Job ID = 1294758 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:53:00 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 ) 2019-06-03T00:53:01 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 : 17,667,108 reads read : 17,667,108 reads written : 17,667,108 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: 00:08:18 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 720127 (4.08%) aligned 0 times 11489864 (65.04%) aligned exactly 1 time 5457117 (30.89%) aligned >1 times 95.92% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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] 1985200 / 16946981 = 0.1171 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 10:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.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 10:15:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.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 10:15:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.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 10:15:33: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:15:33: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:15:42: 1000000 INFO @ Mon, 03 Jun 2019 10:15:43: 1000000 INFO @ Mon, 03 Jun 2019 10:15:43: 1000000 INFO @ Mon, 03 Jun 2019 10:15:51: 2000000 INFO @ Mon, 03 Jun 2019 10:15:52: 2000000 INFO @ Mon, 03 Jun 2019 10:15:52: 2000000 INFO @ Mon, 03 Jun 2019 10:15:59: 3000000 INFO @ Mon, 03 Jun 2019 10:16:02: 3000000 INFO @ Mon, 03 Jun 2019 10:16:02: 3000000 INFO @ Mon, 03 Jun 2019 10:16:08: 4000000 INFO @ Mon, 03 Jun 2019 10:16:11: 4000000 INFO @ Mon, 03 Jun 2019 10:16:12: 4000000 INFO @ Mon, 03 Jun 2019 10:16:17: 5000000 INFO @ Mon, 03 Jun 2019 10:16:21: 5000000 INFO @ Mon, 03 Jun 2019 10:16:21: 5000000 INFO @ Mon, 03 Jun 2019 10:16:25: 6000000 INFO @ Mon, 03 Jun 2019 10:16:29: 6000000 INFO @ Mon, 03 Jun 2019 10:16:31: 6000000 INFO @ Mon, 03 Jun 2019 10:16:33: 7000000 INFO @ Mon, 03 Jun 2019 10:16:38: 7000000 INFO @ Mon, 03 Jun 2019 10:16:39: 7000000 INFO @ Mon, 03 Jun 2019 10:16:42: 8000000 INFO @ Mon, 03 Jun 2019 10:16:46: 8000000 INFO @ Mon, 03 Jun 2019 10:16:47: 8000000 INFO @ Mon, 03 Jun 2019 10:16:50: 9000000 INFO @ Mon, 03 Jun 2019 10:16:54: 9000000 INFO @ Mon, 03 Jun 2019 10:16:55: 9000000 INFO @ Mon, 03 Jun 2019 10:16:58: 10000000 INFO @ Mon, 03 Jun 2019 10:17:01: 10000000 INFO @ Mon, 03 Jun 2019 10:17:03: 10000000 INFO @ Mon, 03 Jun 2019 10:17:07: 11000000 INFO @ Mon, 03 Jun 2019 10:17:09: 11000000 INFO @ Mon, 03 Jun 2019 10:17:11: 11000000 INFO @ Mon, 03 Jun 2019 10:17:15: 12000000 INFO @ Mon, 03 Jun 2019 10:17:16: 12000000 INFO @ Mon, 03 Jun 2019 10:17:19: 12000000 INFO @ Mon, 03 Jun 2019 10:17:23: 13000000 INFO @ Mon, 03 Jun 2019 10:17:23: 13000000 INFO @ Mon, 03 Jun 2019 10:17:28: 13000000 INFO @ Mon, 03 Jun 2019 10:17:30: 14000000 INFO @ Mon, 03 Jun 2019 10:17:31: 14000000 INFO @ Mon, 03 Jun 2019 10:17:36: 14000000 INFO @ Mon, 03 Jun 2019 10:17:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:38: #1 total tags in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:38: #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 10:17:38: #1 tags after filtering in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:38: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:40: #1 total tags in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:40: #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 10:17:40: #2 number of paired peaks: 286 WARNING @ Mon, 03 Jun 2019 10:17:40: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Mon, 03 Jun 2019 10:17:40: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:40: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:40: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:40: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:40: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:17:40: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10_model.r WARNING @ Mon, 03 Jun 2019 10:17:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:17:40: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:17:40: #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 10:17:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:40: #1 tags after filtering in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:40: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:41: #2 number of paired peaks: 286 WARNING @ Mon, 03 Jun 2019 10:17:41: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Mon, 03 Jun 2019 10:17:41: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:41: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:17:41: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05_model.r WARNING @ Mon, 03 Jun 2019 10:17:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:17:41: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:17:41: #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 10:17:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:17:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:17:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:17:44: #1 total tags in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:17:44: #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 10:17:45: #1 tags after filtering in treatment: 14961781 INFO @ Mon, 03 Jun 2019 10:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:17:45: #1 finished! INFO @ Mon, 03 Jun 2019 10:17:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:17:46: #2 number of paired peaks: 286 WARNING @ Mon, 03 Jun 2019 10:17:46: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Mon, 03 Jun 2019 10:17:46: start model_add_line... INFO @ Mon, 03 Jun 2019 10:17:46: start X-correlation... INFO @ Mon, 03 Jun 2019 10:17:46: end of X-cor INFO @ Mon, 03 Jun 2019 10:17:46: #2 finished! INFO @ Mon, 03 Jun 2019 10:17:46: #2 predicted fragment length is 44 bps INFO @ Mon, 03 Jun 2019 10:17:46: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 03 Jun 2019 10:17:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20_model.r WARNING @ Mon, 03 Jun 2019 10:17:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 10:17:46: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 03 Jun 2019 10:17:46: #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 10:17:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:17:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:18:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:18:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.10_summits.bed INFO @ Mon, 03 Jun 2019 10:18:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1859 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.05_summits.bed INFO @ Mon, 03 Jun 2019 10:18:40: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2137 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287862/SRX287862.20_summits.bed INFO @ Mon, 03 Jun 2019 10:18:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1482 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。