Job ID = 1308429 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:56:28 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 ) 2019-06-03T13:56:28 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 : 31,093,103 reads read : 62,186,206 reads written : 31,093,103 reads 0-length : 31,093,103 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: 00:15:05 31093103 reads; of these: 31093103 (100.00%) were unpaired; of these: 2884799 (9.28%) aligned 0 times 20057412 (64.51%) aligned exactly 1 time 8150892 (26.21%) aligned >1 times 90.72% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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 12 files... [bam_rmdupse_core] 9356337 / 28208304 = 0.3317 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 23:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.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 23:20:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:20:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.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 23:20:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:20:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:20:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.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 23:20:42: #1 read tag files... INFO @ Mon, 03 Jun 2019 23:20:42: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 23:20:50: 1000000 INFO @ Mon, 03 Jun 2019 23:20:50: 1000000 INFO @ Mon, 03 Jun 2019 23:20:51: 1000000 INFO @ Mon, 03 Jun 2019 23:20:58: 2000000 INFO @ Mon, 03 Jun 2019 23:20:58: 2000000 INFO @ Mon, 03 Jun 2019 23:20:59: 2000000 INFO @ Mon, 03 Jun 2019 23:21:06: 3000000 INFO @ Mon, 03 Jun 2019 23:21:06: 3000000 INFO @ Mon, 03 Jun 2019 23:21:07: 3000000 INFO @ Mon, 03 Jun 2019 23:21:14: 4000000 INFO @ Mon, 03 Jun 2019 23:21:14: 4000000 INFO @ Mon, 03 Jun 2019 23:21:15: 4000000 INFO @ Mon, 03 Jun 2019 23:21:21: 5000000 INFO @ Mon, 03 Jun 2019 23:21:22: 5000000 INFO @ Mon, 03 Jun 2019 23:21:23: 5000000 INFO @ Mon, 03 Jun 2019 23:21:28: 6000000 INFO @ Mon, 03 Jun 2019 23:21:29: 6000000 INFO @ Mon, 03 Jun 2019 23:21:31: 6000000 INFO @ Mon, 03 Jun 2019 23:21:36: 7000000 INFO @ Mon, 03 Jun 2019 23:21:37: 7000000 INFO @ Mon, 03 Jun 2019 23:21:40: 7000000 INFO @ Mon, 03 Jun 2019 23:21:45: 8000000 INFO @ Mon, 03 Jun 2019 23:21:45: 8000000 INFO @ Mon, 03 Jun 2019 23:21:47: 8000000 INFO @ Mon, 03 Jun 2019 23:21:53: 9000000 INFO @ Mon, 03 Jun 2019 23:21:54: 9000000 INFO @ Mon, 03 Jun 2019 23:21:56: 9000000 INFO @ Mon, 03 Jun 2019 23:22:01: 10000000 INFO @ Mon, 03 Jun 2019 23:22:02: 10000000 INFO @ Mon, 03 Jun 2019 23:22:04: 10000000 INFO @ Mon, 03 Jun 2019 23:22:08: 11000000 INFO @ Mon, 03 Jun 2019 23:22:09: 11000000 INFO @ Mon, 03 Jun 2019 23:22:13: 11000000 INFO @ Mon, 03 Jun 2019 23:22:15: 12000000 INFO @ Mon, 03 Jun 2019 23:22:17: 12000000 INFO @ Mon, 03 Jun 2019 23:22:21: 12000000 INFO @ Mon, 03 Jun 2019 23:22:22: 13000000 INFO @ Mon, 03 Jun 2019 23:22:24: 13000000 INFO @ Mon, 03 Jun 2019 23:22:29: 13000000 INFO @ Mon, 03 Jun 2019 23:22:30: 14000000 INFO @ Mon, 03 Jun 2019 23:22:32: 14000000 INFO @ Mon, 03 Jun 2019 23:22:37: 14000000 INFO @ Mon, 03 Jun 2019 23:22:37: 15000000 INFO @ Mon, 03 Jun 2019 23:22:39: 15000000 INFO @ Mon, 03 Jun 2019 23:22:45: 15000000 INFO @ Mon, 03 Jun 2019 23:22:45: 16000000 INFO @ Mon, 03 Jun 2019 23:22:47: 16000000 INFO @ Mon, 03 Jun 2019 23:22:52: 17000000 INFO @ Mon, 03 Jun 2019 23:22:52: 16000000 INFO @ Mon, 03 Jun 2019 23:22:54: 17000000 INFO @ Mon, 03 Jun 2019 23:23:00: 18000000 INFO @ Mon, 03 Jun 2019 23:23:00: 17000000 INFO @ Mon, 03 Jun 2019 23:23:02: 18000000 INFO @ Mon, 03 Jun 2019 23:23:06: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:23:06: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:23:06: #1 total tags in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:23:06: #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 23:23:06: #1 tags after filtering in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:23:06: #1 finished! INFO @ Mon, 03 Jun 2019 23:23:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:23:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:23:08: 18000000 INFO @ Mon, 03 Jun 2019 23:23:08: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 23:23:08: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 23:23:08: start model_add_line... INFO @ Mon, 03 Jun 2019 23:23:08: start X-correlation... INFO @ Mon, 03 Jun 2019 23:23:08: end of X-cor INFO @ Mon, 03 Jun 2019 23:23:08: #2 finished! INFO @ Mon, 03 Jun 2019 23:23:08: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 23:23:08: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 03 Jun 2019 23:23:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10_model.r WARNING @ Mon, 03 Jun 2019 23:23:08: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:23:08: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 03 Jun 2019 23:23:08: #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 23:23:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:23:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:23:08: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:23:08: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:23:08: #1 total tags in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:23:08: #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 23:23:09: #1 tags after filtering in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:23:09: #1 finished! INFO @ Mon, 03 Jun 2019 23:23:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:23:10: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 23:23:10: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 23:23:10: start model_add_line... INFO @ Mon, 03 Jun 2019 23:23:10: start X-correlation... INFO @ Mon, 03 Jun 2019 23:23:10: end of X-cor INFO @ Mon, 03 Jun 2019 23:23:10: #2 finished! INFO @ Mon, 03 Jun 2019 23:23:10: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 23:23:10: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 03 Jun 2019 23:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05_model.r WARNING @ Mon, 03 Jun 2019 23:23:10: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:23:10: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 03 Jun 2019 23:23:10: #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 23:23:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:23:15: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 23:23:15: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 23:23:15: #1 total tags in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 23:23:15: #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 23:23:15: #1 tags after filtering in treatment: 18851967 INFO @ Mon, 03 Jun 2019 23:23:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 23:23:15: #1 finished! INFO @ Mon, 03 Jun 2019 23:23:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 23:23:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 23:23:17: #2 number of paired peaks: 126 WARNING @ Mon, 03 Jun 2019 23:23:17: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Mon, 03 Jun 2019 23:23:17: start model_add_line... INFO @ Mon, 03 Jun 2019 23:23:17: start X-correlation... INFO @ Mon, 03 Jun 2019 23:23:17: end of X-cor INFO @ Mon, 03 Jun 2019 23:23:17: #2 finished! INFO @ Mon, 03 Jun 2019 23:23:17: #2 predicted fragment length is 66 bps INFO @ Mon, 03 Jun 2019 23:23:17: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 03 Jun 2019 23:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20_model.r WARNING @ Mon, 03 Jun 2019 23:23:17: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 23:23:17: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 03 Jun 2019 23:23:17: #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 23:23:17: #3 Call peaks... INFO @ Mon, 03 Jun 2019 23:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 23:23:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:23:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:24:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 23:24:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10_peaks.xls INFO @ Mon, 03 Jun 2019 23:24:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:24:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.10_summits.bed INFO @ Mon, 03 Jun 2019 23:24:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:24:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05_peaks.xls INFO @ Mon, 03 Jun 2019 23:24:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:24:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.05_summits.bed INFO @ Mon, 03 Jun 2019 23:24:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 23:24:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20_peaks.xls INFO @ Mon, 03 Jun 2019 23:24:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 23:24:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343144/SRX5343144.20_summits.bed INFO @ Mon, 03 Jun 2019 23:24:27: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (865 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。