Job ID = 2009674 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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 ) 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 : 24,664,907 reads read : 24,664,907 reads written : 24,664,907 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364337.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: 00:02:06 24664907 reads; of these: 24664907 (100.00%) were unpaired; of these: 18225346 (73.89%) aligned 0 times 5456665 (22.12%) aligned exactly 1 time 982896 (3.98%) aligned >1 times 26.11% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 4153683 / 6439561 = 0.6450 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 19:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.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 19:31:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:31:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.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 19:31:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:31:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:31:12: 1000000 INFO @ Fri, 05 Jul 2019 19:31:14: 1000000 INFO @ Fri, 05 Jul 2019 19:31:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.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 19:31:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:31:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:31:19: 2000000 INFO @ Fri, 05 Jul 2019 19:31:21: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:31:21: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:31:21: #1 total tags in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:31:21: #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 19:31:21: #1 tags after filtering in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:31:21: #1 finished! INFO @ Fri, 05 Jul 2019 19:31:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:31:21: #2 number of paired peaks: 576 WARNING @ Fri, 05 Jul 2019 19:31:21: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 05 Jul 2019 19:31:21: start model_add_line... INFO @ Fri, 05 Jul 2019 19:31:21: start X-correlation... INFO @ Fri, 05 Jul 2019 19:31:21: end of X-cor INFO @ Fri, 05 Jul 2019 19:31:21: #2 finished! INFO @ Fri, 05 Jul 2019 19:31:21: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 19:31:21: #2 alternative fragment length(s) may be 1,12,65,93,110,133,205,243,449,490,531,563,598 bps INFO @ Fri, 05 Jul 2019 19:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10_model.r WARNING @ Fri, 05 Jul 2019 19:31:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:31:21: #2 You may need to consider one of the other alternative d(s): 1,12,65,93,110,133,205,243,449,490,531,563,598 WARNING @ Fri, 05 Jul 2019 19:31:21: #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 19:31:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:31:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:31:22: 2000000 INFO @ Fri, 05 Jul 2019 19:31:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:31:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:31:24: #1 total tags in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:31:24: #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 19:31:24: #1 tags after filtering in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:31:24: #1 finished! INFO @ Fri, 05 Jul 2019 19:31:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:31:25: #2 number of paired peaks: 576 WARNING @ Fri, 05 Jul 2019 19:31:25: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 05 Jul 2019 19:31:25: start model_add_line... INFO @ Fri, 05 Jul 2019 19:31:25: start X-correlation... INFO @ Fri, 05 Jul 2019 19:31:25: end of X-cor INFO @ Fri, 05 Jul 2019 19:31:25: #2 finished! INFO @ Fri, 05 Jul 2019 19:31:25: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 19:31:25: #2 alternative fragment length(s) may be 1,12,65,93,110,133,205,243,449,490,531,563,598 bps INFO @ Fri, 05 Jul 2019 19:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05_model.r WARNING @ Fri, 05 Jul 2019 19:31:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:31:25: #2 You may need to consider one of the other alternative d(s): 1,12,65,93,110,133,205,243,449,490,531,563,598 WARNING @ Fri, 05 Jul 2019 19:31:25: #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 19:31:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:31:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:31:26: 1000000 INFO @ Fri, 05 Jul 2019 19:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.10_summits.bed INFO @ Fri, 05 Jul 2019 19:31:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:31:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:31:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:31:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:31:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.05_summits.bed INFO @ Fri, 05 Jul 2019 19:31:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:31:34: 2000000 INFO @ Fri, 05 Jul 2019 19:31:37: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:31:37: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:31:37: #1 total tags in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:31:37: #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 19:31:37: #1 tags after filtering in treatment: 2285878 INFO @ Fri, 05 Jul 2019 19:31:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:31:37: #1 finished! INFO @ Fri, 05 Jul 2019 19:31:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:31:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:31:37: #2 number of paired peaks: 576 WARNING @ Fri, 05 Jul 2019 19:31:37: Fewer paired peaks (576) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 576 pairs to build model! INFO @ Fri, 05 Jul 2019 19:31:37: start model_add_line... INFO @ Fri, 05 Jul 2019 19:31:37: start X-correlation... INFO @ Fri, 05 Jul 2019 19:31:37: end of X-cor INFO @ Fri, 05 Jul 2019 19:31:37: #2 finished! INFO @ Fri, 05 Jul 2019 19:31:37: #2 predicted fragment length is 1 bps INFO @ Fri, 05 Jul 2019 19:31:37: #2 alternative fragment length(s) may be 1,12,65,93,110,133,205,243,449,490,531,563,598 bps INFO @ Fri, 05 Jul 2019 19:31:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20_model.r WARNING @ Fri, 05 Jul 2019 19:31:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:31:37: #2 You may need to consider one of the other alternative d(s): 1,12,65,93,110,133,205,243,449,490,531,563,598 WARNING @ Fri, 05 Jul 2019 19:31:37: #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 19:31:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:31:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:31:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105551/SRX105551.20_summits.bed INFO @ Fri, 05 Jul 2019 19:31:43: Done! pass1 - making usageList (0 chroms): 1 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。