Job ID = 1293958 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T18:30:44 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' 2019-06-02T18:30:44 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/SRR504948/SRR504948.1' 2019-06-02T18:30:55 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR504948', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:31:10 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' 2019-06-02T18:31:10 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/SRR504948/SRR504948.1' 2019-06-02T18:31:15 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' 2019-06-02T18:31:15 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/SRR504948/SRR504948.1' 2019-06-02T18:31:15 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR504948' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 45,299,559 reads read : 45,299,559 reads written : 45,299,559 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: 00:24:59 45299559 reads; of these: 45299559 (100.00%) were unpaired; of these: 1509411 (3.33%) aligned 0 times 28753662 (63.47%) aligned exactly 1 time 15036486 (33.19%) aligned >1 times 96.67% overall alignment rate Time searching: 00:24:59 Overall time: 00:24:59 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 20 files... [bam_rmdupse_core] 21976659 / 43790148 = 0.5019 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 04:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.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 04:11:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:11:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.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 04:11:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:11:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.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 04:11:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:11:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:11:48: 1000000 INFO @ Mon, 03 Jun 2019 04:11:48: 1000000 INFO @ Mon, 03 Jun 2019 04:11:50: 1000000 INFO @ Mon, 03 Jun 2019 04:11:55: 2000000 INFO @ Mon, 03 Jun 2019 04:11:56: 2000000 INFO @ Mon, 03 Jun 2019 04:12:00: 2000000 INFO @ Mon, 03 Jun 2019 04:12:02: 3000000 INFO @ Mon, 03 Jun 2019 04:12:04: 3000000 INFO @ Mon, 03 Jun 2019 04:12:09: 4000000 INFO @ Mon, 03 Jun 2019 04:12:09: 3000000 INFO @ Mon, 03 Jun 2019 04:12:12: 4000000 INFO @ Mon, 03 Jun 2019 04:12:16: 5000000 INFO @ Mon, 03 Jun 2019 04:12:19: 4000000 INFO @ Mon, 03 Jun 2019 04:12:20: 5000000 INFO @ Mon, 03 Jun 2019 04:12:24: 6000000 INFO @ Mon, 03 Jun 2019 04:12:28: 6000000 INFO @ Mon, 03 Jun 2019 04:12:28: 5000000 INFO @ Mon, 03 Jun 2019 04:12:31: 7000000 INFO @ Mon, 03 Jun 2019 04:12:36: 7000000 INFO @ Mon, 03 Jun 2019 04:12:38: 8000000 INFO @ Mon, 03 Jun 2019 04:12:38: 6000000 INFO @ Mon, 03 Jun 2019 04:12:44: 8000000 INFO @ Mon, 03 Jun 2019 04:12:45: 9000000 INFO @ Mon, 03 Jun 2019 04:12:47: 7000000 INFO @ Mon, 03 Jun 2019 04:12:52: 9000000 INFO @ Mon, 03 Jun 2019 04:12:52: 10000000 INFO @ Mon, 03 Jun 2019 04:12:57: 8000000 INFO @ Mon, 03 Jun 2019 04:12:59: 10000000 INFO @ Mon, 03 Jun 2019 04:13:00: 11000000 INFO @ Mon, 03 Jun 2019 04:13:07: 12000000 INFO @ Mon, 03 Jun 2019 04:13:07: 9000000 INFO @ Mon, 03 Jun 2019 04:13:08: 11000000 INFO @ Mon, 03 Jun 2019 04:13:14: 13000000 INFO @ Mon, 03 Jun 2019 04:13:15: 12000000 INFO @ Mon, 03 Jun 2019 04:13:17: 10000000 INFO @ Mon, 03 Jun 2019 04:13:21: 14000000 INFO @ Mon, 03 Jun 2019 04:13:23: 13000000 INFO @ Mon, 03 Jun 2019 04:13:26: 11000000 INFO @ Mon, 03 Jun 2019 04:13:28: 15000000 INFO @ Mon, 03 Jun 2019 04:13:31: 14000000 INFO @ Mon, 03 Jun 2019 04:13:36: 16000000 INFO @ Mon, 03 Jun 2019 04:13:36: 12000000 INFO @ Mon, 03 Jun 2019 04:13:40: 15000000 INFO @ Mon, 03 Jun 2019 04:13:43: 17000000 INFO @ Mon, 03 Jun 2019 04:13:46: 13000000 INFO @ Mon, 03 Jun 2019 04:13:48: 16000000 INFO @ Mon, 03 Jun 2019 04:13:50: 18000000 INFO @ Mon, 03 Jun 2019 04:13:55: 14000000 INFO @ Mon, 03 Jun 2019 04:13:56: 17000000 INFO @ Mon, 03 Jun 2019 04:13:58: 19000000 INFO @ Mon, 03 Jun 2019 04:14:04: 18000000 INFO @ Mon, 03 Jun 2019 04:14:05: 20000000 INFO @ Mon, 03 Jun 2019 04:14:05: 15000000 INFO @ Mon, 03 Jun 2019 04:14:12: 21000000 INFO @ Mon, 03 Jun 2019 04:14:12: 19000000 INFO @ Mon, 03 Jun 2019 04:14:15: 16000000 INFO @ Mon, 03 Jun 2019 04:14:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:14:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:14:18: #1 total tags in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:14:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:14:18: #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 04:14:18: #1 tags after filtering in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:14:18: #1 finished! INFO @ Mon, 03 Jun 2019 04:14:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:14:20: 20000000 INFO @ Mon, 03 Jun 2019 04:14:20: #2 number of paired peaks: 509 WARNING @ Mon, 03 Jun 2019 04:14:20: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Mon, 03 Jun 2019 04:14:20: start model_add_line... INFO @ Mon, 03 Jun 2019 04:14:21: start X-correlation... INFO @ Mon, 03 Jun 2019 04:14:21: end of X-cor INFO @ Mon, 03 Jun 2019 04:14:21: #2 finished! INFO @ Mon, 03 Jun 2019 04:14:21: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 04:14:21: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 04:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05_model.r WARNING @ Mon, 03 Jun 2019 04:14:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:14:21: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 04:14:21: #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 04:14:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:14:25: 17000000 INFO @ Mon, 03 Jun 2019 04:14:28: 21000000 INFO @ Mon, 03 Jun 2019 04:14:34: 18000000 INFO @ Mon, 03 Jun 2019 04:14:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:14:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:14:35: #1 total tags in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:14:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:14:35: #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 04:14:35: #1 tags after filtering in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:14:35: #1 finished! INFO @ Mon, 03 Jun 2019 04:14:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:14:37: #2 number of paired peaks: 509 WARNING @ Mon, 03 Jun 2019 04:14:37: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Mon, 03 Jun 2019 04:14:37: start model_add_line... INFO @ Mon, 03 Jun 2019 04:14:37: start X-correlation... INFO @ Mon, 03 Jun 2019 04:14:37: end of X-cor INFO @ Mon, 03 Jun 2019 04:14:37: #2 finished! INFO @ Mon, 03 Jun 2019 04:14:37: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 04:14:37: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 04:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20_model.r WARNING @ Mon, 03 Jun 2019 04:14:37: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:14:37: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 04:14:37: #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 04:14:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:14:44: 19000000 INFO @ Mon, 03 Jun 2019 04:14:53: 20000000 INFO @ Mon, 03 Jun 2019 04:15:02: 21000000 INFO @ Mon, 03 Jun 2019 04:15:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:15:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:15:09: #1 total tags in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:15:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:15:09: #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 04:15:10: #1 tags after filtering in treatment: 21813489 INFO @ Mon, 03 Jun 2019 04:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:15:10: #1 finished! INFO @ Mon, 03 Jun 2019 04:15:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:15:12: #2 number of paired peaks: 509 WARNING @ Mon, 03 Jun 2019 04:15:12: Fewer paired peaks (509) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 509 pairs to build model! INFO @ Mon, 03 Jun 2019 04:15:12: start model_add_line... INFO @ Mon, 03 Jun 2019 04:15:12: start X-correlation... INFO @ Mon, 03 Jun 2019 04:15:12: end of X-cor INFO @ Mon, 03 Jun 2019 04:15:12: #2 finished! INFO @ Mon, 03 Jun 2019 04:15:12: #2 predicted fragment length is 39 bps INFO @ Mon, 03 Jun 2019 04:15:12: #2 alternative fragment length(s) may be 39 bps INFO @ Mon, 03 Jun 2019 04:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10_model.r WARNING @ Mon, 03 Jun 2019 04:15:12: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:15:12: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Mon, 03 Jun 2019 04:15:12: #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 04:15:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:15:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:15:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.05_summits.bed INFO @ Mon, 03 Jun 2019 04:15:42: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7358 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.20_summits.bed INFO @ Mon, 03 Jun 2019 04:15:58: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1598 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:16:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX152092/SRX152092.10_summits.bed INFO @ Mon, 03 Jun 2019 04:16:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4974 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。