Job ID = 2007930 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:29 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 ) 2019-07-05T07:41:15 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' 2019-07-05T07:41:15 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/sos/sra-pub-run-2/ERR506366/ERR506366.1' 2019-07-05T07:41:15 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506366', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:41:20 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' 2019-07-05T07:41:20 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/sos/sra-pub-run-2/ERR506366/ERR506366.1' 2019-07-05T07:41:20 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506366' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:41:25 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' 2019-07-05T07:41:25 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/sos/sra-pub-run-2/ERR506366/ERR506366.1' 2019-07-05T07:41:25 fasterq-dump.2.9.6 err: invalid accession 'ERR506366' spots read : 1,671,540 reads read : 3,343,080 reads written : 3,343,080 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 1671540 reads; of these: 1671540 (100.00%) were paired; of these: 159164 (9.52%) aligned concordantly 0 times 1384192 (82.81%) aligned concordantly exactly 1 time 128184 (7.67%) aligned concordantly >1 times ---- 159164 pairs aligned concordantly 0 times; of these: 35815 (22.50%) aligned discordantly 1 time ---- 123349 pairs aligned 0 times concordantly or discordantly; of these: 246698 mates make up the pairs; of these: 215215 (87.24%) aligned 0 times 21097 (8.55%) aligned exactly 1 time 10386 (4.21%) aligned >1 times 93.56% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 93095 / 1535919 = 0.0606 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 16:52:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam'] # control file = None # effective genome size = 1.21e+07 # 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 16:52:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam'] # control file = None # effective genome size = 1.21e+07 # 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 16:52:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.bam'] # control file = None # effective genome size = 1.21e+07 # 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 16:52:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:46: 1000000 INFO @ Fri, 05 Jul 2019 16:52:48: 1000000 INFO @ Fri, 05 Jul 2019 16:52:50: 1000000 INFO @ Fri, 05 Jul 2019 16:52:53: 2000000 INFO @ Fri, 05 Jul 2019 16:52:58: 2000000 INFO @ Fri, 05 Jul 2019 16:53:00: 2000000 INFO @ Fri, 05 Jul 2019 16:53:00: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:00: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:00: #1 total tags in treatment: 1420022 INFO @ Fri, 05 Jul 2019 16:53:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:00: #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 16:53:00: #1 tags after filtering in treatment: 1349817 INFO @ Fri, 05 Jul 2019 16:53:00: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:00: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:00: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:00: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:00: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:00: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:00: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:00: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:00: #2 predicted fragment length is 221 bps INFO @ Fri, 05 Jul 2019 16:53:00: #2 alternative fragment length(s) may be 2,12,35,82,126,129,160,181,221,245,247,279,302,323,358,376,398,419,447,478,508,528,535,559,582 bps INFO @ Fri, 05 Jul 2019 16:53:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05_model.r INFO @ Fri, 05 Jul 2019 16:53:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:06: Done! pass1 - making usageList (17 chroms): 7 millis pass2 - checking and writing primary data (72 records, 4 fields): 11 millis INFO @ Fri, 05 Jul 2019 16:53:06: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:06: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:06: #1 total tags in treatment: 1420022 INFO @ Fri, 05 Jul 2019 16:53:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:06: #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 16:53:06: #1 tags after filtering in treatment: 1349817 INFO @ Fri, 05 Jul 2019 16:53:06: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:06: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:06: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:06: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:06: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:06: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:06: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:06: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:06: #2 predicted fragment length is 221 bps INFO @ Fri, 05 Jul 2019 16:53:06: #2 alternative fragment length(s) may be 2,12,35,82,126,129,160,181,221,245,247,279,302,323,358,376,398,419,447,478,508,528,535,559,582 bps INFO @ Fri, 05 Jul 2019 16:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10_model.r INFO @ Fri, 05 Jul 2019 16:53:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:09: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:09: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:09: #1 total tags in treatment: 1420022 INFO @ Fri, 05 Jul 2019 16:53:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:09: #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 16:53:09: #1 tags after filtering in treatment: 1349817 INFO @ Fri, 05 Jul 2019 16:53:09: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:53:09: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:09: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:09: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:53:09: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:09: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:09: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:09: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:09: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:09: #2 predicted fragment length is 221 bps INFO @ Fri, 05 Jul 2019 16:53:09: #2 alternative fragment length(s) may be 2,12,35,82,126,129,160,181,221,245,247,279,302,323,358,376,398,419,447,478,508,528,535,559,582 bps INFO @ Fri, 05 Jul 2019 16:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20_model.r INFO @ Fri, 05 Jul 2019 16:53:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:11: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471723/ERX471723.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:15: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。