Job ID = 1294581 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:03:52 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 ) 2019-06-03T00:03:52 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 ) 2019-06-03T00:03:52 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 ) 2019-06-03T00:03:52 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 ) 2019-06-03T00:03:52 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 ) 2019-06-03T00:03:53 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 : 13,145,001 reads read : 13,145,001 reads written : 13,145,001 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: 00:07:16 13145001 reads; of these: 13145001 (100.00%) were unpaired; of these: 524334 (3.99%) aligned 0 times 8741622 (66.50%) aligned exactly 1 time 3879045 (29.51%) aligned >1 times 96.01% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 862992 / 12620667 = 0.0684 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 09:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.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 09:21:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.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 09:21:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.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 09:21:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:21:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:21:23: 1000000 INFO @ Mon, 03 Jun 2019 09:21:23: 1000000 INFO @ Mon, 03 Jun 2019 09:21:24: 1000000 INFO @ Mon, 03 Jun 2019 09:21:33: 2000000 INFO @ Mon, 03 Jun 2019 09:21:33: 2000000 INFO @ Mon, 03 Jun 2019 09:21:34: 2000000 INFO @ Mon, 03 Jun 2019 09:21:42: 3000000 INFO @ Mon, 03 Jun 2019 09:21:42: 3000000 INFO @ Mon, 03 Jun 2019 09:21:43: 3000000 INFO @ Mon, 03 Jun 2019 09:21:51: 4000000 INFO @ Mon, 03 Jun 2019 09:21:52: 4000000 INFO @ Mon, 03 Jun 2019 09:21:53: 4000000 INFO @ Mon, 03 Jun 2019 09:22:01: 5000000 INFO @ Mon, 03 Jun 2019 09:22:01: 5000000 INFO @ Mon, 03 Jun 2019 09:22:03: 5000000 INFO @ Mon, 03 Jun 2019 09:22:10: 6000000 INFO @ Mon, 03 Jun 2019 09:22:10: 6000000 INFO @ Mon, 03 Jun 2019 09:22:13: 6000000 INFO @ Mon, 03 Jun 2019 09:22:20: 7000000 INFO @ Mon, 03 Jun 2019 09:22:20: 7000000 INFO @ Mon, 03 Jun 2019 09:22:23: 7000000 INFO @ Mon, 03 Jun 2019 09:22:29: 8000000 INFO @ Mon, 03 Jun 2019 09:22:29: 8000000 INFO @ Mon, 03 Jun 2019 09:22:33: 8000000 INFO @ Mon, 03 Jun 2019 09:22:38: 9000000 INFO @ Mon, 03 Jun 2019 09:22:38: 9000000 INFO @ Mon, 03 Jun 2019 09:22:43: 9000000 INFO @ Mon, 03 Jun 2019 09:22:48: 10000000 INFO @ Mon, 03 Jun 2019 09:22:48: 10000000 INFO @ Mon, 03 Jun 2019 09:22:53: 10000000 INFO @ Mon, 03 Jun 2019 09:22:57: 11000000 INFO @ Mon, 03 Jun 2019 09:22:58: 11000000 INFO @ Mon, 03 Jun 2019 09:23:03: 11000000 INFO @ Mon, 03 Jun 2019 09:23:04: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:04: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:04: #1 total tags in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:04: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:04: #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 09:23:05: #1 tags after filtering in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:05: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:05: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:05: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:05: #1 total tags in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:05: #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 09:23:05: #1 tags after filtering in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:05: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:06: #2 number of paired peaks: 195 WARNING @ Mon, 03 Jun 2019 09:23:06: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:06: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:06: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:06: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:06: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:06: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 09:23:06: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 09:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05_model.r WARNING @ Mon, 03 Jun 2019 09:23:06: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:23:06: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 09:23:06: #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 09:23:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:06: #2 number of paired peaks: 195 WARNING @ Mon, 03 Jun 2019 09:23:06: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:06: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:07: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:07: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:07: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:07: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 09:23:07: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 09:23:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10_model.r WARNING @ Mon, 03 Jun 2019 09:23:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:23:07: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 09:23:07: #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 09:23:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:23:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:23:10: #1 total tags in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:23:10: #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 09:23:10: #1 tags after filtering in treatment: 11757675 INFO @ Mon, 03 Jun 2019 09:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:23:10: #1 finished! INFO @ Mon, 03 Jun 2019 09:23:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:23:11: #2 number of paired peaks: 195 WARNING @ Mon, 03 Jun 2019 09:23:11: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 03 Jun 2019 09:23:11: start model_add_line... INFO @ Mon, 03 Jun 2019 09:23:11: start X-correlation... INFO @ Mon, 03 Jun 2019 09:23:11: end of X-cor INFO @ Mon, 03 Jun 2019 09:23:11: #2 finished! INFO @ Mon, 03 Jun 2019 09:23:11: #2 predicted fragment length is 52 bps INFO @ Mon, 03 Jun 2019 09:23:11: #2 alternative fragment length(s) may be 52 bps INFO @ Mon, 03 Jun 2019 09:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20_model.r WARNING @ Mon, 03 Jun 2019 09:23:11: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:23:11: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Mon, 03 Jun 2019 09:23:11: #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 09:23:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:23:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:23:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.05_summits.bed INFO @ Mon, 03 Jun 2019 09:23:59: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1546 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:23:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.10_summits.bed INFO @ Mon, 03 Jun 2019 09:23:59: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1279 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287755/SRX287755.20_summits.bed INFO @ Mon, 03 Jun 2019 09:24:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (967 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。