Job ID = 1292798 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T11:35:29 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 : 22,634,552 reads read : 22,634,552 reads written : 22,634,552 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:04:23 22634552 reads; of these: 22634552 (100.00%) were unpaired; of these: 3509011 (15.50%) aligned 0 times 16087731 (71.08%) aligned exactly 1 time 3037810 (13.42%) aligned >1 times 84.50% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 3757566 / 19125541 = 0.1965 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 @ Sun, 02 Jun 2019 20:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.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 @ Sun, 02 Jun 2019 20:56:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.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 @ Sun, 02 Jun 2019 20:56:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:56:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.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 @ Sun, 02 Jun 2019 20:56:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:56:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:08: 1000000 INFO @ Sun, 02 Jun 2019 20:57:08: 1000000 INFO @ Sun, 02 Jun 2019 20:57:08: 1000000 INFO @ Sun, 02 Jun 2019 20:57:17: 2000000 INFO @ Sun, 02 Jun 2019 20:57:17: 2000000 INFO @ Sun, 02 Jun 2019 20:57:17: 2000000 INFO @ Sun, 02 Jun 2019 20:57:25: 3000000 INFO @ Sun, 02 Jun 2019 20:57:25: 3000000 INFO @ Sun, 02 Jun 2019 20:57:25: 3000000 INFO @ Sun, 02 Jun 2019 20:57:33: 4000000 INFO @ Sun, 02 Jun 2019 20:57:33: 4000000 INFO @ Sun, 02 Jun 2019 20:57:34: 4000000 INFO @ Sun, 02 Jun 2019 20:57:42: 5000000 INFO @ Sun, 02 Jun 2019 20:57:42: 5000000 INFO @ Sun, 02 Jun 2019 20:57:43: 5000000 INFO @ Sun, 02 Jun 2019 20:57:49: 6000000 INFO @ Sun, 02 Jun 2019 20:57:50: 6000000 INFO @ Sun, 02 Jun 2019 20:57:51: 6000000 INFO @ Sun, 02 Jun 2019 20:57:57: 7000000 INFO @ Sun, 02 Jun 2019 20:57:58: 7000000 INFO @ Sun, 02 Jun 2019 20:57:59: 7000000 INFO @ Sun, 02 Jun 2019 20:58:05: 8000000 INFO @ Sun, 02 Jun 2019 20:58:06: 8000000 INFO @ Sun, 02 Jun 2019 20:58:07: 8000000 INFO @ Sun, 02 Jun 2019 20:58:13: 9000000 INFO @ Sun, 02 Jun 2019 20:58:14: 9000000 INFO @ Sun, 02 Jun 2019 20:58:16: 9000000 INFO @ Sun, 02 Jun 2019 20:58:20: 10000000 INFO @ Sun, 02 Jun 2019 20:58:22: 10000000 INFO @ Sun, 02 Jun 2019 20:58:24: 10000000 INFO @ Sun, 02 Jun 2019 20:58:28: 11000000 INFO @ Sun, 02 Jun 2019 20:58:30: 11000000 INFO @ Sun, 02 Jun 2019 20:58:33: 11000000 INFO @ Sun, 02 Jun 2019 20:58:37: 12000000 INFO @ Sun, 02 Jun 2019 20:58:38: 12000000 INFO @ Sun, 02 Jun 2019 20:58:41: 12000000 INFO @ Sun, 02 Jun 2019 20:58:45: 13000000 INFO @ Sun, 02 Jun 2019 20:58:46: 13000000 INFO @ Sun, 02 Jun 2019 20:58:50: 13000000 INFO @ Sun, 02 Jun 2019 20:58:52: 14000000 INFO @ Sun, 02 Jun 2019 20:58:54: 14000000 INFO @ Sun, 02 Jun 2019 20:58:58: 14000000 INFO @ Sun, 02 Jun 2019 20:59:00: 15000000 INFO @ Sun, 02 Jun 2019 20:59:02: 15000000 INFO @ Sun, 02 Jun 2019 20:59:03: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:59:03: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:59:03: #1 total tags in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:59:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:59:03: #1 tags after filtering in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:59:03: #1 finished! INFO @ Sun, 02 Jun 2019 20:59:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:59:04: #2 number of paired peaks: 266 WARNING @ Sun, 02 Jun 2019 20:59:04: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 02 Jun 2019 20:59:04: start model_add_line... INFO @ Sun, 02 Jun 2019 20:59:04: start X-correlation... INFO @ Sun, 02 Jun 2019 20:59:04: end of X-cor INFO @ Sun, 02 Jun 2019 20:59:04: #2 finished! INFO @ Sun, 02 Jun 2019 20:59:04: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 20:59:04: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Sun, 02 Jun 2019 20:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20_model.r WARNING @ Sun, 02 Jun 2019 20:59:04: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:59:04: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Sun, 02 Jun 2019 20:59:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:59:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:59:05: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:59:05: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:59:05: #1 total tags in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:59:05: #1 tags after filtering in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:59:05: #1 finished! INFO @ Sun, 02 Jun 2019 20:59:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:59:06: 15000000 INFO @ Sun, 02 Jun 2019 20:59:06: #2 number of paired peaks: 266 WARNING @ Sun, 02 Jun 2019 20:59:06: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 02 Jun 2019 20:59:06: start model_add_line... INFO @ Sun, 02 Jun 2019 20:59:07: start X-correlation... INFO @ Sun, 02 Jun 2019 20:59:07: end of X-cor INFO @ Sun, 02 Jun 2019 20:59:07: #2 finished! INFO @ Sun, 02 Jun 2019 20:59:07: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 20:59:07: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Sun, 02 Jun 2019 20:59:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05_model.r WARNING @ Sun, 02 Jun 2019 20:59:07: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:59:07: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Sun, 02 Jun 2019 20:59:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:59:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:59:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:59:09: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:59:09: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:59:09: #1 total tags in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:59:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:59:10: #1 tags after filtering in treatment: 15367975 INFO @ Sun, 02 Jun 2019 20:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:59:10: #1 finished! INFO @ Sun, 02 Jun 2019 20:59:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:59:11: #2 number of paired peaks: 266 WARNING @ Sun, 02 Jun 2019 20:59:11: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Sun, 02 Jun 2019 20:59:11: start model_add_line... INFO @ Sun, 02 Jun 2019 20:59:11: start X-correlation... INFO @ Sun, 02 Jun 2019 20:59:11: end of X-cor INFO @ Sun, 02 Jun 2019 20:59:11: #2 finished! INFO @ Sun, 02 Jun 2019 20:59:11: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 20:59:11: #2 alternative fragment length(s) may be 2,45,566 bps INFO @ Sun, 02 Jun 2019 20:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10_model.r WARNING @ Sun, 02 Jun 2019 20:59:11: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 20:59:11: #2 You may need to consider one of the other alternative d(s): 2,45,566 WARNING @ Sun, 02 Jun 2019 20:59:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 20:59:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:59:43: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:59:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:59:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.20_summits.bed INFO @ Sun, 02 Jun 2019 21:00:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.05_summits.bed INFO @ Sun, 02 Jun 2019 21:00:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:00:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495046/SRX495046.10_summits.bed INFO @ Sun, 02 Jun 2019 21:00:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (353 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。