Job ID = 2590165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T10:53:05 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 : 19,979,324 reads read : 19,979,324 reads written : 19,979,324 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: 00:05:26 19979324 reads; of these: 19979324 (100.00%) were unpaired; of these: 3178532 (15.91%) aligned 0 times 12450138 (62.32%) aligned exactly 1 time 4350654 (21.78%) aligned >1 times 84.09% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4989203 / 16800792 = 0.2970 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 @ Mon, 12 Aug 2019 20:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 20:09:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 20:09:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 20:09:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:09:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:09:20: 1000000 INFO @ Mon, 12 Aug 2019 20:09:20: 1000000 INFO @ Mon, 12 Aug 2019 20:09:23: 1000000 INFO @ Mon, 12 Aug 2019 20:09:27: 2000000 INFO @ Mon, 12 Aug 2019 20:09:28: 2000000 INFO @ Mon, 12 Aug 2019 20:09:33: 2000000 INFO @ Mon, 12 Aug 2019 20:09:35: 3000000 INFO @ Mon, 12 Aug 2019 20:09:36: 3000000 INFO @ Mon, 12 Aug 2019 20:09:42: 4000000 INFO @ Mon, 12 Aug 2019 20:09:42: 3000000 INFO @ Mon, 12 Aug 2019 20:09:44: 4000000 INFO @ Mon, 12 Aug 2019 20:09:49: 5000000 INFO @ Mon, 12 Aug 2019 20:09:52: 5000000 INFO @ Mon, 12 Aug 2019 20:09:52: 4000000 INFO @ Mon, 12 Aug 2019 20:09:56: 6000000 INFO @ Mon, 12 Aug 2019 20:10:00: 6000000 INFO @ Mon, 12 Aug 2019 20:10:01: 5000000 INFO @ Mon, 12 Aug 2019 20:10:03: 7000000 INFO @ Mon, 12 Aug 2019 20:10:07: 7000000 INFO @ Mon, 12 Aug 2019 20:10:10: 6000000 INFO @ Mon, 12 Aug 2019 20:10:11: 8000000 INFO @ Mon, 12 Aug 2019 20:10:15: 8000000 INFO @ Mon, 12 Aug 2019 20:10:18: 9000000 INFO @ Mon, 12 Aug 2019 20:10:20: 7000000 INFO @ Mon, 12 Aug 2019 20:10:23: 9000000 INFO @ Mon, 12 Aug 2019 20:10:25: 10000000 INFO @ Mon, 12 Aug 2019 20:10:29: 8000000 INFO @ Mon, 12 Aug 2019 20:10:31: 10000000 INFO @ Mon, 12 Aug 2019 20:10:32: 11000000 INFO @ Mon, 12 Aug 2019 20:10:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:10:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:10:38: #1 total tags in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:10:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:10:38: #1 tags after filtering in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:38: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:38: 9000000 INFO @ Mon, 12 Aug 2019 20:10:39: 11000000 INFO @ Mon, 12 Aug 2019 20:10:39: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:10:39: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:39: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:39: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:39: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:39: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:39: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:10:39: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Mon, 12 Aug 2019 20:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10_model.r WARNING @ Mon, 12 Aug 2019 20:10:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:39: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Mon, 12 Aug 2019 20:10:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:10:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:45: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:10:45: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:10:45: #1 total tags in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:10:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:10:45: #1 tags after filtering in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:45: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:47: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:10:47: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:47: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:47: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:47: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:47: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:47: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:10:47: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Mon, 12 Aug 2019 20:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05_model.r WARNING @ Mon, 12 Aug 2019 20:10:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:47: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Mon, 12 Aug 2019 20:10:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:10:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:48: 10000000 INFO @ Mon, 12 Aug 2019 20:10:57: 11000000 INFO @ Mon, 12 Aug 2019 20:11:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:04: #1 total tags in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:11:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:11:04: #1 tags after filtering in treatment: 11811589 INFO @ Mon, 12 Aug 2019 20:11:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:04: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:05: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 20:11:05: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 20:11:05: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:06: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:11:06: #2 alternative fragment length(s) may be 3,50,598 bps INFO @ Mon, 12 Aug 2019 20:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20_model.r WARNING @ Mon, 12 Aug 2019 20:11:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:11:06: #2 You may need to consider one of the other alternative d(s): 3,50,598 WARNING @ Mon, 12 Aug 2019 20:11:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:11:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.10_summits.bed INFO @ Mon, 12 Aug 2019 20:11:26: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1245 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:11:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.05_summits.bed INFO @ Mon, 12 Aug 2019 20:11:33: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3859 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:11:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495039/SRX495039.20_summits.bed INFO @ Mon, 12 Aug 2019 20:11:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。