Job ID = 1294310 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T21:19:53 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 ) 2019-06-02T21:19:53 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 : 20,305,835 reads read : 20,305,835 reads written : 20,305,835 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: 00:09:44 20305835 reads; of these: 20305835 (100.00%) were unpaired; of these: 457736 (2.25%) aligned 0 times 13581240 (66.88%) aligned exactly 1 time 6266859 (30.86%) aligned >1 times 97.75% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 1812637 / 19848099 = 0.0913 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 06:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.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 06:40:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.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 06:40:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.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 06:40:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:40:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:40:24: 1000000 INFO @ Mon, 03 Jun 2019 06:40:25: 1000000 INFO @ Mon, 03 Jun 2019 06:40:26: 1000000 INFO @ Mon, 03 Jun 2019 06:40:33: 2000000 INFO @ Mon, 03 Jun 2019 06:40:35: 2000000 INFO @ Mon, 03 Jun 2019 06:40:37: 2000000 INFO @ Mon, 03 Jun 2019 06:40:41: 3000000 INFO @ Mon, 03 Jun 2019 06:40:44: 3000000 INFO @ Mon, 03 Jun 2019 06:40:48: 3000000 INFO @ Mon, 03 Jun 2019 06:40:50: 4000000 INFO @ Mon, 03 Jun 2019 06:40:53: 4000000 INFO @ Mon, 03 Jun 2019 06:40:58: 5000000 INFO @ Mon, 03 Jun 2019 06:40:58: 4000000 INFO @ Mon, 03 Jun 2019 06:41:02: 5000000 INFO @ Mon, 03 Jun 2019 06:41:06: 6000000 INFO @ Mon, 03 Jun 2019 06:41:08: 5000000 INFO @ Mon, 03 Jun 2019 06:41:11: 6000000 INFO @ Mon, 03 Jun 2019 06:41:14: 7000000 INFO @ Mon, 03 Jun 2019 06:41:18: 6000000 INFO @ Mon, 03 Jun 2019 06:41:20: 7000000 INFO @ Mon, 03 Jun 2019 06:41:22: 8000000 INFO @ Mon, 03 Jun 2019 06:41:28: 7000000 INFO @ Mon, 03 Jun 2019 06:41:29: 8000000 INFO @ Mon, 03 Jun 2019 06:41:30: 9000000 INFO @ Mon, 03 Jun 2019 06:41:38: 10000000 INFO @ Mon, 03 Jun 2019 06:41:38: 9000000 INFO @ Mon, 03 Jun 2019 06:41:39: 8000000 INFO @ Mon, 03 Jun 2019 06:41:46: 11000000 INFO @ Mon, 03 Jun 2019 06:41:47: 10000000 INFO @ Mon, 03 Jun 2019 06:41:49: 9000000 INFO @ Mon, 03 Jun 2019 06:41:54: 12000000 INFO @ Mon, 03 Jun 2019 06:41:56: 11000000 INFO @ Mon, 03 Jun 2019 06:41:59: 10000000 INFO @ Mon, 03 Jun 2019 06:42:02: 13000000 INFO @ Mon, 03 Jun 2019 06:42:06: 12000000 INFO @ Mon, 03 Jun 2019 06:42:10: 14000000 INFO @ Mon, 03 Jun 2019 06:42:10: 11000000 INFO @ Mon, 03 Jun 2019 06:42:15: 13000000 INFO @ Mon, 03 Jun 2019 06:42:18: 15000000 INFO @ Mon, 03 Jun 2019 06:42:21: 12000000 INFO @ Mon, 03 Jun 2019 06:42:24: 14000000 INFO @ Mon, 03 Jun 2019 06:42:26: 16000000 INFO @ Mon, 03 Jun 2019 06:42:31: 13000000 INFO @ Mon, 03 Jun 2019 06:42:33: 15000000 INFO @ Mon, 03 Jun 2019 06:42:34: 17000000 INFO @ Mon, 03 Jun 2019 06:42:42: 18000000 INFO @ Mon, 03 Jun 2019 06:42:42: 14000000 INFO @ Mon, 03 Jun 2019 06:42:42: 16000000 INFO @ Mon, 03 Jun 2019 06:42:42: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:42:42: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:42:42: #1 total tags in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:42:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:42:42: #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 06:42:43: #1 tags after filtering in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:42:43: #1 finished! INFO @ Mon, 03 Jun 2019 06:42:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:42:44: #2 number of paired peaks: 754 WARNING @ Mon, 03 Jun 2019 06:42:44: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Mon, 03 Jun 2019 06:42:44: start model_add_line... INFO @ Mon, 03 Jun 2019 06:42:44: start X-correlation... INFO @ Mon, 03 Jun 2019 06:42:44: end of X-cor INFO @ Mon, 03 Jun 2019 06:42:44: #2 finished! INFO @ Mon, 03 Jun 2019 06:42:44: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 06:42:44: #2 alternative fragment length(s) may be 4,114 bps INFO @ Mon, 03 Jun 2019 06:42:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10_model.r WARNING @ Mon, 03 Jun 2019 06:42:44: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:42:44: #2 You may need to consider one of the other alternative d(s): 4,114 WARNING @ Mon, 03 Jun 2019 06:42:44: #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 06:42:44: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:42:51: 17000000 INFO @ Mon, 03 Jun 2019 06:42:52: 15000000 INFO @ Mon, 03 Jun 2019 06:43:00: 18000000 INFO @ Mon, 03 Jun 2019 06:43:01: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:43:01: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:43:01: #1 total tags in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:43:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:43:01: #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 06:43:01: #1 tags after filtering in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:43:01: #1 finished! INFO @ Mon, 03 Jun 2019 06:43:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:43:02: 16000000 INFO @ Mon, 03 Jun 2019 06:43:03: #2 number of paired peaks: 754 WARNING @ Mon, 03 Jun 2019 06:43:03: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Mon, 03 Jun 2019 06:43:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:43:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:43:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:43:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:43:03: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 06:43:03: #2 alternative fragment length(s) may be 4,114 bps INFO @ Mon, 03 Jun 2019 06:43:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20_model.r WARNING @ Mon, 03 Jun 2019 06:43:03: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:43:03: #2 You may need to consider one of the other alternative d(s): 4,114 WARNING @ Mon, 03 Jun 2019 06:43:03: #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 06:43:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:43:13: 17000000 INFO @ Mon, 03 Jun 2019 06:43:24: 18000000 INFO @ Mon, 03 Jun 2019 06:43:25: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:43:25: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:43:25: #1 total tags in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:43:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:43:25: #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 06:43:25: #1 tags after filtering in treatment: 18035462 INFO @ Mon, 03 Jun 2019 06:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:43:25: #1 finished! INFO @ Mon, 03 Jun 2019 06:43:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:43:27: #2 number of paired peaks: 754 WARNING @ Mon, 03 Jun 2019 06:43:27: Fewer paired peaks (754) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 754 pairs to build model! INFO @ Mon, 03 Jun 2019 06:43:27: start model_add_line... INFO @ Mon, 03 Jun 2019 06:43:27: start X-correlation... INFO @ Mon, 03 Jun 2019 06:43:27: end of X-cor INFO @ Mon, 03 Jun 2019 06:43:27: #2 finished! INFO @ Mon, 03 Jun 2019 06:43:27: #2 predicted fragment length is 114 bps INFO @ Mon, 03 Jun 2019 06:43:27: #2 alternative fragment length(s) may be 4,114 bps INFO @ Mon, 03 Jun 2019 06:43:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05_model.r WARNING @ Mon, 03 Jun 2019 06:43:27: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:43:27: #2 You may need to consider one of the other alternative d(s): 4,114 WARNING @ Mon, 03 Jun 2019 06:43:27: #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 06:43:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:43:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:43:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.10_summits.bed INFO @ Mon, 03 Jun 2019 06:43:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2718 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:44:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.20_summits.bed INFO @ Mon, 03 Jun 2019 06:44:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1403 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:44:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422639/SRX2422639.05_summits.bed INFO @ Mon, 03 Jun 2019 06:44:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4824 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。