Job ID = 2010523 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T13:49:53 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' 2019-07-05T13:49:53 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/sra15/SRR/001011/SRR1035327' 2019-07-05T13:49:53 fasterq-dump.2.9.6 err: invalid accession 'SRR1035327' 2019-07-05T13:50:08 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' 2019-07-05T13:50:08 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/sra15/SRR/001011/SRR1035327' 2019-07-05T13:50:08 fasterq-dump.2.9.6 err: invalid accession 'SRR1035327' 2019-07-05T13:50:23 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' 2019-07-05T13:50:23 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/sra15/SRR/001011/SRR1035327' 2019-07-05T13:50:23 fasterq-dump.2.9.6 err: invalid accession 'SRR1035327' 2019-07-05T14:02:36 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 ) 2019-07-05T14:02:36 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 : 11,349,300 reads read : 22,698,600 reads written : 22,698,600 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: 00:06:51 11349300 reads; of these: 11349300 (100.00%) were paired; of these: 4977409 (43.86%) aligned concordantly 0 times 3602562 (31.74%) aligned concordantly exactly 1 time 2769329 (24.40%) aligned concordantly >1 times ---- 4977409 pairs aligned concordantly 0 times; of these: 58475 (1.17%) aligned discordantly 1 time ---- 4918934 pairs aligned 0 times concordantly or discordantly; of these: 9837868 mates make up the pairs; of these: 9476400 (96.33%) aligned 0 times 172395 (1.75%) aligned exactly 1 time 189073 (1.92%) aligned >1 times 58.25% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 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_sort_core] merging from 8 files... [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] 2208260 / 6423621 = 0.3438 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 23:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.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 23:16:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.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 23:16:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.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 23:16:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:16:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:16:26: 1000000 INFO @ Fri, 05 Jul 2019 23:16:28: 1000000 INFO @ Fri, 05 Jul 2019 23:16:29: 1000000 INFO @ Fri, 05 Jul 2019 23:16:33: 2000000 INFO @ Fri, 05 Jul 2019 23:16:35: 2000000 INFO @ Fri, 05 Jul 2019 23:16:36: 2000000 INFO @ Fri, 05 Jul 2019 23:16:39: 3000000 INFO @ Fri, 05 Jul 2019 23:16:42: 3000000 INFO @ Fri, 05 Jul 2019 23:16:43: 3000000 INFO @ Fri, 05 Jul 2019 23:16:45: 4000000 INFO @ Fri, 05 Jul 2019 23:16:49: 4000000 INFO @ Fri, 05 Jul 2019 23:16:50: 4000000 INFO @ Fri, 05 Jul 2019 23:16:52: 5000000 INFO @ Fri, 05 Jul 2019 23:16:58: 6000000 INFO @ Fri, 05 Jul 2019 23:16:59: 5000000 INFO @ Fri, 05 Jul 2019 23:17:00: 5000000 INFO @ Fri, 05 Jul 2019 23:17:04: 7000000 INFO @ Fri, 05 Jul 2019 23:17:07: 6000000 INFO @ Fri, 05 Jul 2019 23:17:09: 6000000 INFO @ Fri, 05 Jul 2019 23:17:11: 8000000 INFO @ Fri, 05 Jul 2019 23:17:14: 7000000 INFO @ Fri, 05 Jul 2019 23:17:16: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:16: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:16: #1 total tags in treatment: 4167366 INFO @ Fri, 05 Jul 2019 23:17:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:16: #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 23:17:16: #1 tags after filtering in treatment: 2566463 INFO @ Fri, 05 Jul 2019 23:17:16: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:17:16: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:16: #2 number of paired peaks: 345 WARNING @ Fri, 05 Jul 2019 23:17:16: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:16: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:16: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:16: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:16: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:16: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 23:17:16: #2 alternative fragment length(s) may be 3,183 bps INFO @ Fri, 05 Jul 2019 23:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05_model.r INFO @ Fri, 05 Jul 2019 23:17:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:17:17: 7000000 INFO @ Fri, 05 Jul 2019 23:17:21: 8000000 INFO @ Fri, 05 Jul 2019 23:17:26: 8000000 INFO @ Fri, 05 Jul 2019 23:17:27: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:27: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:27: #1 total tags in treatment: 4167366 INFO @ Fri, 05 Jul 2019 23:17:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:27: #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 23:17:27: #1 tags after filtering in treatment: 2566463 INFO @ Fri, 05 Jul 2019 23:17:27: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:17:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:27: #2 number of paired peaks: 345 WARNING @ Fri, 05 Jul 2019 23:17:27: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:27: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 23:17:27: #2 alternative fragment length(s) may be 3,183 bps INFO @ Fri, 05 Jul 2019 23:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20_model.r INFO @ Fri, 05 Jul 2019 23:17:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:17:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.05_summits.bed INFO @ Fri, 05 Jul 2019 23:17:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (562 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:17:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:17:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:17:32: #1 total tags in treatment: 4167366 INFO @ Fri, 05 Jul 2019 23:17:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:17:32: #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 23:17:32: #1 tags after filtering in treatment: 2566463 INFO @ Fri, 05 Jul 2019 23:17:32: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:17:32: #1 finished! INFO @ Fri, 05 Jul 2019 23:17:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:17:32: #2 number of paired peaks: 345 WARNING @ Fri, 05 Jul 2019 23:17:32: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Fri, 05 Jul 2019 23:17:32: start model_add_line... INFO @ Fri, 05 Jul 2019 23:17:32: start X-correlation... INFO @ Fri, 05 Jul 2019 23:17:32: end of X-cor INFO @ Fri, 05 Jul 2019 23:17:32: #2 finished! INFO @ Fri, 05 Jul 2019 23:17:32: #2 predicted fragment length is 183 bps INFO @ Fri, 05 Jul 2019 23:17:32: #2 alternative fragment length(s) may be 3,183 bps INFO @ Fri, 05 Jul 2019 23:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10_model.r INFO @ Fri, 05 Jul 2019 23:17:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:17:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.20_summits.bed INFO @ Fri, 05 Jul 2019 23:17:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:17:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381226/SRX381226.10_summits.bed INFO @ Fri, 05 Jul 2019 23:17:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。