Job ID = 2009683 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T10:25:57 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 : 7,549,353 reads read : 7,549,353 reads written : 7,549,353 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364342.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: 00:01:56 7549353 reads; of these: 7549353 (100.00%) were unpaired; of these: 1950461 (25.84%) aligned 0 times 5168374 (68.46%) aligned exactly 1 time 430518 (5.70%) aligned >1 times 74.16% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 3347738 / 5598892 = 0.5979 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 19:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.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 19:33:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:33:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.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 19:33:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:33:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.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 19:33:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:33:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:33:40: 1000000 INFO @ Fri, 05 Jul 2019 19:33:40: 1000000 INFO @ Fri, 05 Jul 2019 19:33:45: 1000000 INFO @ Fri, 05 Jul 2019 19:33:47: 2000000 INFO @ Fri, 05 Jul 2019 19:33:48: 2000000 INFO @ Fri, 05 Jul 2019 19:33:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:33:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:33:49: #1 total tags in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:33:49: #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 19:33:49: #1 tags after filtering in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:33:49: #1 finished! INFO @ Fri, 05 Jul 2019 19:33:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:33:49: #2 number of paired peaks: 612 WARNING @ Fri, 05 Jul 2019 19:33:49: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 05 Jul 2019 19:33:49: start model_add_line... INFO @ Fri, 05 Jul 2019 19:33:49: start X-correlation... INFO @ Fri, 05 Jul 2019 19:33:49: end of X-cor INFO @ Fri, 05 Jul 2019 19:33:49: #2 finished! INFO @ Fri, 05 Jul 2019 19:33:49: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 19:33:49: #2 alternative fragment length(s) may be 1,128,154,181,243,513,557 bps INFO @ Fri, 05 Jul 2019 19:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10_model.r INFO @ Fri, 05 Jul 2019 19:33:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:33:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:33:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:33:49: #1 total tags in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:33:49: #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 19:33:49: #1 tags after filtering in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:33:49: #1 finished! INFO @ Fri, 05 Jul 2019 19:33:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:33:50: #2 number of paired peaks: 612 WARNING @ Fri, 05 Jul 2019 19:33:50: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 05 Jul 2019 19:33:50: start model_add_line... INFO @ Fri, 05 Jul 2019 19:33:50: start X-correlation... INFO @ Fri, 05 Jul 2019 19:33:50: end of X-cor INFO @ Fri, 05 Jul 2019 19:33:50: #2 finished! INFO @ Fri, 05 Jul 2019 19:33:50: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 19:33:50: #2 alternative fragment length(s) may be 1,128,154,181,243,513,557 bps INFO @ Fri, 05 Jul 2019 19:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05_model.r INFO @ Fri, 05 Jul 2019 19:33:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:33:53: 2000000 INFO @ Fri, 05 Jul 2019 19:33:54: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:33:54: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:33:54: #1 total tags in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:54: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:33:54: #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 19:33:54: #1 tags after filtering in treatment: 2251154 INFO @ Fri, 05 Jul 2019 19:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:33:54: #1 finished! INFO @ Fri, 05 Jul 2019 19:33:54: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:33:55: #2 number of paired peaks: 612 WARNING @ Fri, 05 Jul 2019 19:33:55: Fewer paired peaks (612) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 612 pairs to build model! INFO @ Fri, 05 Jul 2019 19:33:55: start model_add_line... INFO @ Fri, 05 Jul 2019 19:33:55: start X-correlation... INFO @ Fri, 05 Jul 2019 19:33:55: end of X-cor INFO @ Fri, 05 Jul 2019 19:33:55: #2 finished! INFO @ Fri, 05 Jul 2019 19:33:55: #2 predicted fragment length is 154 bps INFO @ Fri, 05 Jul 2019 19:33:55: #2 alternative fragment length(s) may be 1,128,154,181,243,513,557 bps INFO @ Fri, 05 Jul 2019 19:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20_model.r INFO @ Fri, 05 Jul 2019 19:33:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:34:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:34:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.10_summits.bed INFO @ Fri, 05 Jul 2019 19:34:03: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (718 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 19:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.05_summits.bed INFO @ Fri, 05 Jul 2019 19:34:04: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1136 records, 4 fields): 5 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:34:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:34:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105556/SRX105556.20_summits.bed INFO @ Fri, 05 Jul 2019 19:34:13: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。