Job ID = 1292964 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T12:17:21 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 ) 2019-06-02T12:17:21 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 : 20,115,882 reads read : 40,231,764 reads written : 20,115,882 reads 0-length : 20,115,882 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: 00:07:33 20115882 reads; of these: 20115882 (100.00%) were unpaired; of these: 234530 (1.17%) aligned 0 times 15615445 (77.63%) aligned exactly 1 time 4265907 (21.21%) aligned >1 times 98.83% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 2957554 / 19881352 = 0.1488 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 21:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.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 21:36:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.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 21:36:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.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 21:36:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:36:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:36:49: 1000000 INFO @ Sun, 02 Jun 2019 21:36:49: 1000000 INFO @ Sun, 02 Jun 2019 21:36:51: 1000000 INFO @ Sun, 02 Jun 2019 21:36:56: 2000000 INFO @ Sun, 02 Jun 2019 21:36:56: 2000000 INFO @ Sun, 02 Jun 2019 21:36:59: 2000000 INFO @ Sun, 02 Jun 2019 21:37:03: 3000000 INFO @ Sun, 02 Jun 2019 21:37:03: 3000000 INFO @ Sun, 02 Jun 2019 21:37:08: 3000000 INFO @ Sun, 02 Jun 2019 21:37:10: 4000000 INFO @ Sun, 02 Jun 2019 21:37:10: 4000000 INFO @ Sun, 02 Jun 2019 21:37:17: 4000000 INFO @ Sun, 02 Jun 2019 21:37:17: 5000000 INFO @ Sun, 02 Jun 2019 21:37:18: 5000000 INFO @ Sun, 02 Jun 2019 21:37:25: 6000000 INFO @ Sun, 02 Jun 2019 21:37:26: 5000000 INFO @ Sun, 02 Jun 2019 21:37:26: 6000000 INFO @ Sun, 02 Jun 2019 21:37:33: 7000000 INFO @ Sun, 02 Jun 2019 21:37:34: 7000000 INFO @ Sun, 02 Jun 2019 21:37:35: 6000000 INFO @ Sun, 02 Jun 2019 21:37:42: 8000000 INFO @ Sun, 02 Jun 2019 21:37:42: 8000000 INFO @ Sun, 02 Jun 2019 21:37:43: 7000000 INFO @ Sun, 02 Jun 2019 21:37:50: 9000000 INFO @ Sun, 02 Jun 2019 21:37:50: 9000000 INFO @ Sun, 02 Jun 2019 21:37:52: 8000000 INFO @ Sun, 02 Jun 2019 21:37:58: 10000000 INFO @ Sun, 02 Jun 2019 21:37:58: 10000000 INFO @ Sun, 02 Jun 2019 21:38:01: 9000000 INFO @ Sun, 02 Jun 2019 21:38:06: 11000000 INFO @ Sun, 02 Jun 2019 21:38:07: 11000000 INFO @ Sun, 02 Jun 2019 21:38:10: 10000000 INFO @ Sun, 02 Jun 2019 21:38:14: 12000000 INFO @ Sun, 02 Jun 2019 21:38:15: 12000000 INFO @ Sun, 02 Jun 2019 21:38:19: 11000000 INFO @ Sun, 02 Jun 2019 21:38:22: 13000000 INFO @ Sun, 02 Jun 2019 21:38:23: 13000000 INFO @ Sun, 02 Jun 2019 21:38:28: 12000000 INFO @ Sun, 02 Jun 2019 21:38:31: 14000000 INFO @ Sun, 02 Jun 2019 21:38:31: 14000000 INFO @ Sun, 02 Jun 2019 21:38:36: 13000000 INFO @ Sun, 02 Jun 2019 21:38:39: 15000000 INFO @ Sun, 02 Jun 2019 21:38:40: 15000000 INFO @ Sun, 02 Jun 2019 21:38:45: 14000000 INFO @ Sun, 02 Jun 2019 21:38:48: 16000000 INFO @ Sun, 02 Jun 2019 21:38:48: 16000000 INFO @ Sun, 02 Jun 2019 21:38:54: 15000000 INFO @ Sun, 02 Jun 2019 21:38:56: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:38:56: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:38:56: #1 total tags in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:38:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:38:56: #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 21:38:56: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:38:56: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:38:56: #1 total tags in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:38:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:38:56: #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 21:38:56: #1 tags after filtering in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:38:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:38:56: #1 finished! INFO @ Sun, 02 Jun 2019 21:38:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:38:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:38:56: #1 tags after filtering in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:38:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:38:56: #1 finished! INFO @ Sun, 02 Jun 2019 21:38:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:38:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:38:58: #2 number of paired peaks: 458 WARNING @ Sun, 02 Jun 2019 21:38:58: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 02 Jun 2019 21:38:58: start model_add_line... INFO @ Sun, 02 Jun 2019 21:38:58: #2 number of paired peaks: 458 WARNING @ Sun, 02 Jun 2019 21:38:58: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 02 Jun 2019 21:38:58: start model_add_line... INFO @ Sun, 02 Jun 2019 21:38:58: start X-correlation... INFO @ Sun, 02 Jun 2019 21:38:58: end of X-cor INFO @ Sun, 02 Jun 2019 21:38:58: #2 finished! INFO @ Sun, 02 Jun 2019 21:38:58: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 21:38:58: #2 alternative fragment length(s) may be 2,80 bps INFO @ Sun, 02 Jun 2019 21:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05_model.r WARNING @ Sun, 02 Jun 2019 21:38:58: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:38:58: #2 You may need to consider one of the other alternative d(s): 2,80 WARNING @ Sun, 02 Jun 2019 21:38:58: #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 21:38:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:38:58: start X-correlation... INFO @ Sun, 02 Jun 2019 21:38:58: end of X-cor INFO @ Sun, 02 Jun 2019 21:38:58: #2 finished! INFO @ Sun, 02 Jun 2019 21:38:58: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 21:38:58: #2 alternative fragment length(s) may be 2,80 bps INFO @ Sun, 02 Jun 2019 21:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10_model.r WARNING @ Sun, 02 Jun 2019 21:38:58: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:38:58: #2 You may need to consider one of the other alternative d(s): 2,80 WARNING @ Sun, 02 Jun 2019 21:38:58: #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 21:38:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:38:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:03: 16000000 INFO @ Sun, 02 Jun 2019 21:39:11: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:39:11: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:39:11: #1 total tags in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:39:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:11: #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 21:39:11: #1 tags after filtering in treatment: 16923798 INFO @ Sun, 02 Jun 2019 21:39:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:11: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:12: #2 number of paired peaks: 458 WARNING @ Sun, 02 Jun 2019 21:39:12: Fewer paired peaks (458) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 458 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:12: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:13: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:13: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:13: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:13: #2 predicted fragment length is 80 bps INFO @ Sun, 02 Jun 2019 21:39:13: #2 alternative fragment length(s) may be 2,80 bps INFO @ Sun, 02 Jun 2019 21:39:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20_model.r WARNING @ Sun, 02 Jun 2019 21:39:13: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:39:13: #2 You may need to consider one of the other alternative d(s): 2,80 WARNING @ Sun, 02 Jun 2019 21:39:13: #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 21:39:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:39:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:39:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.05_summits.bed INFO @ Sun, 02 Jun 2019 21:40:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1570 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.10_summits.bed INFO @ Sun, 02 Jun 2019 21:40:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020744/SRX5020744.20_summits.bed INFO @ Sun, 02 Jun 2019 21:40:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 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。