Job ID = 1294660 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:36:16 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 ) 2019-06-03T00:36:16 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 ) 2019-06-03T00:36:16 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 ) 2019-06-03T00:36:16 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 ) 2019-06-03T00:36:16 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: 00:09:32 17667108 reads; of these: 17667108 (100.00%) were unpaired; of these: 720191 (4.08%) aligned 0 times 11489720 (65.03%) aligned exactly 1 time 5457197 (30.89%) aligned >1 times 95.92% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 1985178 / 16946917 = 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 09:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.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 09:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.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 09:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.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 09:53:51: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:53:51: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:53:59: 1000000 INFO @ Mon, 03 Jun 2019 09:53:59: 1000000 INFO @ Mon, 03 Jun 2019 09:54:01: 1000000 INFO @ Mon, 03 Jun 2019 09:54:06: 2000000 INFO @ Mon, 03 Jun 2019 09:54:07: 2000000 INFO @ Mon, 03 Jun 2019 09:54:10: 2000000 INFO @ Mon, 03 Jun 2019 09:54:13: 3000000 INFO @ Mon, 03 Jun 2019 09:54:15: 3000000 INFO @ Mon, 03 Jun 2019 09:54:18: 3000000 INFO @ Mon, 03 Jun 2019 09:54:21: 4000000 INFO @ Mon, 03 Jun 2019 09:54:23: 4000000 INFO @ Mon, 03 Jun 2019 09:54:27: 4000000 INFO @ Mon, 03 Jun 2019 09:54:28: 5000000 INFO @ Mon, 03 Jun 2019 09:54:31: 5000000 INFO @ Mon, 03 Jun 2019 09:54:35: 6000000 INFO @ Mon, 03 Jun 2019 09:54:36: 5000000 INFO @ Mon, 03 Jun 2019 09:54:38: 6000000 INFO @ Mon, 03 Jun 2019 09:54:43: 7000000 INFO @ Mon, 03 Jun 2019 09:54:45: 6000000 INFO @ Mon, 03 Jun 2019 09:54:46: 7000000 INFO @ Mon, 03 Jun 2019 09:54:50: 8000000 INFO @ Mon, 03 Jun 2019 09:54:54: 7000000 INFO @ Mon, 03 Jun 2019 09:54:54: 8000000 INFO @ Mon, 03 Jun 2019 09:54:57: 9000000 INFO @ Mon, 03 Jun 2019 09:55:02: 9000000 INFO @ Mon, 03 Jun 2019 09:55:03: 8000000 INFO @ Mon, 03 Jun 2019 09:55:05: 10000000 INFO @ Mon, 03 Jun 2019 09:55:10: 10000000 INFO @ Mon, 03 Jun 2019 09:55:12: 9000000 INFO @ Mon, 03 Jun 2019 09:55:12: 11000000 INFO @ Mon, 03 Jun 2019 09:55:17: 11000000 INFO @ Mon, 03 Jun 2019 09:55:19: 12000000 INFO @ Mon, 03 Jun 2019 09:55:20: 10000000 INFO @ Mon, 03 Jun 2019 09:55:25: 12000000 INFO @ Mon, 03 Jun 2019 09:55:26: 13000000 INFO @ Mon, 03 Jun 2019 09:55:29: 11000000 INFO @ Mon, 03 Jun 2019 09:55:32: 13000000 INFO @ Mon, 03 Jun 2019 09:55:33: 14000000 INFO @ Mon, 03 Jun 2019 09:55:38: 12000000 INFO @ Mon, 03 Jun 2019 09:55:39: 14000000 INFO @ Mon, 03 Jun 2019 09:55:40: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:55:40: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:55:40: #1 total tags in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:55:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:55:40: #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 09:55:40: #1 tags after filtering in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:55:40: #1 finished! INFO @ Mon, 03 Jun 2019 09:55:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:55:42: #2 number of paired peaks: 290 WARNING @ Mon, 03 Jun 2019 09:55:42: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Mon, 03 Jun 2019 09:55:42: start model_add_line... INFO @ Mon, 03 Jun 2019 09:55:42: start X-correlation... INFO @ Mon, 03 Jun 2019 09:55:42: end of X-cor INFO @ Mon, 03 Jun 2019 09:55:42: #2 finished! INFO @ Mon, 03 Jun 2019 09:55:42: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:55:42: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20_model.r WARNING @ Mon, 03 Jun 2019 09:55:42: #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 09:55:42: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:55:42: #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 09:55:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:55:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:55:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:55:46: #1 total tags in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:55:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:55:46: #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 09:55:47: 13000000 INFO @ Mon, 03 Jun 2019 09:55:47: #1 tags after filtering in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:55:47: #1 finished! INFO @ Mon, 03 Jun 2019 09:55:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:55:48: #2 number of paired peaks: 290 WARNING @ Mon, 03 Jun 2019 09:55:48: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Mon, 03 Jun 2019 09:55:48: start model_add_line... INFO @ Mon, 03 Jun 2019 09:55:48: start X-correlation... INFO @ Mon, 03 Jun 2019 09:55:48: end of X-cor INFO @ Mon, 03 Jun 2019 09:55:48: #2 finished! INFO @ Mon, 03 Jun 2019 09:55:48: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:55:48: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:55:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10_model.r WARNING @ Mon, 03 Jun 2019 09:55:48: #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 09:55:48: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:55:48: #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 09:55:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:55:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:55:55: 14000000 INFO @ Mon, 03 Jun 2019 09:56:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:56:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:56:04: #1 total tags in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:56:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:56:04: #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 09:56:04: #1 tags after filtering in treatment: 14961739 INFO @ Mon, 03 Jun 2019 09:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:56:04: #1 finished! INFO @ Mon, 03 Jun 2019 09:56:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:56:06: #2 number of paired peaks: 290 WARNING @ Mon, 03 Jun 2019 09:56:06: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Mon, 03 Jun 2019 09:56:06: start model_add_line... INFO @ Mon, 03 Jun 2019 09:56:06: start X-correlation... INFO @ Mon, 03 Jun 2019 09:56:06: end of X-cor INFO @ Mon, 03 Jun 2019 09:56:06: #2 finished! INFO @ Mon, 03 Jun 2019 09:56:06: #2 predicted fragment length is 43 bps INFO @ Mon, 03 Jun 2019 09:56:06: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 03 Jun 2019 09:56:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05_model.r WARNING @ Mon, 03 Jun 2019 09:56:06: #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 09:56:06: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 03 Jun 2019 09:56:06: #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 09:56:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:56:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.20_summits.bed INFO @ Mon, 03 Jun 2019 09:56:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:56:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.10_summits.bed INFO @ Mon, 03 Jun 2019 09:56:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1888 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:57:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:57:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:57:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287810/SRX287810.05_summits.bed INFO @ Mon, 03 Jun 2019 09:57:10: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2142 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。