Job ID = 2007944 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:40:36 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' 2019-07-05T07:40:41 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' 2019-07-05T07:40:41 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/ERR506380/ERR506380.1' 2019-07-05T07:40:41 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506380' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: sorter.c run_producer_pool() : processed lookup rows: 1592433 of 3184864 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: sorter.c execute_lookup_production() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:54 fasterq-dump.2.9.6 err: fasterq-dump.c produce_lookup_files() -> RC(rcVDB,rcNoTarg,rcConstructing,rcSize,rcInvalid) 2019-07-05T07:40:59 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' 2019-07-05T07:40:59 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/ERR506380/ERR506380.1' 2019-07-05T07:40:59 fasterq-dump.2.9.6 err: invalid accession 'ERR506380' 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/ERR506380/ERR506380.1' 2019-07-05T07:41:14 fasterq-dump.2.9.6 err: invalid accession 'ERR506380' spots read : 1,667,617 reads read : 3,335,234 reads written : 3,335,234 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: 00:01:58 1667617 reads; of these: 1667617 (100.00%) were paired; of these: 122903 (7.37%) aligned concordantly 0 times 1387990 (83.23%) aligned concordantly exactly 1 time 156724 (9.40%) aligned concordantly >1 times ---- 122903 pairs aligned concordantly 0 times; of these: 34849 (28.35%) aligned discordantly 1 time ---- 88054 pairs aligned 0 times concordantly or discordantly; of these: 176108 mates make up the pairs; of these: 145319 (82.52%) aligned 0 times 18874 (10.72%) aligned exactly 1 time 11915 (6.77%) aligned >1 times 95.64% overall alignment rate Time searching: 00:01:58 Overall time: 00:01:58 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] 51904 / 1568141 = 0.0331 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 16:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.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 16:52:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.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 16:52:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.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 16:52:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:52:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:00: 1000000 INFO @ Fri, 05 Jul 2019 16:53:01: 1000000 INFO @ Fri, 05 Jul 2019 16:53:02: 1000000 INFO @ Fri, 05 Jul 2019 16:53:13: 2000000 INFO @ Fri, 05 Jul 2019 16:53:15: 2000000 INFO @ Fri, 05 Jul 2019 16:53:16: 2000000 INFO @ Fri, 05 Jul 2019 16:53:26: 3000000 INFO @ Fri, 05 Jul 2019 16:53:27: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:27: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:27: #1 total tags in treatment: 1493232 INFO @ Fri, 05 Jul 2019 16:53:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:27: #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 16:53:27: #1 tags after filtering in treatment: 1390435 INFO @ Fri, 05 Jul 2019 16:53:27: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:27: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:27: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 16:53:27: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:27: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:27: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:27: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:27: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:27: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 16:53:27: #2 alternative fragment length(s) may be 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 bps INFO @ Fri, 05 Jul 2019 16:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10_model.r WARNING @ Fri, 05 Jul 2019 16:53:27: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:27: #2 You may need to consider one of the other alternative d(s): 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 WARNING @ Fri, 05 Jul 2019 16:53:27: #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 16:53:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:28: 3000000 INFO @ Fri, 05 Jul 2019 16:53:29: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:29: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:29: #1 total tags in treatment: 1493232 INFO @ Fri, 05 Jul 2019 16:53:29: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:29: #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 16:53:29: #1 tags after filtering in treatment: 1390435 INFO @ Fri, 05 Jul 2019 16:53:29: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:29: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:29: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 16:53:29: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:29: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:29: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:29: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:29: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:29: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 16:53:29: #2 alternative fragment length(s) may be 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 bps INFO @ Fri, 05 Jul 2019 16:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20_model.r WARNING @ Fri, 05 Jul 2019 16:53:29: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:29: #2 You may need to consider one of the other alternative d(s): 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 WARNING @ Fri, 05 Jul 2019 16:53:29: #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 16:53:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:32: 3000000 INFO @ Fri, 05 Jul 2019 16:53:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:33: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:53:33: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:53:33: #1 total tags in treatment: 1493232 INFO @ Fri, 05 Jul 2019 16:53:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:53:33: #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 16:53:33: #1 tags after filtering in treatment: 1390435 INFO @ Fri, 05 Jul 2019 16:53:33: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 16:53:33: #1 finished! INFO @ Fri, 05 Jul 2019 16:53:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:53:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:53:33: #2 number of paired peaks: 182 WARNING @ Fri, 05 Jul 2019 16:53:33: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 05 Jul 2019 16:53:33: start model_add_line... INFO @ Fri, 05 Jul 2019 16:53:33: start X-correlation... INFO @ Fri, 05 Jul 2019 16:53:33: end of X-cor INFO @ Fri, 05 Jul 2019 16:53:33: #2 finished! INFO @ Fri, 05 Jul 2019 16:53:33: #2 predicted fragment length is 173 bps INFO @ Fri, 05 Jul 2019 16:53:33: #2 alternative fragment length(s) may be 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 bps INFO @ Fri, 05 Jul 2019 16:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05_model.r WARNING @ Fri, 05 Jul 2019 16:53:33: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:53:33: #2 You may need to consider one of the other alternative d(s): 0,91,96,103,125,152,173,203,223,231,239,253,279,310,358,372,408,472,487,507,540,560,569,572 WARNING @ Fri, 05 Jul 2019 16:53:33: #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 16:53:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:53:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.10_summits.bed INFO @ Fri, 05 Jul 2019 16:53:34: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.20_summits.bed INFO @ Fri, 05 Jul 2019 16:53:35: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:53:37: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471737/ERX471737.05_summits.bed INFO @ Fri, 05 Jul 2019 16:53:39: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。