Job ID = 2010008 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:51:02 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 : 6,351,789 reads read : 12,703,578 reads written : 12,703,578 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: 00:04:07 6351789 reads; of these: 6351789 (100.00%) were paired; of these: 2225716 (35.04%) aligned concordantly 0 times 2494135 (39.27%) aligned concordantly exactly 1 time 1631938 (25.69%) aligned concordantly >1 times ---- 2225716 pairs aligned concordantly 0 times; of these: 60403 (2.71%) aligned discordantly 1 time ---- 2165313 pairs aligned 0 times concordantly or discordantly; of these: 4330626 mates make up the pairs; of these: 4145866 (95.73%) aligned 0 times 62436 (1.44%) aligned exactly 1 time 122324 (2.82%) aligned >1 times 67.36% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 2745347 / 4181779 = 0.6565 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 21:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.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 21:07:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.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 21:07:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.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 21:07:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:07:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:07:10: 1000000 INFO @ Fri, 05 Jul 2019 21:07:11: 1000000 INFO @ Fri, 05 Jul 2019 21:07:11: 1000000 INFO @ Fri, 05 Jul 2019 21:07:17: 2000000 INFO @ Fri, 05 Jul 2019 21:07:21: 2000000 INFO @ Fri, 05 Jul 2019 21:07:21: 2000000 INFO @ Fri, 05 Jul 2019 21:07:25: 3000000 INFO @ Fri, 05 Jul 2019 21:07:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:07:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:07:25: #1 total tags in treatment: 1406063 INFO @ Fri, 05 Jul 2019 21:07:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:25: #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 21:07:25: #1 tags after filtering in treatment: 785503 INFO @ Fri, 05 Jul 2019 21:07:25: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 05 Jul 2019 21:07:25: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:25: #2 number of paired peaks: 592 WARNING @ Fri, 05 Jul 2019 21:07:25: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Fri, 05 Jul 2019 21:07:25: start model_add_line... INFO @ Fri, 05 Jul 2019 21:07:25: start X-correlation... INFO @ Fri, 05 Jul 2019 21:07:25: end of X-cor INFO @ Fri, 05 Jul 2019 21:07:25: #2 finished! INFO @ Fri, 05 Jul 2019 21:07:25: #2 predicted fragment length is 168 bps INFO @ Fri, 05 Jul 2019 21:07:25: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 05 Jul 2019 21:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20_model.r INFO @ Fri, 05 Jul 2019 21:07:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:07:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.20_summits.bed INFO @ Fri, 05 Jul 2019 21:07:30: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (369 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 21:07:31: 3000000 INFO @ Fri, 05 Jul 2019 21:07:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:07:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:07:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:07:31: #1 total tags in treatment: 1406063 INFO @ Fri, 05 Jul 2019 21:07:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:31: #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 21:07:31: #1 tags after filtering in treatment: 785503 INFO @ Fri, 05 Jul 2019 21:07:31: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 05 Jul 2019 21:07:31: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:07:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:07:31: #1 total tags in treatment: 1406063 INFO @ Fri, 05 Jul 2019 21:07:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:07:31: #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 21:07:31: #2 number of paired peaks: 592 WARNING @ Fri, 05 Jul 2019 21:07:31: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Fri, 05 Jul 2019 21:07:31: start model_add_line... INFO @ Fri, 05 Jul 2019 21:07:31: start X-correlation... INFO @ Fri, 05 Jul 2019 21:07:31: #1 tags after filtering in treatment: 785503 INFO @ Fri, 05 Jul 2019 21:07:31: #1 Redundant rate of treatment: 0.44 INFO @ Fri, 05 Jul 2019 21:07:31: #1 finished! INFO @ Fri, 05 Jul 2019 21:07:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:07:31: end of X-cor INFO @ Fri, 05 Jul 2019 21:07:31: #2 finished! INFO @ Fri, 05 Jul 2019 21:07:31: #2 predicted fragment length is 168 bps INFO @ Fri, 05 Jul 2019 21:07:31: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 05 Jul 2019 21:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05_model.r INFO @ Fri, 05 Jul 2019 21:07:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:07:32: #2 number of paired peaks: 592 WARNING @ Fri, 05 Jul 2019 21:07:32: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Fri, 05 Jul 2019 21:07:32: start model_add_line... INFO @ Fri, 05 Jul 2019 21:07:32: start X-correlation... INFO @ Fri, 05 Jul 2019 21:07:32: end of X-cor INFO @ Fri, 05 Jul 2019 21:07:32: #2 finished! INFO @ Fri, 05 Jul 2019 21:07:32: #2 predicted fragment length is 168 bps INFO @ Fri, 05 Jul 2019 21:07:32: #2 alternative fragment length(s) may be 4,168 bps INFO @ Fri, 05 Jul 2019 21:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10_model.r INFO @ Fri, 05 Jul 2019 21:07:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:07:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:07:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.05_summits.bed INFO @ Fri, 05 Jul 2019 21:07:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339870/SRX2339870.10_summits.bed INFO @ Fri, 05 Jul 2019 21:07:36: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling