Job ID = 2009681 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 ) 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 ) 2019-07-05T10:26:19 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 : 15,791,938 reads read : 15,791,938 reads written : 15,791,938 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364341.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: 00:01:17 15791938 reads; of these: 15791938 (100.00%) were unpaired; of these: 14107955 (89.34%) aligned 0 times 1474085 (9.33%) aligned exactly 1 time 209898 (1.33%) aligned >1 times 10.66% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 560751 / 1683983 = 0.3330 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 19:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.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 19:29:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:29:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:29:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.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 19:29:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:29:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:29:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.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 19:29:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:29:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:29:48: 1000000 INFO @ Fri, 05 Jul 2019 19:29:49: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:49: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:49: #1 total tags in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:49: #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 19:29:49: #1 tags after filtering in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:49: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:49: #2 number of paired peaks: 658 WARNING @ Fri, 05 Jul 2019 19:29:49: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:49: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:49: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:49: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:49: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:49: #2 predicted fragment length is 240 bps INFO @ Fri, 05 Jul 2019 19:29:49: #2 alternative fragment length(s) may be 3,227,240,255 bps INFO @ Fri, 05 Jul 2019 19:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05_model.r INFO @ Fri, 05 Jul 2019 19:29:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:29:50: 1000000 INFO @ Fri, 05 Jul 2019 19:29:50: 1000000 INFO @ Fri, 05 Jul 2019 19:29:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:51: #1 total tags in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:51: #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 19:29:51: #1 tags after filtering in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:51: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:51: #2 number of paired peaks: 658 WARNING @ Fri, 05 Jul 2019 19:29:51: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:51: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:51: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:51: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:51: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:51: #2 predicted fragment length is 240 bps INFO @ Fri, 05 Jul 2019 19:29:51: #2 alternative fragment length(s) may be 3,227,240,255 bps INFO @ Fri, 05 Jul 2019 19:29:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20_model.r INFO @ Fri, 05 Jul 2019 19:29:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:29:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:29:51: #1 total tags in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:29:51: #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 19:29:51: #1 tags after filtering in treatment: 1123232 INFO @ Fri, 05 Jul 2019 19:29:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:29:51: #1 finished! INFO @ Fri, 05 Jul 2019 19:29:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:29:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:29:51: #2 number of paired peaks: 658 WARNING @ Fri, 05 Jul 2019 19:29:51: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Fri, 05 Jul 2019 19:29:51: start model_add_line... INFO @ Fri, 05 Jul 2019 19:29:51: start X-correlation... INFO @ Fri, 05 Jul 2019 19:29:52: end of X-cor INFO @ Fri, 05 Jul 2019 19:29:52: #2 finished! INFO @ Fri, 05 Jul 2019 19:29:52: #2 predicted fragment length is 240 bps INFO @ Fri, 05 Jul 2019 19:29:52: #2 alternative fragment length(s) may be 3,227,240,255 bps INFO @ Fri, 05 Jul 2019 19:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10_model.r INFO @ Fri, 05 Jul 2019 19:29:56: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:30:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:30:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:30:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:30:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.05_summits.bed INFO @ Fri, 05 Jul 2019 19:30:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 10 millis BigWig に変換しました。 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:30:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:30:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.10_summits.bed INFO @ Fri, 05 Jul 2019 19:30:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105555/SRX105555.20_summits.bed INFO @ Fri, 05 Jul 2019 19:30:28: Done! INFO @ Fri, 05 Jul 2019 19:30:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (398 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling