Job ID = 2007938 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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/ERR506374/ERR506374.1' 2019-07-05T07:41:00 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'ERR506374', 'SEQUENCE', 'NAME' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:41:05 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' 2019-07-05T07:41:05 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/ERR506374/ERR506374.1' 2019-07-05T07:41:05 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'ERR506374' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcBusy) 2019-07-05T07:41:11 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' 2019-07-05T07:41:11 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/sos/sra-pub-run-2/ERR506374/ERR506374.1' 2019-07-05T07:41:11 fasterq-dump.2.9.6 err: invalid accession 'ERR506374' spots read : 1,839,152 reads read : 3,678,304 reads written : 3,678,304 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: 00:02:34 1839152 reads; of these: 1839152 (100.00%) were paired; of these: 258196 (14.04%) aligned concordantly 0 times 1453341 (79.02%) aligned concordantly exactly 1 time 127615 (6.94%) aligned concordantly >1 times ---- 258196 pairs aligned concordantly 0 times; of these: 30647 (11.87%) aligned discordantly 1 time ---- 227549 pairs aligned 0 times concordantly or discordantly; of these: 455098 mates make up the pairs; of these: 430213 (94.53%) aligned 0 times 16259 (3.57%) aligned exactly 1 time 8626 (1.90%) aligned >1 times 88.30% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 235709 / 1607587 = 0.1466 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 16:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.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 16:53:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.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 16:53:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:53:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.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 16:53:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:53:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:54:01: 1000000 INFO @ Fri, 05 Jul 2019 16:54:01: 1000000 INFO @ Fri, 05 Jul 2019 16:54:03: 1000000 INFO @ Fri, 05 Jul 2019 16:54:09: 2000000 INFO @ Fri, 05 Jul 2019 16:54:10: 2000000 INFO @ Fri, 05 Jul 2019 16:54:12: 2000000 INFO @ Fri, 05 Jul 2019 16:54:15: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:15: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:15: #1 total tags in treatment: 1347232 INFO @ Fri, 05 Jul 2019 16:54:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:15: #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 16:54:15: #1 tags after filtering in treatment: 1287617 INFO @ Fri, 05 Jul 2019 16:54:15: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:15: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:15: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:54:15: 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 16:54:15: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:15: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:15: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:15: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:15: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:54:15: #2 alternative fragment length(s) may be 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 bps INFO @ Fri, 05 Jul 2019 16:54:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10_model.r WARNING @ Fri, 05 Jul 2019 16:54:15: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:15: #2 You may need to consider one of the other alternative d(s): 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 WARNING @ Fri, 05 Jul 2019 16:54:15: #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 16:54:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:17: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:17: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:17: #1 total tags in treatment: 1347232 INFO @ Fri, 05 Jul 2019 16:54:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:17: #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 16:54:17: #1 tags after filtering in treatment: 1287617 INFO @ Fri, 05 Jul 2019 16:54:17: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:17: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:18: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:54:18: 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 16:54:18: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:18: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:18: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:18: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:18: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:54:18: #2 alternative fragment length(s) may be 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 bps INFO @ Fri, 05 Jul 2019 16:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05_model.r WARNING @ Fri, 05 Jul 2019 16:54:18: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:18: #2 You may need to consider one of the other alternative d(s): 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 WARNING @ Fri, 05 Jul 2019 16:54:18: #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 16:54:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:19: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 16:54:19: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 16:54:19: #1 total tags in treatment: 1347232 INFO @ Fri, 05 Jul 2019 16:54:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:54:19: #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 16:54:19: #1 tags after filtering in treatment: 1287617 INFO @ Fri, 05 Jul 2019 16:54:19: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 16:54:19: #1 finished! INFO @ Fri, 05 Jul 2019 16:54:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:54:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:19: #2 number of paired peaks: 160 WARNING @ Fri, 05 Jul 2019 16:54:19: 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 16:54:19: start model_add_line... INFO @ Fri, 05 Jul 2019 16:54:19: start X-correlation... INFO @ Fri, 05 Jul 2019 16:54:19: end of X-cor INFO @ Fri, 05 Jul 2019 16:54:19: #2 finished! INFO @ Fri, 05 Jul 2019 16:54:19: #2 predicted fragment length is 182 bps INFO @ Fri, 05 Jul 2019 16:54:19: #2 alternative fragment length(s) may be 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 bps INFO @ Fri, 05 Jul 2019 16:54:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20_model.r WARNING @ Fri, 05 Jul 2019 16:54:19: #2 Since the d (182) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:54:19: #2 You may need to consider one of the other alternative d(s): 1,32,52,72,114,136,164,182,215,258,278,304,324,348,371,395,428,433,447,500,531,553,575,582,587 WARNING @ Fri, 05 Jul 2019 16:54:19: #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 16:54:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:54:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.10_summits.bed INFO @ Fri, 05 Jul 2019 16:54:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 16:54:22: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.05_summits.bed INFO @ Fri, 05 Jul 2019 16:54:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (56 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:54:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:54:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:54:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:54:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471731/ERX471731.20_summits.bed INFO @ Fri, 05 Jul 2019 16:54:25: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。