Job ID = 2007632 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,462,368 reads read : 4,462,368 reads written : 4,462,368 spots read : 4,257,296 reads read : 4,257,296 reads written : 4,257,296 spots read : 4,216,219 reads read : 4,216,219 reads written : 4,216,219 2019-07-05T07:18:11 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 ) 2019-07-05T07:18:11 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 : 4,424,977 reads read : 4,424,977 reads written : 4,424,977 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529754.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529755.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529756.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: 00:06:50 17360860 reads; of these: 17360860 (100.00%) were unpaired; of these: 3479647 (20.04%) aligned 0 times 11250441 (64.80%) aligned exactly 1 time 2630772 (15.15%) aligned >1 times 79.96% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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 12 files... [bam_rmdupse_core] 13729885 / 13881213 = 0.9891 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 16:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.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 16:36:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.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 16:36:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:15: #1 tag size is determined as 144 bps INFO @ Fri, 05 Jul 2019 16:36:15: #1 tag size = 144 INFO @ Fri, 05 Jul 2019 16:36:15: #1 total tags in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:15: #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 16:36:15: #1 tags after filtering in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:36:15: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:15: #2 number of paired peaks: 351 WARNING @ Fri, 05 Jul 2019 16:36:15: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:15: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:15: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:15: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:15: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:15: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 16:36:15: #2 alternative fragment length(s) may be 89,111,156,177,201,220,246,267,290,423,581 bps INFO @ Fri, 05 Jul 2019 16:36:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05_model.r WARNING @ Fri, 05 Jul 2019 16:36:15: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:36:15: #2 You may need to consider one of the other alternative d(s): 89,111,156,177,201,220,246,267,290,423,581 WARNING @ Fri, 05 Jul 2019 16:36:15: #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 16:36:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.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 16:36:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:36:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:36:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.05_summits.bed INFO @ Fri, 05 Jul 2019 16:36:16: Done! INFO @ Fri, 05 Jul 2019 16:36:16: #1 tag size is determined as 144 bps INFO @ Fri, 05 Jul 2019 16:36:16: #1 tag size = 144 INFO @ Fri, 05 Jul 2019 16:36:16: #1 total tags in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:16: #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 16:36:16: #1 tags after filtering in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:36:16: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:16: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 1 millis INFO @ Fri, 05 Jul 2019 16:36:16: #2 number of paired peaks: 351 WARNING @ Fri, 05 Jul 2019 16:36:16: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:16: start model_add_line... pass2 - checking and writing primary data (65 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 16:36:16: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:16: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:16: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:16: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 16:36:16: #2 alternative fragment length(s) may be 89,111,156,177,201,220,246,267,290,423,581 bps INFO @ Fri, 05 Jul 2019 16:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10_model.r WARNING @ Fri, 05 Jul 2019 16:36:16: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:36:16: #2 You may need to consider one of the other alternative d(s): 89,111,156,177,201,220,246,267,290,423,581 WARNING @ Fri, 05 Jul 2019 16:36:16: #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 16:36:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 16:36:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.10_summits.bed INFO @ Fri, 05 Jul 2019 16:36:17: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 16:36:17: #1 tag size is determined as 144 bps INFO @ Fri, 05 Jul 2019 16:36:17: #1 tag size = 144 INFO @ Fri, 05 Jul 2019 16:36:17: #1 total tags in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:36:17: #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 16:36:17: #1 tags after filtering in treatment: 151328 INFO @ Fri, 05 Jul 2019 16:36:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:36:17: #1 finished! INFO @ Fri, 05 Jul 2019 16:36:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:36:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:36:17: #2 number of paired peaks: 351 WARNING @ Fri, 05 Jul 2019 16:36:17: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 05 Jul 2019 16:36:17: start model_add_line... INFO @ Fri, 05 Jul 2019 16:36:17: start X-correlation... INFO @ Fri, 05 Jul 2019 16:36:17: end of X-cor INFO @ Fri, 05 Jul 2019 16:36:17: #2 finished! INFO @ Fri, 05 Jul 2019 16:36:17: #2 predicted fragment length is 156 bps INFO @ Fri, 05 Jul 2019 16:36:17: #2 alternative fragment length(s) may be 89,111,156,177,201,220,246,267,290,423,581 bps INFO @ Fri, 05 Jul 2019 16:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20_model.r WARNING @ Fri, 05 Jul 2019 16:36:17: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:36:17: #2 You may need to consider one of the other alternative d(s): 89,111,156,177,201,220,246,267,290,423,581 WARNING @ Fri, 05 Jul 2019 16:36:17: #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 16:36:17: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:36:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:36:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548234/ERX2548234.20_summits.bed INFO @ Fri, 05 Jul 2019 16:36:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling