Job ID = 2009687 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 : 4,007,582 reads read : 4,007,582 reads written : 4,007,582 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR364343.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: 00:00:27 4007582 reads; of these: 4007582 (100.00%) were unpaired; of these: 1701713 (42.46%) aligned 0 times 2081414 (51.94%) aligned exactly 1 time 224455 (5.60%) aligned >1 times 57.54% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 1080037 / 2305869 = 0.4684 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 19:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.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 19:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.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 19:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.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 19:27:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:27:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:27:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:27:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:28:05: 1000000 INFO @ Fri, 05 Jul 2019 19:28:07: 1000000 INFO @ Fri, 05 Jul 2019 19:28:07: 1000000 INFO @ Fri, 05 Jul 2019 19:28:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 19:28:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:18: #1 total tags in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 19:28:18: #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 19:28:18: #1 total tags in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 total tags in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:28:18: #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 19:28:18: #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 19:28:18: #1 tags after filtering in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:18: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:18: #1 tags after filtering in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:18: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:18: #1 tags after filtering in treatment: 1225832 INFO @ Fri, 05 Jul 2019 19:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:28:18: #1 finished! INFO @ Fri, 05 Jul 2019 19:28:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:28:18: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 19:28:18: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:18: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:18: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 19:28:18: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:18: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:18: #2 number of paired peaks: 397 WARNING @ Fri, 05 Jul 2019 19:28:18: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Fri, 05 Jul 2019 19:28:18: start model_add_line... INFO @ Fri, 05 Jul 2019 19:28:18: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:18: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:18: start X-correlation... INFO @ Fri, 05 Jul 2019 19:28:18: end of X-cor INFO @ Fri, 05 Jul 2019 19:28:18: #2 finished! INFO @ Fri, 05 Jul 2019 19:28:18: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 19:28:18: end of X-cor INFO @ Fri, 05 Jul 2019 19:28:18: #2 alternative fragment length(s) may be 2,17,80,106,186,216,246,462,483,525,555,569 bps INFO @ Fri, 05 Jul 2019 19:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05_model.r INFO @ Fri, 05 Jul 2019 19:28:18: #2 finished! INFO @ Fri, 05 Jul 2019 19:28:18: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 19:28:18: #2 alternative fragment length(s) may be 2,17,80,106,186,216,246,462,483,525,555,569 bps INFO @ Fri, 05 Jul 2019 19:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20_model.r INFO @ Fri, 05 Jul 2019 19:28:18: end of X-cor WARNING @ Fri, 05 Jul 2019 19:28:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:28:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:28:22: #2 You may need to consider one of the other alternative d(s): 2,17,80,106,186,216,246,462,483,525,555,569 INFO @ Fri, 05 Jul 2019 19:28:22: #2 finished! WARNING @ Fri, 05 Jul 2019 19:28:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Fri, 05 Jul 2019 19:28:22: #2 You may need to consider one of the other alternative d(s): 2,17,80,106,186,216,246,462,483,525,555,569 INFO @ Fri, 05 Jul 2019 19:28:22: #3 Call peaks... WARNING @ Fri, 05 Jul 2019 19:28:22: #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 19:28:22: #2 predicted fragment length is 2 bps INFO @ Fri, 05 Jul 2019 19:28:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:28:22: #2 alternative fragment length(s) may be 2,17,80,106,186,216,246,462,483,525,555,569 bps INFO @ Fri, 05 Jul 2019 19:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10_model.r INFO @ Fri, 05 Jul 2019 19:28:22: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 05 Jul 2019 19:28:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:28:22: #2 You may need to consider one of the other alternative d(s): 2,17,80,106,186,216,246,462,483,525,555,569 WARNING @ Fri, 05 Jul 2019 19:28:22: #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 19:28:22: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:28:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.05_summits.bed INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.10_summits.bed INFO @ Fri, 05 Jul 2019 19:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX105557/SRX105557.20_summits.bed INFO @ Fri, 05 Jul 2019 19:28:29: Done! INFO @ Fri, 05 Jul 2019 19:28:29: Done! INFO @ Fri, 05 Jul 2019 19:28:29: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 3 millis : 2 millis : 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184)needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。