Job ID = 1294441 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T22:53:54 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 ) 2019-06-02T22:53:55 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 ) 2019-06-02T22:58:21 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 ) 2019-06-02T22:59:07 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 : 16,205,141 reads read : 16,205,141 reads written : 16,205,141 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: 00:05:57 16205141 reads; of these: 16205141 (100.00%) were unpaired; of these: 1277314 (7.88%) aligned 0 times 11341664 (69.99%) aligned exactly 1 time 3586163 (22.13%) aligned >1 times 92.12% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1540212 / 14927827 = 0.1032 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, 03 Jun 2019 08:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:13:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:13:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:13:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:13:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 08:13:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:13:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:13:32: 1000000 INFO @ Mon, 03 Jun 2019 08:13:34: 1000000 INFO @ Mon, 03 Jun 2019 08:13:34: 1000000 INFO @ Mon, 03 Jun 2019 08:13:40: 2000000 INFO @ Mon, 03 Jun 2019 08:13:42: 2000000 INFO @ Mon, 03 Jun 2019 08:13:42: 2000000 INFO @ Mon, 03 Jun 2019 08:13:47: 3000000 INFO @ Mon, 03 Jun 2019 08:13:50: 3000000 INFO @ Mon, 03 Jun 2019 08:13:50: 3000000 INFO @ Mon, 03 Jun 2019 08:13:54: 4000000 INFO @ Mon, 03 Jun 2019 08:13:58: 4000000 INFO @ Mon, 03 Jun 2019 08:13:58: 4000000 INFO @ Mon, 03 Jun 2019 08:14:02: 5000000 INFO @ Mon, 03 Jun 2019 08:14:07: 5000000 INFO @ Mon, 03 Jun 2019 08:14:07: 5000000 INFO @ Mon, 03 Jun 2019 08:14:10: 6000000 INFO @ Mon, 03 Jun 2019 08:14:16: 6000000 INFO @ Mon, 03 Jun 2019 08:14:16: 6000000 INFO @ Mon, 03 Jun 2019 08:14:17: 7000000 INFO @ Mon, 03 Jun 2019 08:14:25: 7000000 INFO @ Mon, 03 Jun 2019 08:14:25: 7000000 INFO @ Mon, 03 Jun 2019 08:14:25: 8000000 INFO @ Mon, 03 Jun 2019 08:14:32: 9000000 INFO @ Mon, 03 Jun 2019 08:14:33: 8000000 INFO @ Mon, 03 Jun 2019 08:14:33: 8000000 INFO @ Mon, 03 Jun 2019 08:14:40: 10000000 INFO @ Mon, 03 Jun 2019 08:14:41: 9000000 INFO @ Mon, 03 Jun 2019 08:14:41: 9000000 INFO @ Mon, 03 Jun 2019 08:14:47: 11000000 INFO @ Mon, 03 Jun 2019 08:14:50: 10000000 INFO @ Mon, 03 Jun 2019 08:14:50: 10000000 INFO @ Mon, 03 Jun 2019 08:14:54: 12000000 INFO @ Mon, 03 Jun 2019 08:14:58: 11000000 INFO @ Mon, 03 Jun 2019 08:14:58: 11000000 INFO @ Mon, 03 Jun 2019 08:15:02: 13000000 INFO @ Mon, 03 Jun 2019 08:15:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:15:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:15:05: #1 total tags in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:15:05: #1 tags after filtering in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:15:05: #1 finished! INFO @ Mon, 03 Jun 2019 08:15:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:15:06: #2 number of paired peaks: 172 WARNING @ Mon, 03 Jun 2019 08:15:06: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 03 Jun 2019 08:15:06: start model_add_line... INFO @ Mon, 03 Jun 2019 08:15:06: start X-correlation... INFO @ Mon, 03 Jun 2019 08:15:06: end of X-cor INFO @ Mon, 03 Jun 2019 08:15:06: #2 finished! INFO @ Mon, 03 Jun 2019 08:15:06: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 08:15:06: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 08:15:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10_model.r WARNING @ Mon, 03 Jun 2019 08:15:06: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:15:06: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 08:15:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:15:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:15:06: 12000000 INFO @ Mon, 03 Jun 2019 08:15:06: 12000000 INFO @ Mon, 03 Jun 2019 08:15:15: 13000000 INFO @ Mon, 03 Jun 2019 08:15:15: 13000000 INFO @ Mon, 03 Jun 2019 08:15:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:15:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:15:18: #1 total tags in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:15:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:15:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:15:18: #1 total tags in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:15:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 08:15:18: #1 tags after filtering in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:15:18: #1 finished! INFO @ Mon, 03 Jun 2019 08:15:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:15:18: #1 tags after filtering in treatment: 13387615 INFO @ Mon, 03 Jun 2019 08:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:15:18: #1 finished! INFO @ Mon, 03 Jun 2019 08:15:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:15:19: #2 number of paired peaks: 172 WARNING @ Mon, 03 Jun 2019 08:15:19: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 03 Jun 2019 08:15:19: start model_add_line... INFO @ Mon, 03 Jun 2019 08:15:19: #2 number of paired peaks: 172 WARNING @ Mon, 03 Jun 2019 08:15:19: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Mon, 03 Jun 2019 08:15:19: start model_add_line... INFO @ Mon, 03 Jun 2019 08:15:19: start X-correlation... INFO @ Mon, 03 Jun 2019 08:15:19: end of X-cor INFO @ Mon, 03 Jun 2019 08:15:19: #2 finished! INFO @ Mon, 03 Jun 2019 08:15:19: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 08:15:19: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 08:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20_model.r WARNING @ Mon, 03 Jun 2019 08:15:19: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:15:19: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 08:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:15:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:15:19: start X-correlation... INFO @ Mon, 03 Jun 2019 08:15:19: end of X-cor INFO @ Mon, 03 Jun 2019 08:15:19: #2 finished! INFO @ Mon, 03 Jun 2019 08:15:19: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 08:15:19: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 08:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05_model.r WARNING @ Mon, 03 Jun 2019 08:15:19: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:15:19: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 08:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 08:15:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:15:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:15:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:15:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.10_summits.bed INFO @ Mon, 03 Jun 2019 08:16:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1515 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.20_summits.bed INFO @ Mon, 03 Jun 2019 08:16:13: Done! INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287651/SRX287651.05_summits.bed INFO @ Mon, 03 Jun 2019 08:16:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (927 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2011 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。