Job ID = 1307191 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T13:06:05 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T13:06:05 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/sos/sra-pub-run-2/SRR8433312/SRR8433312.1' 2019-06-03T13:06:05 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR8433312' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T13:06:05 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 16,716,245 reads read : 33,432,490 reads written : 16,716,245 reads 0-length : 16,716,245 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: 00:10:22 16716245 reads; of these: 16716245 (100.00%) were unpaired; of these: 697162 (4.17%) aligned 0 times 12331107 (73.77%) aligned exactly 1 time 3687976 (22.06%) aligned >1 times 95.83% overall alignment rate Time searching: 00:10:22 Overall time: 00:10:22 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] 1642094 / 16019083 = 0.1025 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 22:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.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 22:36:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.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 22:36:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.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 22:36:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:36:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:36:37: 1000000 INFO @ Mon, 03 Jun 2019 22:36:39: 1000000 INFO @ Mon, 03 Jun 2019 22:36:39: 1000000 INFO @ Mon, 03 Jun 2019 22:36:45: 2000000 INFO @ Mon, 03 Jun 2019 22:36:48: 2000000 INFO @ Mon, 03 Jun 2019 22:36:48: 2000000 INFO @ Mon, 03 Jun 2019 22:36:53: 3000000 INFO @ Mon, 03 Jun 2019 22:36:57: 3000000 INFO @ Mon, 03 Jun 2019 22:36:57: 3000000 INFO @ Mon, 03 Jun 2019 22:37:01: 4000000 INFO @ Mon, 03 Jun 2019 22:37:06: 4000000 INFO @ Mon, 03 Jun 2019 22:37:07: 4000000 INFO @ Mon, 03 Jun 2019 22:37:09: 5000000 INFO @ Mon, 03 Jun 2019 22:37:14: 5000000 INFO @ Mon, 03 Jun 2019 22:37:16: 5000000 INFO @ Mon, 03 Jun 2019 22:37:16: 6000000 INFO @ Mon, 03 Jun 2019 22:37:23: 6000000 INFO @ Mon, 03 Jun 2019 22:37:24: 7000000 INFO @ Mon, 03 Jun 2019 22:37:25: 6000000 INFO @ Mon, 03 Jun 2019 22:37:31: 8000000 INFO @ Mon, 03 Jun 2019 22:37:33: 7000000 INFO @ Mon, 03 Jun 2019 22:37:34: 7000000 INFO @ Mon, 03 Jun 2019 22:37:39: 9000000 INFO @ Mon, 03 Jun 2019 22:37:42: 8000000 INFO @ Mon, 03 Jun 2019 22:37:43: 8000000 INFO @ Mon, 03 Jun 2019 22:37:46: 10000000 INFO @ Mon, 03 Jun 2019 22:37:51: 9000000 INFO @ Mon, 03 Jun 2019 22:37:52: 9000000 INFO @ Mon, 03 Jun 2019 22:37:54: 11000000 INFO @ Mon, 03 Jun 2019 22:37:59: 10000000 INFO @ Mon, 03 Jun 2019 22:38:01: 10000000 INFO @ Mon, 03 Jun 2019 22:38:01: 12000000 INFO @ Mon, 03 Jun 2019 22:38:08: 11000000 INFO @ Mon, 03 Jun 2019 22:38:09: 13000000 INFO @ Mon, 03 Jun 2019 22:38:10: 11000000 INFO @ Mon, 03 Jun 2019 22:38:17: 14000000 INFO @ Mon, 03 Jun 2019 22:38:17: 12000000 INFO @ Mon, 03 Jun 2019 22:38:19: 12000000 INFO @ Mon, 03 Jun 2019 22:38:20: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:38:20: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:38:20: #1 total tags in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:20: #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 22:38:20: #1 tags after filtering in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:20: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:21: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 22:38:21: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 22:38:21: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:21: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:21: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:21: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:21: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 22:38:21: #2 alternative fragment length(s) may be 4,78 bps INFO @ Mon, 03 Jun 2019 22:38:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10_model.r WARNING @ Mon, 03 Jun 2019 22:38:21: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:38:21: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Mon, 03 Jun 2019 22:38:21: #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 22:38:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:38:26: 13000000 INFO @ Mon, 03 Jun 2019 22:38:28: 13000000 INFO @ Mon, 03 Jun 2019 22:38:35: 14000000 INFO @ Mon, 03 Jun 2019 22:38:37: 14000000 INFO @ Mon, 03 Jun 2019 22:38:38: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:38:38: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:38:38: #1 total tags in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:38: #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 22:38:39: #1 tags after filtering in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:39: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:40: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 22:38:40: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 22:38:40: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:40: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:40: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:40: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:40: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 22:38:40: #2 alternative fragment length(s) may be 4,78 bps INFO @ Mon, 03 Jun 2019 22:38:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20_model.r WARNING @ Mon, 03 Jun 2019 22:38:40: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:38:40: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Mon, 03 Jun 2019 22:38:40: #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 22:38:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:38:41: #1 tag size is determined as 76 bps INFO @ Mon, 03 Jun 2019 22:38:41: #1 tag size = 76 INFO @ Mon, 03 Jun 2019 22:38:41: #1 total tags in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:38:41: #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 22:38:41: #1 tags after filtering in treatment: 14376989 INFO @ Mon, 03 Jun 2019 22:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:38:41: #1 finished! INFO @ Mon, 03 Jun 2019 22:38:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:38:42: #2 number of paired peaks: 120 WARNING @ Mon, 03 Jun 2019 22:38:42: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Mon, 03 Jun 2019 22:38:42: start model_add_line... INFO @ Mon, 03 Jun 2019 22:38:42: start X-correlation... INFO @ Mon, 03 Jun 2019 22:38:42: end of X-cor INFO @ Mon, 03 Jun 2019 22:38:42: #2 finished! INFO @ Mon, 03 Jun 2019 22:38:42: #2 predicted fragment length is 78 bps INFO @ Mon, 03 Jun 2019 22:38:42: #2 alternative fragment length(s) may be 4,78 bps INFO @ Mon, 03 Jun 2019 22:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05_model.r WARNING @ Mon, 03 Jun 2019 22:38:42: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 22:38:42: #2 You may need to consider one of the other alternative d(s): 4,78 WARNING @ Mon, 03 Jun 2019 22:38:42: #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 22:38:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:39:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.10_summits.bed INFO @ Mon, 03 Jun 2019 22:39:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:39:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:39:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.20_summits.bed INFO @ Mon, 03 Jun 2019 22:39:39: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:39:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:39:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:39:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5241031/SRX5241031.05_summits.bed INFO @ Mon, 03 Jun 2019 22:39:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1734 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。