Job ID = 2007656 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,562,625 reads read : 4,562,625 reads written : 4,562,625 2019-07-05T07:07:06 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 ) 2019-07-05T07:07:07 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 : 4,432,403 reads read : 4,432,403 reads written : 4,432,403 spots read : 4,586,132 reads read : 4,586,132 reads written : 4,586,132 spots read : 4,263,323 reads read : 4,263,323 reads written : 4,263,323 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529818.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529819.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529820.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: 00:09:02 17844483 reads; of these: 17844483 (100.00%) were unpaired; of these: 834645 (4.68%) aligned 0 times 13525987 (75.80%) aligned exactly 1 time 3483851 (19.52%) aligned >1 times 95.32% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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] 16685417 / 17009838 = 0.9809 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 16:27:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.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 16:27:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:27:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.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 16:27:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:27:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.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 16:27:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:27:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:27:52: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:27:52: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:27:52: #1 total tags in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:27:52: #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 16:27:52: #1 tags after filtering in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:27:52: #1 finished! INFO @ Fri, 05 Jul 2019 16:27:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:27:52: #2 number of paired peaks: 425 WARNING @ Fri, 05 Jul 2019 16:27:52: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Fri, 05 Jul 2019 16:27:52: start model_add_line... INFO @ Fri, 05 Jul 2019 16:27:52: start X-correlation... INFO @ Fri, 05 Jul 2019 16:27:52: end of X-cor INFO @ Fri, 05 Jul 2019 16:27:52: #2 finished! INFO @ Fri, 05 Jul 2019 16:27:52: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:27:52: #2 alternative fragment length(s) may be 73,99 bps INFO @ Fri, 05 Jul 2019 16:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05_model.r WARNING @ Fri, 05 Jul 2019 16:27:52: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:27:52: #2 You may need to consider one of the other alternative d(s): 73,99 WARNING @ Fri, 05 Jul 2019 16:27:52: #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 16:27:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:27:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:27:53: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:27:53: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:27:53: #1 total tags in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:27:53: #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 16:27:53: #1 tags after filtering in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:27:53: #1 finished! INFO @ Fri, 05 Jul 2019 16:27:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:27:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:27:53: #2 number of paired peaks: 425 WARNING @ Fri, 05 Jul 2019 16:27:53: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Fri, 05 Jul 2019 16:27:53: start model_add_line... INFO @ Fri, 05 Jul 2019 16:27:53: start X-correlation... INFO @ Fri, 05 Jul 2019 16:27:53: end of X-cor INFO @ Fri, 05 Jul 2019 16:27:53: #2 finished! INFO @ Fri, 05 Jul 2019 16:27:53: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:27:53: #2 alternative fragment length(s) may be 73,99 bps INFO @ Fri, 05 Jul 2019 16:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10_model.r WARNING @ Fri, 05 Jul 2019 16:27:53: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:27:53: #2 You may need to consider one of the other alternative d(s): 73,99 WARNING @ Fri, 05 Jul 2019 16:27:53: #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 16:27:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:27:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:27:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:27:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:27:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.05_summits.bed INFO @ Fri, 05 Jul 2019 16:27:54: Done! INFO @ Fri, 05 Jul 2019 16:27:54: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:27:54: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:27:54: #1 total tags in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:27:54: #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 16:27:54: #1 tags after filtering in treatment: 324421 INFO @ Fri, 05 Jul 2019 16:27:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:27:54: #1 finished! INFO @ Fri, 05 Jul 2019 16:27:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:27:54: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:27:54: #2 number of paired peaks: 425 WARNING @ Fri, 05 Jul 2019 16:27:54: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Fri, 05 Jul 2019 16:27:54: start model_add_line... INFO @ Fri, 05 Jul 2019 16:27:54: start X-correlation... INFO @ Fri, 05 Jul 2019 16:27:54: end of X-cor INFO @ Fri, 05 Jul 2019 16:27:54: #2 finished! INFO @ Fri, 05 Jul 2019 16:27:54: #2 predicted fragment length is 73 bps INFO @ Fri, 05 Jul 2019 16:27:54: #2 alternative fragment length(s) may be 73,99 bps INFO @ Fri, 05 Jul 2019 16:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20_model.r WARNING @ Fri, 05 Jul 2019 16:27:54: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:27:54: #2 You may need to consider one of the other alternative d(s): 73,99 WARNING @ Fri, 05 Jul 2019 16:27:54: #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 16:27:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:27:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.10_summits.bed INFO @ Fri, 05 Jul 2019 16:27:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:27:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548250/ERX2548250.20_summits.bed INFO @ Fri, 05 Jul 2019 16:27:56: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (89 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling