Job ID = 2007684 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T07:21:05 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 : 74,037 reads read : 148,074 reads written : 148,074 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: 00:00:03 74037 reads; of these: 74037 (100.00%) were paired; of these: 5048 (6.82%) aligned concordantly 0 times 63288 (85.48%) aligned concordantly exactly 1 time 5701 (7.70%) aligned concordantly >1 times ---- 5048 pairs aligned concordantly 0 times; of these: 1900 (37.64%) aligned discordantly 1 time ---- 3148 pairs aligned 0 times concordantly or discordantly; of these: 6296 mates make up the pairs; of these: 5056 (80.30%) aligned 0 times 789 (12.53%) aligned exactly 1 time 451 (7.16%) aligned >1 times 96.59% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 88 / 70455 = 0.0012 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 16:21:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.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 16:21:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:28: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:21:28: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:21:28: #1 total tags in treatment: 68901 INFO @ Fri, 05 Jul 2019 16:21:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:28: #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 16:21:28: #1 tags after filtering in treatment: 68559 INFO @ Fri, 05 Jul 2019 16:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:28: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 16:21:28: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:28: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:28: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:28: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:28: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:28: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:21:28: #2 alternative fragment length(s) may be 58,146,193,226,313,391,567 bps INFO @ Fri, 05 Jul 2019 16:21:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05_model.r INFO @ Fri, 05 Jul 2019 16:21:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.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 16:21:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.05_summits.bed INFO @ Fri, 05 Jul 2019 16:21:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:21:28: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:21:28: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:21:28: #1 total tags in treatment: 68901 INFO @ Fri, 05 Jul 2019 16:21:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:28: #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 16:21:28: #1 tags after filtering in treatment: 68559 INFO @ Fri, 05 Jul 2019 16:21:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:28: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:29: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 16:21:29: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:29: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:29: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:29: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:29: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:29: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:21:29: #2 alternative fragment length(s) may be 58,146,193,226,313,391,567 bps INFO @ Fri, 05 Jul 2019 16:21:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10_model.r INFO @ Fri, 05 Jul 2019 16:21:29: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.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 16:21:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:21:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:21:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.10_summits.bed INFO @ Fri, 05 Jul 2019 16:21:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:21:30: #1 tag size is determined as 25 bps INFO @ Fri, 05 Jul 2019 16:21:30: #1 tag size = 25 INFO @ Fri, 05 Jul 2019 16:21:30: #1 total tags in treatment: 68901 INFO @ Fri, 05 Jul 2019 16:21:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:21:30: #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 16:21:30: #1 tags after filtering in treatment: 68559 INFO @ Fri, 05 Jul 2019 16:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:21:30: #1 finished! INFO @ Fri, 05 Jul 2019 16:21:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:21:30: #2 number of paired peaks: 400 WARNING @ Fri, 05 Jul 2019 16:21:30: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Fri, 05 Jul 2019 16:21:30: start model_add_line... INFO @ Fri, 05 Jul 2019 16:21:30: start X-correlation... INFO @ Fri, 05 Jul 2019 16:21:30: end of X-cor INFO @ Fri, 05 Jul 2019 16:21:30: #2 finished! INFO @ Fri, 05 Jul 2019 16:21:30: #2 predicted fragment length is 226 bps INFO @ Fri, 05 Jul 2019 16:21:30: #2 alternative fragment length(s) may be 58,146,193,226,313,391,567 bps INFO @ Fri, 05 Jul 2019 16:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20_model.r INFO @ Fri, 05 Jul 2019 16:21:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:21:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:21:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:21:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:21:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX433659/ERX433659.20_summits.bed INFO @ Fri, 05 Jul 2019 16:21:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling