatment: 13268977 INFO @ Fri, 05 Jul 2019 06:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 06:49:56: #1 finished! INFO @ Fri, 05 Jul 2019 06:49:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 06:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 06:49:58: #2 number of paired peaks: 67533 INFO @ Fri, 05 Jul 2019 06:49:58: start model_add_line... INFO @ Fri, 05 Jul 2019 06:49:59: start X-correlation... INFO @ Fri, 05 Jul 2019 06:49:59: end of X-cor INFO @ Fri, 05 Jul 2019 06:49:59: #2 finished! INFO @ Fri, 05 Jul 2019 06:49:59: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:49:59: #2 alternative fragment length(s) may be 4,130,292 bps INFO @ Fri, 05 Jul 2019 06:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10_model.r INFO @ Fri, 05 Jul 2019 06:49:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:49:59: #2 number of paired peaks: 67533 INFO @ Fri, 05 Jul 2019 06:49:59: start model_add_line... INFO @ Fri, 05 Jul 2019 06:49:59: start X-correlation... INFO @ Fri, 05 Jul 2019 06:49:59: end of X-cor INFO @ Fri, 05 Jul 2019 06:49:59: #2 finished! INFO @ Fri, 05 Jul 2019 06:49:59: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:49:59: #2 alternative fragment length(s) may be 4,130,292 bps INFO @ Fri, 05 Jul 2019 06:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20_model.r INFO @ Fri, 05 Jul 2019 06:49:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:50:00: #2 number of paired peaks: 67533 INFO @ Fri, 05 Jul 2019 06:50:00: start model_add_line... INFO @ Fri, 05 Jul 2019 06:50:01: start X-correlation... INFO @ Fri, 05 Jul 2019 06:50:01: end of X-cor INFO @ Fri, 05 Jul 2019 06:50:01: #2 finished! INFO @ Fri, 05 Jul 2019 06:50:01: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:50:01: #2 alternative fragment length(s) may be 4,130,292 bps INFO @ Fri, 05 Jul 2019 06:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05_model.r INFO @ Fri, 05 Jul 2019 06:50:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:50:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:50:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:50:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.10_summits.bed INFO @ Fri, 05 Jul 2019 06:51:02: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (178 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:51:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:51:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:51:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.20_summits.bed INFO @ Fri, 05 Jul 2019 06:51:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101949/ERX101949.05_summits.bed INFO @ Fri, 05 Jul 2019 06:51:05: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (974 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。