Job ID = 1293650 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:15:25 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' 2019-06-02T16:15:25 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/traces/sra7/SRR/000354/SRR363408' 2019-06-02T16:15:35 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR363408' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T16:15:35 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T16:30:34 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' 2019-06-02T16:30:34 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/traces/sra7/SRR/000354/SRR363408' 2019-06-02T16:30:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR363408' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T16:30:43 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 37,480,643 reads read : 37,480,643 reads written : 37,480,643 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: 00:09:06 37480643 reads; of these: 37480643 (100.00%) were unpaired; of these: 3263123 (8.71%) aligned 0 times 29295446 (78.16%) aligned exactly 1 time 4922074 (13.13%) aligned >1 times 91.29% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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] 8669596 / 34217520 = 0.2534 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 02:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.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 02:04:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:04:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.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 02:04:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:04:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.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 02:04:15: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:04:15: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:04:24: 1000000 INFO @ Mon, 03 Jun 2019 02:04:24: 1000000 INFO @ Mon, 03 Jun 2019 02:04:24: 1000000 INFO @ Mon, 03 Jun 2019 02:04:33: 2000000 INFO @ Mon, 03 Jun 2019 02:04:33: 2000000 INFO @ Mon, 03 Jun 2019 02:04:33: 2000000 INFO @ Mon, 03 Jun 2019 02:04:41: 3000000 INFO @ Mon, 03 Jun 2019 02:04:42: 3000000 INFO @ Mon, 03 Jun 2019 02:04:42: 3000000 INFO @ Mon, 03 Jun 2019 02:04:50: 4000000 INFO @ Mon, 03 Jun 2019 02:04:50: 4000000 INFO @ Mon, 03 Jun 2019 02:04:50: 4000000 INFO @ Mon, 03 Jun 2019 02:04:58: 5000000 INFO @ Mon, 03 Jun 2019 02:04:59: 5000000 INFO @ Mon, 03 Jun 2019 02:04:59: 5000000 INFO @ Mon, 03 Jun 2019 02:05:07: 6000000 INFO @ Mon, 03 Jun 2019 02:05:07: 6000000 INFO @ Mon, 03 Jun 2019 02:05:07: 6000000 INFO @ Mon, 03 Jun 2019 02:05:15: 7000000 INFO @ Mon, 03 Jun 2019 02:05:16: 7000000 INFO @ Mon, 03 Jun 2019 02:05:16: 7000000 INFO @ Mon, 03 Jun 2019 02:05:23: 8000000 INFO @ Mon, 03 Jun 2019 02:05:24: 8000000 INFO @ Mon, 03 Jun 2019 02:05:25: 8000000 INFO @ Mon, 03 Jun 2019 02:05:31: 9000000 INFO @ Mon, 03 Jun 2019 02:05:32: 9000000 INFO @ Mon, 03 Jun 2019 02:05:33: 9000000 INFO @ Mon, 03 Jun 2019 02:05:39: 10000000 INFO @ Mon, 03 Jun 2019 02:05:40: 10000000 INFO @ Mon, 03 Jun 2019 02:05:41: 10000000 INFO @ Mon, 03 Jun 2019 02:05:47: 11000000 INFO @ Mon, 03 Jun 2019 02:05:49: 11000000 INFO @ Mon, 03 Jun 2019 02:05:50: 11000000 INFO @ Mon, 03 Jun 2019 02:05:55: 12000000 INFO @ Mon, 03 Jun 2019 02:05:57: 12000000 INFO @ Mon, 03 Jun 2019 02:05:58: 12000000 INFO @ Mon, 03 Jun 2019 02:06:03: 13000000 INFO @ Mon, 03 Jun 2019 02:06:05: 13000000 INFO @ Mon, 03 Jun 2019 02:06:06: 13000000 INFO @ Mon, 03 Jun 2019 02:06:11: 14000000 INFO @ Mon, 03 Jun 2019 02:06:13: 14000000 INFO @ Mon, 03 Jun 2019 02:06:15: 14000000 INFO @ Mon, 03 Jun 2019 02:06:20: 15000000 INFO @ Mon, 03 Jun 2019 02:06:21: 15000000 INFO @ Mon, 03 Jun 2019 02:06:23: 15000000 INFO @ Mon, 03 Jun 2019 02:06:28: 16000000 INFO @ Mon, 03 Jun 2019 02:06:29: 16000000 INFO @ Mon, 03 Jun 2019 02:06:31: 16000000 INFO @ Mon, 03 Jun 2019 02:06:36: 17000000 INFO @ Mon, 03 Jun 2019 02:06:38: 17000000 INFO @ Mon, 03 Jun 2019 02:06:40: 17000000 INFO @ Mon, 03 Jun 2019 02:06:44: 18000000 INFO @ Mon, 03 Jun 2019 02:06:46: 18000000 INFO @ Mon, 03 Jun 2019 02:06:48: 18000000 INFO @ Mon, 03 Jun 2019 02:06:52: 19000000 INFO @ Mon, 03 Jun 2019 02:06:54: 19000000 INFO @ Mon, 03 Jun 2019 02:06:57: 19000000 INFO @ Mon, 03 Jun 2019 02:07:00: 20000000 INFO @ Mon, 03 Jun 2019 02:07:03: 20000000 INFO @ Mon, 03 Jun 2019 02:07:06: 20000000 INFO @ Mon, 03 Jun 2019 02:07:09: 21000000 INFO @ Mon, 03 Jun 2019 02:07:11: 21000000 INFO @ Mon, 03 Jun 2019 02:07:14: 21000000 INFO @ Mon, 03 Jun 2019 02:07:17: 22000000 INFO @ Mon, 03 Jun 2019 02:07:19: 22000000 INFO @ Mon, 03 Jun 2019 02:07:23: 22000000 INFO @ Mon, 03 Jun 2019 02:07:25: 23000000 INFO @ Mon, 03 Jun 2019 02:07:27: 23000000 INFO @ Mon, 03 Jun 2019 02:07:31: 23000000 INFO @ Mon, 03 Jun 2019 02:07:33: 24000000 INFO @ Mon, 03 Jun 2019 02:07:36: 24000000 INFO @ Mon, 03 Jun 2019 02:07:39: 24000000 INFO @ Mon, 03 Jun 2019 02:07:41: 25000000 INFO @ Mon, 03 Jun 2019 02:07:44: 25000000 INFO @ Mon, 03 Jun 2019 02:07:46: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:07:46: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:07:46: #1 total tags in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:07:46: #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 02:07:46: #1 tags after filtering in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:07:46: #1 finished! INFO @ Mon, 03 Jun 2019 02:07:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:07:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:07:48: 25000000 INFO @ Mon, 03 Jun 2019 02:07:48: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:07:48: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:07:48: #1 total tags in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:07:48: #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 02:07:49: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 02:07:49: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 02:07:49: start model_add_line... INFO @ Mon, 03 Jun 2019 02:07:49: start X-correlation... INFO @ Mon, 03 Jun 2019 02:07:49: end of X-cor INFO @ Mon, 03 Jun 2019 02:07:49: #2 finished! INFO @ Mon, 03 Jun 2019 02:07:49: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 02:07:49: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 02:07:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10_model.r INFO @ Mon, 03 Jun 2019 02:07:49: #1 tags after filtering in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:07:49: #1 finished! INFO @ Mon, 03 Jun 2019 02:07:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:07:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:07:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:07:51: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 02:07:51: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 02:07:51: start model_add_line... INFO @ Mon, 03 Jun 2019 02:07:51: start X-correlation... INFO @ Mon, 03 Jun 2019 02:07:51: end of X-cor INFO @ Mon, 03 Jun 2019 02:07:51: #2 finished! INFO @ Mon, 03 Jun 2019 02:07:51: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 02:07:51: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 02:07:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20_model.r INFO @ Mon, 03 Jun 2019 02:07:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:07:52: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 02:07:52: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 02:07:52: #1 total tags in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:07:52: #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 02:07:53: #1 tags after filtering in treatment: 25547924 INFO @ Mon, 03 Jun 2019 02:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:07:53: #1 finished! INFO @ Mon, 03 Jun 2019 02:07:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:07:55: #2 number of paired peaks: 131 WARNING @ Mon, 03 Jun 2019 02:07:55: Fewer paired peaks (131) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 131 pairs to build model! INFO @ Mon, 03 Jun 2019 02:07:55: start model_add_line... INFO @ Mon, 03 Jun 2019 02:07:55: start X-correlation... INFO @ Mon, 03 Jun 2019 02:07:55: end of X-cor INFO @ Mon, 03 Jun 2019 02:07:55: #2 finished! INFO @ Mon, 03 Jun 2019 02:07:55: #2 predicted fragment length is 98 bps INFO @ Mon, 03 Jun 2019 02:07:55: #2 alternative fragment length(s) may be 98 bps INFO @ Mon, 03 Jun 2019 02:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05_model.r INFO @ Mon, 03 Jun 2019 02:07:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:08:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:08:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:08:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.10_summits.bed INFO @ Mon, 03 Jun 2019 02:09:24: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4538 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.20_summits.bed INFO @ Mon, 03 Jun 2019 02:09:27: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1748 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX104964/SRX104964.05_summits.bed INFO @ Mon, 03 Jun 2019 02:09:33: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11559 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。