Job ID = 2011787 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-07-05T17:37:11 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 ) 2019-07-05T17:37:11 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 ) 2019-07-05T17:37:11 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 ) 2019-07-05T17:37:11 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 : 6,515,546 reads read : 13,031,092 reads written : 6,515,546 reads 0-length : 6,515,546 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:16 6515546 reads; of these: 6515546 (100.00%) were unpaired; of these: 2070625 (31.78%) aligned 0 times 4073450 (62.52%) aligned exactly 1 time 371471 (5.70%) aligned >1 times 68.22% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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_rmdupse_core] 3562350 / 4444921 = 0.8014 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 @ Sat, 06 Jul 2019 02:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.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 @ Sat, 06 Jul 2019 02:42:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:42:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.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 @ Sat, 06 Jul 2019 02:42:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:42:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.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 @ Sat, 06 Jul 2019 02:42:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:42:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:42:23: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:42:23: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:42:23: #1 total tags in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:42:23: #1 tags after filtering in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:42:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:42:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:42:23: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:42:23: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:42:23: #1 total tags in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:23: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:42:23: #1 tags after filtering in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:42:23: #1 finished! INFO @ Sat, 06 Jul 2019 02:42:23: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:42:23: #2 number of paired peaks: 129 WARNING @ Sat, 06 Jul 2019 02:42:23: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 06 Jul 2019 02:42:23: start model_add_line... INFO @ Sat, 06 Jul 2019 02:42:23: start X-correlation... INFO @ Sat, 06 Jul 2019 02:42:23: end of X-cor INFO @ Sat, 06 Jul 2019 02:42:23: #2 finished! INFO @ Sat, 06 Jul 2019 02:42:23: #2 predicted fragment length is 78 bps INFO @ Sat, 06 Jul 2019 02:42:23: #2 alternative fragment length(s) may be 4,78,98,114,142,156,175,226,242,479 bps INFO @ Sat, 06 Jul 2019 02:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10_model.r WARNING @ Sat, 06 Jul 2019 02:42:23: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:42:23: #2 You may need to consider one of the other alternative d(s): 4,78,98,114,142,156,175,226,242,479 WARNING @ Sat, 06 Jul 2019 02:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:42:23: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:42:23: #2 number of paired peaks: 129 WARNING @ Sat, 06 Jul 2019 02:42:23: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 06 Jul 2019 02:42:23: start model_add_line... INFO @ Sat, 06 Jul 2019 02:42:23: start X-correlation... INFO @ Sat, 06 Jul 2019 02:42:23: end of X-cor INFO @ Sat, 06 Jul 2019 02:42:23: #2 finished! INFO @ Sat, 06 Jul 2019 02:42:23: #2 predicted fragment length is 78 bps INFO @ Sat, 06 Jul 2019 02:42:23: #2 alternative fragment length(s) may be 4,78,98,114,142,156,175,226,242,479 bps INFO @ Sat, 06 Jul 2019 02:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05_model.r WARNING @ Sat, 06 Jul 2019 02:42:23: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:42:23: #2 You may need to consider one of the other alternative d(s): 4,78,98,114,142,156,175,226,242,479 WARNING @ Sat, 06 Jul 2019 02:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:42:23: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:42:25: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:42:25: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:42:25: #1 total tags in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:25: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:42:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:42:25: #1 tags after filtering in treatment: 882571 INFO @ Sat, 06 Jul 2019 02:42:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:42:25: #1 finished! INFO @ Sat, 06 Jul 2019 02:42:25: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:42:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:42:25: #2 number of paired peaks: 129 WARNING @ Sat, 06 Jul 2019 02:42:25: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 06 Jul 2019 02:42:25: start model_add_line... INFO @ Sat, 06 Jul 2019 02:42:25: start X-correlation... INFO @ Sat, 06 Jul 2019 02:42:25: end of X-cor INFO @ Sat, 06 Jul 2019 02:42:25: #2 finished! INFO @ Sat, 06 Jul 2019 02:42:25: #2 predicted fragment length is 78 bps INFO @ Sat, 06 Jul 2019 02:42:25: #2 alternative fragment length(s) may be 4,78,98,114,142,156,175,226,242,479 bps INFO @ Sat, 06 Jul 2019 02:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20_model.r WARNING @ Sat, 06 Jul 2019 02:42:25: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 06 Jul 2019 02:42:25: #2 You may need to consider one of the other alternative d(s): 4,78,98,114,142,156,175,226,242,479 WARNING @ Sat, 06 Jul 2019 02:42:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 06 Jul 2019 02:42:25: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:42:26: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:42:26: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.10_summits.bed INFO @ Sat, 06 Jul 2019 02:42:27: Done! INFO @ Sat, 06 Jul 2019 02:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05_peaks.xls pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 3 millis INFO @ Sat, 06 Jul 2019 02:42:28: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:42:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.05_summits.bed INFO @ Sat, 06 Jul 2019 02:42:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:42:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:42:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:42:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028218/SRX5028218.20_summits.bed INFO @ Sat, 06 Jul 2019 02:42:29: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。