Job ID = 2007915 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:39:12 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-07-05T07:40:35 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' 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 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' 2019-07-05T07:40:40 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/ERR506355/ERR506355.1' 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506355' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:40 fasterq-dump.2.9.6 err: perform_fastq_split_file_join().make_fastq_csra_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:44 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' 2019-07-05T07:40:44 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/ERR506355/ERR506355.1' 2019-07-05T07:40:44 fasterq-dump.2.9.6 err: invalid accession 'ERR506355' 2019-07-05T07:41:00 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' 2019-07-05T07:41:00 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/ERR506355/ERR506355.1' 2019-07-05T07:41:00 fasterq-dump.2.9.6 err: invalid accession 'ERR506355' 2019-07-05T07:41:14 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' 2019-07-05T07:41:14 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/ERR506355/ERR506355.1' 2019-07-05T07:41:14 fasterq-dump.2.9.6 err: invalid accession 'ERR506355' 2019-07-05T07:43:47 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 : 1,665,035 reads read : 3,330,070 reads written : 3,330,070 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: 00:01:54 1665035 reads; of these: 1665035 (100.00%) were paired; of these: 139608 (8.38%) aligned concordantly 0 times 1397644 (83.94%) aligned concordantly exactly 1 time 127783 (7.67%) aligned concordantly >1 times ---- 139608 pairs aligned concordantly 0 times; of these: 35352 (25.32%) aligned discordantly 1 time ---- 104256 pairs aligned 0 times concordantly or discordantly; of these: 208512 mates make up the pairs; of these: 181057 (86.83%) aligned 0 times 17505 (8.40%) aligned exactly 1 time 9950 (4.77%) aligned >1 times 94.56% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 127790 / 1553491 = 0.0823 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 16:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.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 16:52:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.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 16:52:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.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 16:52:09: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:09: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:17: 1000000 INFO @ Fri, 05 Jul 2019 16:52:18: 1000000 INFO @ Fri, 05 Jul 2019 16:52:18: 1000000 INFO @ Fri, 05 Jul 2019 16:52:27: 2000000 INFO @ Fri, 05 Jul 2019 16:52:27: 2000000 INFO @ Fri, 05 Jul 2019 16:52:29: 2000000 INFO @ Fri, 05 Jul 2019 16:52:34: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:52:34: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:52:34: #1 total tags in treatment: 1399028 INFO @ Fri, 05 Jul 2019 16:52:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:52:34: #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 16:52:34: #1 tags after filtering in treatment: 1326898 INFO @ Fri, 05 Jul 2019 16:52:34: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:52:34: #1 finished! INFO @ Fri, 05 Jul 2019 16:52:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:52:34: #2 number of paired peaks: 159 WARNING @ Fri, 05 Jul 2019 16:52:34: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 05 Jul 2019 16:52:34: start model_add_line... INFO @ Fri, 05 Jul 2019 16:52:34: start X-correlation... INFO @ Fri, 05 Jul 2019 16:52:34: end of X-cor INFO @ Fri, 05 Jul 2019 16:52:34: #2 finished! INFO @ Fri, 05 Jul 2019 16:52:34: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 16:52:34: #2 alternative fragment length(s) may be 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 bps INFO @ Fri, 05 Jul 2019 16:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20_model.r WARNING @ Fri, 05 Jul 2019 16:52:34: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:52:34: #2 You may need to consider one of the other alternative d(s): 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 WARNING @ Fri, 05 Jul 2019 16:52:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:52:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:52:36: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:52:36: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:52:36: #1 total tags in treatment: 1399028 INFO @ Fri, 05 Jul 2019 16:52:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:52:36: #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 16:52:36: #1 tags after filtering in treatment: 1326898 INFO @ Fri, 05 Jul 2019 16:52:36: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:52:36: #1 finished! INFO @ Fri, 05 Jul 2019 16:52:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:52:36: #2 number of paired peaks: 159 WARNING @ Fri, 05 Jul 2019 16:52:36: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 05 Jul 2019 16:52:36: start model_add_line... INFO @ Fri, 05 Jul 2019 16:52:36: start X-correlation... INFO @ Fri, 05 Jul 2019 16:52:36: end of X-cor INFO @ Fri, 05 Jul 2019 16:52:36: #2 finished! INFO @ Fri, 05 Jul 2019 16:52:36: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 16:52:36: #2 alternative fragment length(s) may be 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 bps INFO @ Fri, 05 Jul 2019 16:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10_model.r WARNING @ Fri, 05 Jul 2019 16:52:36: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:52:36: #2 You may need to consider one of the other alternative d(s): 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 WARNING @ Fri, 05 Jul 2019 16:52:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:52:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:52:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:52:39: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:52:39: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:52:39: #1 total tags in treatment: 1399028 INFO @ Fri, 05 Jul 2019 16:52:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:52:39: #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 16:52:39: #1 tags after filtering in treatment: 1326898 INFO @ Fri, 05 Jul 2019 16:52:39: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 16:52:39: #1 finished! INFO @ Fri, 05 Jul 2019 16:52:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:52:39: #2 number of paired peaks: 159 WARNING @ Fri, 05 Jul 2019 16:52:39: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Fri, 05 Jul 2019 16:52:39: start model_add_line... INFO @ Fri, 05 Jul 2019 16:52:39: start X-correlation... INFO @ Fri, 05 Jul 2019 16:52:39: end of X-cor INFO @ Fri, 05 Jul 2019 16:52:39: #2 finished! INFO @ Fri, 05 Jul 2019 16:52:39: #2 predicted fragment length is 199 bps INFO @ Fri, 05 Jul 2019 16:52:39: #2 alternative fragment length(s) may be 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 bps INFO @ Fri, 05 Jul 2019 16:52:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05_model.r WARNING @ Fri, 05 Jul 2019 16:52:39: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:52:39: #2 You may need to consider one of the other alternative d(s): 1,51,126,130,173,199,213,227,263,365,506,537,557,566,572,588,591 WARNING @ Fri, 05 Jul 2019 16:52:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:52:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.20_summits.bed INFO @ Fri, 05 Jul 2019 16:52:40: Done! INFO @ Fri, 05 Jul 2019 16:52:40: #3 Call peaks for each chromosome... pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.10_summits.bed INFO @ Fri, 05 Jul 2019 16:52:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:52:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:52:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:52:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:52:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471712/ERX471712.05_summits.bed INFO @ Fri, 05 Jul 2019 16:52:45: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。