Job ID = 2001581 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-04T20:25:34 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' 2019-07-04T20:25:34 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/ERR125825' 2019-07-04T20:25:34 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR125825', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-04T20:25:38 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' 2019-07-04T20:25:38 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/ERR125825' 2019-07-04T20:25:38 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR125825' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-04T20:25:43 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' 2019-07-04T20:25:43 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/ERR125825' 2019-07-04T20:25:43 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:25:56 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' 2019-07-04T20:25:56 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/ERR125825' 2019-07-04T20:25:56 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:26:11 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' 2019-07-04T20:26:11 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/ERR125825' 2019-07-04T20:26:11 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:26:27 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' 2019-07-04T20:26:27 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/ERR125825' 2019-07-04T20:26:27 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:26:42 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' 2019-07-04T20:26:42 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/ERR125825' 2019-07-04T20:26:42 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:26:57 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' 2019-07-04T20:26:57 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/ERR125825' 2019-07-04T20:26:57 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' 2019-07-04T20:27:13 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' 2019-07-04T20:27:13 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/ERR125825' 2019-07-04T20:27:13 fasterq-dump.2.9.6 err: invalid accession 'ERR125825' spots read : 22,884,065 reads read : 22,884,065 reads written : 22,884,065 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: 00:00:00 Multiseed full-index search: 00:10:08 22884065 reads; of these: 22884065 (100.00%) were unpaired; of these: 602477 (2.63%) aligned 0 times 16959128 (74.11%) aligned exactly 1 time 5322460 (23.26%) aligned >1 times 97.37% overall alignment rate Time searching: 00:10:10 Overall time: 00:10:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1248911 / 22281588 = 0.0561 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 05:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.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 05:56:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.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 05:56:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.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 05:56:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:56:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:56:31: 1000000 INFO @ Fri, 05 Jul 2019 05:56:33: 1000000 INFO @ Fri, 05 Jul 2019 05:56:33: 1000000 INFO @ Fri, 05 Jul 2019 05:56:42: 2000000 INFO @ Fri, 05 Jul 2019 05:56:42: 2000000 INFO @ Fri, 05 Jul 2019 05:56:43: 2000000 INFO @ Fri, 05 Jul 2019 05:56:51: 3000000 INFO @ Fri, 05 Jul 2019 05:56:52: 3000000 INFO @ Fri, 05 Jul 2019 05:56:53: 3000000 INFO @ Fri, 05 Jul 2019 05:57:01: 4000000 INFO @ Fri, 05 Jul 2019 05:57:02: 4000000 INFO @ Fri, 05 Jul 2019 05:57:03: 4000000 INFO @ Fri, 05 Jul 2019 05:57:10: 5000000 INFO @ Fri, 05 Jul 2019 05:57:12: 5000000 INFO @ Fri, 05 Jul 2019 05:57:13: 5000000 INFO @ Fri, 05 Jul 2019 05:57:19: 6000000 INFO @ Fri, 05 Jul 2019 05:57:21: 6000000 INFO @ Fri, 05 Jul 2019 05:57:23: 6000000 INFO @ Fri, 05 Jul 2019 05:57:27: 7000000 INFO @ Fri, 05 Jul 2019 05:57:31: 7000000 INFO @ Fri, 05 Jul 2019 05:57:33: 7000000 INFO @ Fri, 05 Jul 2019 05:57:38: 8000000 INFO @ Fri, 05 Jul 2019 05:57:42: 8000000 INFO @ Fri, 05 Jul 2019 05:57:43: 8000000 INFO @ Fri, 05 Jul 2019 05:57:49: 9000000 INFO @ Fri, 05 Jul 2019 05:57:53: 9000000 INFO @ Fri, 05 Jul 2019 05:57:54: 9000000 INFO @ Fri, 05 Jul 2019 05:57:58: 10000000 INFO @ Fri, 05 Jul 2019 05:58:03: 10000000 INFO @ Fri, 05 Jul 2019 05:58:05: 10000000 INFO @ Fri, 05 Jul 2019 05:58:06: 11000000 INFO @ Fri, 05 Jul 2019 05:58:13: 11000000 INFO @ Fri, 05 Jul 2019 05:58:15: 12000000 INFO @ Fri, 05 Jul 2019 05:58:15: 11000000 INFO @ Fri, 05 Jul 2019 05:58:23: 13000000 INFO @ Fri, 05 Jul 2019 05:58:23: 12000000 INFO @ Fri, 05 Jul 2019 05:58:24: 12000000 INFO @ Fri, 05 Jul 2019 05:58:32: 14000000 INFO @ Fri, 05 Jul 2019 05:58:33: 13000000 INFO @ Fri, 05 Jul 2019 05:58:34: 13000000 INFO @ Fri, 05 Jul 2019 05:58:41: 15000000 INFO @ Fri, 05 Jul 2019 05:58:43: 14000000 INFO @ Fri, 05 Jul 2019 05:58:44: 14000000 INFO @ Fri, 05 Jul 2019 05:58:50: 16000000 INFO @ Fri, 05 Jul 2019 05:58:53: 15000000 INFO @ Fri, 05 Jul 2019 05:58:54: 15000000 INFO @ Fri, 05 Jul 2019 05:59:00: 17000000 INFO @ Fri, 05 Jul 2019 05:59:03: 16000000 INFO @ Fri, 05 Jul 2019 05:59:04: 16000000 INFO @ Fri, 05 Jul 2019 05:59:09: 18000000 INFO @ Fri, 05 Jul 2019 05:59:13: 17000000 INFO @ Fri, 05 Jul 2019 05:59:14: 17000000 INFO @ Fri, 05 Jul 2019 05:59:18: 19000000 INFO @ Fri, 05 Jul 2019 05:59:23: 18000000 INFO @ Fri, 05 Jul 2019 05:59:23: 18000000 INFO @ Fri, 05 Jul 2019 05:59:28: 20000000 INFO @ Fri, 05 Jul 2019 05:59:33: 19000000 INFO @ Fri, 05 Jul 2019 05:59:34: 19000000 INFO @ Fri, 05 Jul 2019 05:59:38: 21000000 INFO @ Fri, 05 Jul 2019 05:59:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:59:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:59:38: #1 total tags in treatment: 21032677 INFO @ Fri, 05 Jul 2019 05:59:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:59:38: #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 05:59:39: #1 tags after filtering in treatment: 21032509 INFO @ Fri, 05 Jul 2019 05:59:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:59:39: #1 finished! INFO @ Fri, 05 Jul 2019 05:59:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:59:43: 20000000 INFO @ Fri, 05 Jul 2019 05:59:44: 20000000 INFO @ Fri, 05 Jul 2019 05:59:44: #2 number of paired peaks: 48731 INFO @ Fri, 05 Jul 2019 05:59:44: start model_add_line... INFO @ Fri, 05 Jul 2019 05:59:45: start X-correlation... INFO @ Fri, 05 Jul 2019 05:59:45: end of X-cor INFO @ Fri, 05 Jul 2019 05:59:45: #2 finished! INFO @ Fri, 05 Jul 2019 05:59:45: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:59:45: #2 alternative fragment length(s) may be 2,130,293 bps INFO @ Fri, 05 Jul 2019 05:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20_model.r INFO @ Fri, 05 Jul 2019 05:59:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:59:53: 21000000 INFO @ Fri, 05 Jul 2019 05:59:53: 21000000 INFO @ Fri, 05 Jul 2019 05:59:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:59:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:59:54: #1 total tags in treatment: 21032677 INFO @ Fri, 05 Jul 2019 05:59:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:59:54: #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 05:59:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:59:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:59:54: #1 total tags in treatment: 21032677 INFO @ Fri, 05 Jul 2019 05:59:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:59:54: #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 05:59:54: #1 tags after filtering in treatment: 21032509 INFO @ Fri, 05 Jul 2019 05:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:59:54: #1 finished! INFO @ Fri, 05 Jul 2019 05:59:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:59:54: #1 tags after filtering in treatment: 21032509 INFO @ Fri, 05 Jul 2019 05:59:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:59:54: #1 finished! INFO @ Fri, 05 Jul 2019 05:59:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:59:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:59:59: #2 number of paired peaks: 48731 INFO @ Fri, 05 Jul 2019 05:59:59: start model_add_line... INFO @ Fri, 05 Jul 2019 05:59:59: start X-correlation... INFO @ Fri, 05 Jul 2019 05:59:59: end of X-cor INFO @ Fri, 05 Jul 2019 05:59:59: #2 finished! INFO @ Fri, 05 Jul 2019 05:59:59: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:59:59: #2 alternative fragment length(s) may be 2,130,293 bps INFO @ Fri, 05 Jul 2019 05:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10_model.r INFO @ Fri, 05 Jul 2019 05:59:59: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:59:59: #2 number of paired peaks: 48731 INFO @ Fri, 05 Jul 2019 05:59:59: start model_add_line... INFO @ Fri, 05 Jul 2019 06:00:00: start X-correlation... INFO @ Fri, 05 Jul 2019 06:00:00: end of X-cor INFO @ Fri, 05 Jul 2019 06:00:00: #2 finished! INFO @ Fri, 05 Jul 2019 06:00:00: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 06:00:00: #2 alternative fragment length(s) may be 2,130,293 bps INFO @ Fri, 05 Jul 2019 06:00:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05_model.r INFO @ Fri, 05 Jul 2019 06:00:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 06:00:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 06:01:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:01:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:01:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 06:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20_peaks.xls INFO @ Fri, 05 Jul 2019 06:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.20_summits.bed INFO @ Fri, 05 Jul 2019 06:01:45: Done! pass1 - making usageList (20 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:01:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10_peaks.xls INFO @ Fri, 05 Jul 2019 06:01:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:01:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.10_summits.bed INFO @ Fri, 05 Jul 2019 06:01:47: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 06:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05_peaks.xls INFO @ Fri, 05 Jul 2019 06:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 06:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101922/ERX101922.05_summits.bed INFO @ Fri, 05 Jul 2019 06:01:53: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1867 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。