Job ID = 2008198 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T08:35:35 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 : 6,131,025 reads read : 12,262,050 reads written : 12,262,050 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628927.sra.cache’: 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: 00:04:32 6131025 reads; of these: 6131025 (100.00%) were paired; of these: 498342 (8.13%) aligned concordantly 0 times 5233621 (85.36%) aligned concordantly exactly 1 time 399062 (6.51%) aligned concordantly >1 times ---- 498342 pairs aligned concordantly 0 times; of these: 32306 (6.48%) aligned discordantly 1 time ---- 466036 pairs aligned 0 times concordantly or discordantly; of these: 932072 mates make up the pairs; of these: 906915 (97.30%) aligned 0 times 16731 (1.80%) aligned exactly 1 time 8426 (0.90%) aligned >1 times 92.60% overall alignment rate Time searching: 00:04:32 Overall time: 00:04:32 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] 5189529 / 5661582 = 0.9166 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 17:45:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.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 17:45:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:45:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.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 17:45:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:45:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:45:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.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 17:45:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:45:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:45:21: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:45:21: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:45:21: #1 total tags in treatment: 453129 INFO @ Fri, 05 Jul 2019 17:45:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:45:21: #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 17:45:21: #1 tags after filtering in treatment: 390968 INFO @ Fri, 05 Jul 2019 17:45:21: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 05 Jul 2019 17:45:21: #1 finished! INFO @ Fri, 05 Jul 2019 17:45:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:45:21: #2 number of paired peaks: 247 WARNING @ Fri, 05 Jul 2019 17:45:21: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Fri, 05 Jul 2019 17:45:21: start model_add_line... INFO @ Fri, 05 Jul 2019 17:45:21: start X-correlation... INFO @ Fri, 05 Jul 2019 17:45:21: end of X-cor INFO @ Fri, 05 Jul 2019 17:45:21: #2 finished! INFO @ Fri, 05 Jul 2019 17:45:21: #2 predicted fragment length is 188 bps INFO @ Fri, 05 Jul 2019 17:45:21: #2 alternative fragment length(s) may be 52,95,188,275,364,415,464,523,539,594 bps INFO @ Fri, 05 Jul 2019 17:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05_model.r INFO @ Fri, 05 Jul 2019 17:45:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:45:22: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:45:22: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:45:22: #1 total tags in treatment: 453129 INFO @ Fri, 05 Jul 2019 17:45:22: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:45:22: #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 17:45:22: #1 tags after filtering in treatment: 390968 INFO @ Fri, 05 Jul 2019 17:45:22: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 05 Jul 2019 17:45:22: #1 finished! INFO @ Fri, 05 Jul 2019 17:45:22: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:45:22: #2 number of paired peaks: 247 WARNING @ Fri, 05 Jul 2019 17:45:22: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Fri, 05 Jul 2019 17:45:22: start model_add_line... INFO @ Fri, 05 Jul 2019 17:45:22: start X-correlation... INFO @ Fri, 05 Jul 2019 17:45:22: end of X-cor INFO @ Fri, 05 Jul 2019 17:45:22: #2 finished! INFO @ Fri, 05 Jul 2019 17:45:22: #2 predicted fragment length is 188 bps INFO @ Fri, 05 Jul 2019 17:45:22: #2 alternative fragment length(s) may be 52,95,188,275,364,415,464,523,539,594 bps INFO @ Fri, 05 Jul 2019 17:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10_model.r INFO @ Fri, 05 Jul 2019 17:45:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:45:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:45:23: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 17:45:23: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 17:45:23: #1 total tags in treatment: 453129 INFO @ Fri, 05 Jul 2019 17:45:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:45:23: #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 17:45:23: #1 tags after filtering in treatment: 390968 INFO @ Fri, 05 Jul 2019 17:45:23: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 05 Jul 2019 17:45:23: #1 finished! INFO @ Fri, 05 Jul 2019 17:45:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:45:23: #2 number of paired peaks: 247 WARNING @ Fri, 05 Jul 2019 17:45:23: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Fri, 05 Jul 2019 17:45:23: start model_add_line... INFO @ Fri, 05 Jul 2019 17:45:23: start X-correlation... INFO @ Fri, 05 Jul 2019 17:45:23: end of X-cor INFO @ Fri, 05 Jul 2019 17:45:23: #2 finished! INFO @ Fri, 05 Jul 2019 17:45:23: #2 predicted fragment length is 188 bps INFO @ Fri, 05 Jul 2019 17:45:23: #2 alternative fragment length(s) may be 52,95,188,275,364,415,464,523,539,594 bps INFO @ Fri, 05 Jul 2019 17:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20_model.r INFO @ Fri, 05 Jul 2019 17:45:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:45:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.05_summits.bed INFO @ Fri, 05 Jul 2019 17:45:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.10_summits.bed INFO @ Fri, 05 Jul 2019 17:45:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:45:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX585733/ERX585733.20_summits.bed INFO @ Fri, 05 Jul 2019 17:45:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。