Job ID = 2589949 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-12T09:51:32 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 ) 2019-08-12T09:51:40 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 : 34,284,849 reads read : 34,284,849 reads written : 34,284,849 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1163524.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: 00:07:12 34284849 reads; of these: 34284849 (100.00%) were unpaired; of these: 6795370 (19.82%) aligned 0 times 23736191 (69.23%) aligned exactly 1 time 3753288 (10.95%) aligned >1 times 80.18% overall alignment rate Time searching: 00:07:12 Overall time: 00:07:12 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 12 files... [bam_rmdupse_core] 10218746 / 27489479 = 0.3717 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 19:07:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.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 19:07:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.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 19:07:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.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 19:07:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:07:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:07:42: 1000000 INFO @ Mon, 12 Aug 2019 19:07:43: 1000000 INFO @ Mon, 12 Aug 2019 19:07:44: 1000000 INFO @ Mon, 12 Aug 2019 19:07:50: 2000000 INFO @ Mon, 12 Aug 2019 19:07:52: 2000000 INFO @ Mon, 12 Aug 2019 19:07:53: 2000000 INFO @ Mon, 12 Aug 2019 19:07:57: 3000000 INFO @ Mon, 12 Aug 2019 19:08:02: 3000000 INFO @ Mon, 12 Aug 2019 19:08:03: 3000000 INFO @ Mon, 12 Aug 2019 19:08:05: 4000000 INFO @ Mon, 12 Aug 2019 19:08:12: 4000000 INFO @ Mon, 12 Aug 2019 19:08:12: 5000000 INFO @ Mon, 12 Aug 2019 19:08:13: 4000000 INFO @ Mon, 12 Aug 2019 19:08:20: 6000000 INFO @ Mon, 12 Aug 2019 19:08:21: 5000000 INFO @ Mon, 12 Aug 2019 19:08:22: 5000000 INFO @ Mon, 12 Aug 2019 19:08:27: 7000000 INFO @ Mon, 12 Aug 2019 19:08:31: 6000000 INFO @ Mon, 12 Aug 2019 19:08:32: 6000000 INFO @ Mon, 12 Aug 2019 19:08:34: 8000000 INFO @ Mon, 12 Aug 2019 19:08:41: 7000000 INFO @ Mon, 12 Aug 2019 19:08:42: 7000000 INFO @ Mon, 12 Aug 2019 19:08:42: 9000000 INFO @ Mon, 12 Aug 2019 19:08:49: 8000000 INFO @ Mon, 12 Aug 2019 19:08:50: 10000000 INFO @ Mon, 12 Aug 2019 19:08:51: 8000000 INFO @ Mon, 12 Aug 2019 19:08:57: 11000000 INFO @ Mon, 12 Aug 2019 19:08:58: 9000000 INFO @ Mon, 12 Aug 2019 19:08:59: 9000000 INFO @ Mon, 12 Aug 2019 19:09:05: 12000000 INFO @ Mon, 12 Aug 2019 19:09:07: 10000000 INFO @ Mon, 12 Aug 2019 19:09:08: 10000000 INFO @ Mon, 12 Aug 2019 19:09:13: 13000000 INFO @ Mon, 12 Aug 2019 19:09:16: 11000000 INFO @ Mon, 12 Aug 2019 19:09:17: 11000000 INFO @ Mon, 12 Aug 2019 19:09:21: 14000000 INFO @ Mon, 12 Aug 2019 19:09:25: 12000000 INFO @ Mon, 12 Aug 2019 19:09:26: 12000000 INFO @ Mon, 12 Aug 2019 19:09:28: 15000000 INFO @ Mon, 12 Aug 2019 19:09:34: 13000000 INFO @ Mon, 12 Aug 2019 19:09:35: 13000000 INFO @ Mon, 12 Aug 2019 19:09:36: 16000000 INFO @ Mon, 12 Aug 2019 19:09:43: 14000000 INFO @ Mon, 12 Aug 2019 19:09:44: 17000000 INFO @ Mon, 12 Aug 2019 19:09:44: 14000000 INFO @ Mon, 12 Aug 2019 19:09:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:09:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:09:46: #1 total tags in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:09:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:09:46: #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 19:09:46: #1 tags after filtering in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:09:46: #1 finished! INFO @ Mon, 12 Aug 2019 19:09:46: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:09:48: #2 number of paired peaks: 186 WARNING @ Mon, 12 Aug 2019 19:09:48: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 12 Aug 2019 19:09:48: start model_add_line... INFO @ Mon, 12 Aug 2019 19:09:48: start X-correlation... INFO @ Mon, 12 Aug 2019 19:09:48: end of X-cor INFO @ Mon, 12 Aug 2019 19:09:48: #2 finished! INFO @ Mon, 12 Aug 2019 19:09:48: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:09:48: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:09:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20_model.r WARNING @ Mon, 12 Aug 2019 19:09:48: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:09:48: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:09:48: #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 19:09:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:09:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:09:52: 15000000 INFO @ Mon, 12 Aug 2019 19:09:53: 15000000 INFO @ Mon, 12 Aug 2019 19:10:01: 16000000 INFO @ Mon, 12 Aug 2019 19:10:01: 16000000 INFO @ Mon, 12 Aug 2019 19:10:09: 17000000 INFO @ Mon, 12 Aug 2019 19:10:10: 17000000 INFO @ Mon, 12 Aug 2019 19:10:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:12: #1 total tags in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:10:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:12: #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 19:10:12: #1 tags after filtering in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:10:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:12: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 19:10:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 19:10:12: #1 total tags in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:10:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:10:12: #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 19:10:13: #1 tags after filtering in treatment: 17270733 INFO @ Mon, 12 Aug 2019 19:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:10:13: #1 finished! INFO @ Mon, 12 Aug 2019 19:10:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:10:13: #2 number of paired peaks: 186 WARNING @ Mon, 12 Aug 2019 19:10:13: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 12 Aug 2019 19:10:13: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:14: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:10:14: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05_model.r WARNING @ Mon, 12 Aug 2019 19:10:14: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:10:14: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:10:14: #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 19:10:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:14: #2 number of paired peaks: 186 WARNING @ Mon, 12 Aug 2019 19:10:14: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Mon, 12 Aug 2019 19:10:14: start model_add_line... INFO @ Mon, 12 Aug 2019 19:10:14: start X-correlation... INFO @ Mon, 12 Aug 2019 19:10:14: end of X-cor INFO @ Mon, 12 Aug 2019 19:10:14: #2 finished! INFO @ Mon, 12 Aug 2019 19:10:14: #2 predicted fragment length is 46 bps INFO @ Mon, 12 Aug 2019 19:10:14: #2 alternative fragment length(s) may be 2,46 bps INFO @ Mon, 12 Aug 2019 19:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10_model.r WARNING @ Mon, 12 Aug 2019 19:10:14: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:10:14: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Mon, 12 Aug 2019 19:10:14: #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 19:10:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:10:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.20_summits.bed INFO @ Mon, 12 Aug 2019 19:10:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:10:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:10:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.05_summits.bed INFO @ Mon, 12 Aug 2019 19:11:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1399 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:11:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:11:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:11:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466458/SRX466458.10_summits.bed INFO @ Mon, 12 Aug 2019 19:11:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。