Job ID = 1293040 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:30:30 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 ) 2019-06-02T12:30:30 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 : 22,530,091 reads read : 45,060,182 reads written : 22,530,091 reads 0-length : 22,530,091 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:46 22530091 reads; of these: 22530091 (100.00%) were unpaired; of these: 875806 (3.89%) aligned 0 times 18108757 (80.38%) aligned exactly 1 time 3545528 (15.74%) aligned >1 times 96.11% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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] 3067920 / 21654285 = 0.1417 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 21:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.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 21:52:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.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 21:52:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.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 21:52:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:52:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:52:57: 1000000 INFO @ Sun, 02 Jun 2019 21:53:00: 1000000 INFO @ Sun, 02 Jun 2019 21:53:01: 1000000 INFO @ Sun, 02 Jun 2019 21:53:05: 2000000 INFO @ Sun, 02 Jun 2019 21:53:10: 2000000 INFO @ Sun, 02 Jun 2019 21:53:12: 2000000 INFO @ Sun, 02 Jun 2019 21:53:13: 3000000 INFO @ Sun, 02 Jun 2019 21:53:21: 3000000 INFO @ Sun, 02 Jun 2019 21:53:21: 4000000 INFO @ Sun, 02 Jun 2019 21:53:23: 3000000 INFO @ Sun, 02 Jun 2019 21:53:29: 5000000 INFO @ Sun, 02 Jun 2019 21:53:31: 4000000 INFO @ Sun, 02 Jun 2019 21:53:35: 4000000 INFO @ Sun, 02 Jun 2019 21:53:37: 6000000 INFO @ Sun, 02 Jun 2019 21:53:42: 5000000 INFO @ Sun, 02 Jun 2019 21:53:45: 7000000 INFO @ Sun, 02 Jun 2019 21:53:47: 5000000 INFO @ Sun, 02 Jun 2019 21:53:52: 6000000 INFO @ Sun, 02 Jun 2019 21:53:53: 8000000 INFO @ Sun, 02 Jun 2019 21:53:58: 6000000 INFO @ Sun, 02 Jun 2019 21:54:01: 9000000 INFO @ Sun, 02 Jun 2019 21:54:03: 7000000 INFO @ Sun, 02 Jun 2019 21:54:09: 10000000 INFO @ Sun, 02 Jun 2019 21:54:10: 7000000 INFO @ Sun, 02 Jun 2019 21:54:14: 8000000 INFO @ Sun, 02 Jun 2019 21:54:17: 11000000 INFO @ Sun, 02 Jun 2019 21:54:22: 8000000 INFO @ Sun, 02 Jun 2019 21:54:24: 9000000 INFO @ Sun, 02 Jun 2019 21:54:26: 12000000 INFO @ Sun, 02 Jun 2019 21:54:33: 9000000 INFO @ Sun, 02 Jun 2019 21:54:34: 13000000 INFO @ Sun, 02 Jun 2019 21:54:35: 10000000 INFO @ Sun, 02 Jun 2019 21:54:41: 14000000 INFO @ Sun, 02 Jun 2019 21:54:45: 10000000 INFO @ Sun, 02 Jun 2019 21:54:45: 11000000 INFO @ Sun, 02 Jun 2019 21:54:50: 15000000 INFO @ Sun, 02 Jun 2019 21:54:55: 11000000 INFO @ Sun, 02 Jun 2019 21:54:56: 12000000 INFO @ Sun, 02 Jun 2019 21:54:58: 16000000 INFO @ Sun, 02 Jun 2019 21:55:06: 17000000 INFO @ Sun, 02 Jun 2019 21:55:07: 12000000 INFO @ Sun, 02 Jun 2019 21:55:07: 13000000 INFO @ Sun, 02 Jun 2019 21:55:14: 18000000 INFO @ Sun, 02 Jun 2019 21:55:18: 14000000 INFO @ Sun, 02 Jun 2019 21:55:18: 13000000 INFO @ Sun, 02 Jun 2019 21:55:19: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:55:19: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:55:19: #1 total tags in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:55:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:55:19: #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 21:55:19: #1 tags after filtering in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:55:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:55:19: #1 finished! INFO @ Sun, 02 Jun 2019 21:55:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:55:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:55:21: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 21:55:21: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 21:55:21: start model_add_line... INFO @ Sun, 02 Jun 2019 21:55:21: start X-correlation... INFO @ Sun, 02 Jun 2019 21:55:21: end of X-cor INFO @ Sun, 02 Jun 2019 21:55:21: #2 finished! INFO @ Sun, 02 Jun 2019 21:55:21: #2 predicted fragment length is 64 bps INFO @ Sun, 02 Jun 2019 21:55:21: #2 alternative fragment length(s) may be 2,64,561 bps INFO @ Sun, 02 Jun 2019 21:55:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10_model.r WARNING @ Sun, 02 Jun 2019 21:55:21: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:55:21: #2 You may need to consider one of the other alternative d(s): 2,64,561 WARNING @ Sun, 02 Jun 2019 21:55:21: #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 21:55:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:55:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:55:28: 15000000 INFO @ Sun, 02 Jun 2019 21:55:29: 14000000 INFO @ Sun, 02 Jun 2019 21:55:39: 16000000 INFO @ Sun, 02 Jun 2019 21:55:41: 15000000 INFO @ Sun, 02 Jun 2019 21:55:49: 17000000 INFO @ Sun, 02 Jun 2019 21:55:51: 16000000 INFO @ Sun, 02 Jun 2019 21:55:59: 18000000 INFO @ Sun, 02 Jun 2019 21:56:02: 17000000 INFO @ Sun, 02 Jun 2019 21:56:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:56:05: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:56:05: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:56:05: #1 total tags in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:56:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:56:05: #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 21:56:06: #1 tags after filtering in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:56:06: #1 finished! INFO @ Sun, 02 Jun 2019 21:56:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:56:07: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 21:56:07: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 21:56:07: start model_add_line... INFO @ Sun, 02 Jun 2019 21:56:07: start X-correlation... INFO @ Sun, 02 Jun 2019 21:56:07: end of X-cor INFO @ Sun, 02 Jun 2019 21:56:07: #2 finished! INFO @ Sun, 02 Jun 2019 21:56:07: #2 predicted fragment length is 64 bps INFO @ Sun, 02 Jun 2019 21:56:07: #2 alternative fragment length(s) may be 2,64,561 bps INFO @ Sun, 02 Jun 2019 21:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20_model.r WARNING @ Sun, 02 Jun 2019 21:56:07: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:56:07: #2 You may need to consider one of the other alternative d(s): 2,64,561 WARNING @ Sun, 02 Jun 2019 21:56:07: #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 21:56:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:56:14: 18000000 INFO @ Sun, 02 Jun 2019 21:56:20: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:56:20: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:56:20: #1 total tags in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:56:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:56:20: #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 21:56:20: #1 tags after filtering in treatment: 18586365 INFO @ Sun, 02 Jun 2019 21:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:56:20: #1 finished! INFO @ Sun, 02 Jun 2019 21:56:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:56:22: #2 number of paired peaks: 209 WARNING @ Sun, 02 Jun 2019 21:56:22: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Sun, 02 Jun 2019 21:56:22: start model_add_line... INFO @ Sun, 02 Jun 2019 21:56:22: start X-correlation... INFO @ Sun, 02 Jun 2019 21:56:22: end of X-cor INFO @ Sun, 02 Jun 2019 21:56:22: #2 finished! INFO @ Sun, 02 Jun 2019 21:56:22: #2 predicted fragment length is 64 bps INFO @ Sun, 02 Jun 2019 21:56:22: #2 alternative fragment length(s) may be 2,64,561 bps INFO @ Sun, 02 Jun 2019 21:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05_model.r WARNING @ Sun, 02 Jun 2019 21:56:22: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:56:22: #2 You may need to consider one of the other alternative d(s): 2,64,561 WARNING @ Sun, 02 Jun 2019 21:56:22: #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 21:56:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.10_summits.bed INFO @ Sun, 02 Jun 2019 21:56:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (480 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:56:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:57:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.20_summits.bed INFO @ Sun, 02 Jun 2019 21:57:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (252 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020805/SRX5020805.05_summits.bed INFO @ Sun, 02 Jun 2019 21:57:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (709 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。