Job ID = 2007647 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,675,409 reads read : 1,675,409 reads written : 1,675,409 spots read : 1,609,122 reads read : 1,609,122 reads written : 1,609,122 2019-07-05T07:08:55 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 : 1,656,003 reads read : 1,656,003 reads written : 1,656,003 2019-07-05T07:13:59 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 : 1,663,500 reads read : 1,663,500 reads written : 1,663,500 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529794.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529795.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529796.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: 00:03:16 6604034 reads; of these: 6604034 (100.00%) were unpaired; of these: 312557 (4.73%) aligned 0 times 5189250 (78.58%) aligned exactly 1 time 1102227 (16.69%) aligned >1 times 95.27% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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_rmdupse_core] 6227330 / 6291477 = 0.9898 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 16:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.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 16:22:10: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:10: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:10: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 16:22:10: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 16:22:10: #1 total tags in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:10: #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 16:22:10: #1 tags after filtering in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:10: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:10: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:22:10: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:10: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:10: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:11: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:11: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:11: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 16:22:11: #2 alternative fragment length(s) may be 0,144,172,198,275,367,454,482,545,574 bps INFO @ Fri, 05 Jul 2019 16:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05_model.r WARNING @ Fri, 05 Jul 2019 16:22:11: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:22:11: #2 You may need to consider one of the other alternative d(s): 0,144,172,198,275,367,454,482,545,574 WARNING @ Fri, 05 Jul 2019 16:22:11: #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 16:22:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:11: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.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 16:22:11: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:11: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:22:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 16:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.05_summits.bed INFO @ Fri, 05 Jul 2019 16:22:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:22:11: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 16:22:11: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 16:22:11: #1 total tags in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:11: #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 16:22:11: #1 tags after filtering in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:11: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:11: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:22:11: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:11: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:11: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:11: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:11: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:11: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 16:22:11: #2 alternative fragment length(s) may be 0,144,172,198,275,367,454,482,545,574 bps INFO @ Fri, 05 Jul 2019 16:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10_model.r WARNING @ Fri, 05 Jul 2019 16:22:11: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:22:11: #2 You may need to consider one of the other alternative d(s): 0,144,172,198,275,367,454,482,545,574 WARNING @ Fri, 05 Jul 2019 16:22:11: #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 16:22:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.10_summits.bed INFO @ Fri, 05 Jul 2019 16:22:12: Done! INFO @ Fri, 05 Jul 2019 16:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.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 16:22:12: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:22:12: #1 read treatment tags... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:22:12: #1 tag size is determined as 128 bps INFO @ Fri, 05 Jul 2019 16:22:12: #1 tag size = 128 INFO @ Fri, 05 Jul 2019 16:22:12: #1 total tags in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:12: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:22:12: #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 16:22:12: #1 tags after filtering in treatment: 64147 INFO @ Fri, 05 Jul 2019 16:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:22:12: #1 finished! INFO @ Fri, 05 Jul 2019 16:22:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:22:12: #2 number of paired peaks: 267 WARNING @ Fri, 05 Jul 2019 16:22:12: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Fri, 05 Jul 2019 16:22:12: start model_add_line... INFO @ Fri, 05 Jul 2019 16:22:12: start X-correlation... INFO @ Fri, 05 Jul 2019 16:22:12: end of X-cor INFO @ Fri, 05 Jul 2019 16:22:12: #2 finished! INFO @ Fri, 05 Jul 2019 16:22:12: #2 predicted fragment length is 144 bps INFO @ Fri, 05 Jul 2019 16:22:12: #2 alternative fragment length(s) may be 0,144,172,198,275,367,454,482,545,574 bps INFO @ Fri, 05 Jul 2019 16:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20_model.r WARNING @ Fri, 05 Jul 2019 16:22:12: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:22:12: #2 You may need to consider one of the other alternative d(s): 0,144,172,198,275,367,454,482,545,574 WARNING @ Fri, 05 Jul 2019 16:22:12: #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 16:22:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:22:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:22:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:22:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:22:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548244/ERX2548244.20_summits.bed INFO @ Fri, 05 Jul 2019 16:22:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling