Job ID = 1293986 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 3,985,480 reads read : 3,985,480 reads written : 3,985,480 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 2019-06-02T18:56:32 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' 2019-06-02T18:56:32 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-1/SRR3130893/SRR3130893.1' 2019-06-02T18:56:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR3130893' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T18:56:43 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 spots read : 4,000,000 reads read : 4,000,000 reads written : 4,000,000 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: 00:15:40 39985480 reads; of these: 39985480 (100.00%) were unpaired; of these: 2171702 (5.43%) aligned 0 times 30209279 (75.55%) aligned exactly 1 time 7604499 (19.02%) aligned >1 times 94.57% overall alignment rate Time searching: 00:15:40 Overall time: 00:15:40 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 16 files... [bam_rmdupse_core] 7071044 / 37813778 = 0.1870 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 04:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.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 04:35:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:35:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.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 04:35:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:35:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:35:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.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 04:35:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:35:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:35:45: 1000000 INFO @ Mon, 03 Jun 2019 04:35:45: 1000000 INFO @ Mon, 03 Jun 2019 04:35:45: 1000000 INFO @ Mon, 03 Jun 2019 04:35:52: 2000000 INFO @ Mon, 03 Jun 2019 04:35:53: 2000000 INFO @ Mon, 03 Jun 2019 04:35:53: 2000000 INFO @ Mon, 03 Jun 2019 04:36:00: 3000000 INFO @ Mon, 03 Jun 2019 04:36:01: 3000000 INFO @ Mon, 03 Jun 2019 04:36:01: 3000000 INFO @ Mon, 03 Jun 2019 04:36:07: 4000000 INFO @ Mon, 03 Jun 2019 04:36:09: 4000000 INFO @ Mon, 03 Jun 2019 04:36:09: 4000000 INFO @ Mon, 03 Jun 2019 04:36:14: 5000000 INFO @ Mon, 03 Jun 2019 04:36:17: 5000000 INFO @ Mon, 03 Jun 2019 04:36:17: 5000000 INFO @ Mon, 03 Jun 2019 04:36:21: 6000000 INFO @ Mon, 03 Jun 2019 04:36:25: 6000000 INFO @ Mon, 03 Jun 2019 04:36:25: 6000000 INFO @ Mon, 03 Jun 2019 04:36:28: 7000000 INFO @ Mon, 03 Jun 2019 04:36:32: 7000000 INFO @ Mon, 03 Jun 2019 04:36:32: 7000000 INFO @ Mon, 03 Jun 2019 04:36:35: 8000000 INFO @ Mon, 03 Jun 2019 04:36:40: 8000000 INFO @ Mon, 03 Jun 2019 04:36:40: 8000000 INFO @ Mon, 03 Jun 2019 04:36:42: 9000000 INFO @ Mon, 03 Jun 2019 04:36:47: 9000000 INFO @ Mon, 03 Jun 2019 04:36:48: 9000000 INFO @ Mon, 03 Jun 2019 04:36:50: 10000000 INFO @ Mon, 03 Jun 2019 04:36:55: 10000000 INFO @ Mon, 03 Jun 2019 04:36:55: 10000000 INFO @ Mon, 03 Jun 2019 04:36:57: 11000000 INFO @ Mon, 03 Jun 2019 04:37:02: 11000000 INFO @ Mon, 03 Jun 2019 04:37:03: 11000000 INFO @ Mon, 03 Jun 2019 04:37:04: 12000000 INFO @ Mon, 03 Jun 2019 04:37:10: 12000000 INFO @ Mon, 03 Jun 2019 04:37:10: 12000000 INFO @ Mon, 03 Jun 2019 04:37:11: 13000000 INFO @ Mon, 03 Jun 2019 04:37:18: 13000000 INFO @ Mon, 03 Jun 2019 04:37:18: 13000000 INFO @ Mon, 03 Jun 2019 04:37:18: 14000000 INFO @ Mon, 03 Jun 2019 04:37:25: 14000000 INFO @ Mon, 03 Jun 2019 04:37:25: 14000000 INFO @ Mon, 03 Jun 2019 04:37:26: 15000000 INFO @ Mon, 03 Jun 2019 04:37:32: 15000000 INFO @ Mon, 03 Jun 2019 04:37:33: 15000000 INFO @ Mon, 03 Jun 2019 04:37:34: 16000000 INFO @ Mon, 03 Jun 2019 04:37:39: 16000000 INFO @ Mon, 03 Jun 2019 04:37:41: 16000000 INFO @ Mon, 03 Jun 2019 04:37:42: 17000000 INFO @ Mon, 03 Jun 2019 04:37:47: 17000000 INFO @ Mon, 03 Jun 2019 04:37:49: 17000000 INFO @ Mon, 03 Jun 2019 04:37:50: 18000000 INFO @ Mon, 03 Jun 2019 04:37:54: 18000000 INFO @ Mon, 03 Jun 2019 04:37:57: 18000000 INFO @ Mon, 03 Jun 2019 04:37:58: 19000000 INFO @ Mon, 03 Jun 2019 04:38:01: 19000000 INFO @ Mon, 03 Jun 2019 04:38:05: 19000000 INFO @ Mon, 03 Jun 2019 04:38:06: 20000000 INFO @ Mon, 03 Jun 2019 04:38:08: 20000000 INFO @ Mon, 03 Jun 2019 04:38:13: 20000000 INFO @ Mon, 03 Jun 2019 04:38:13: 21000000 INFO @ Mon, 03 Jun 2019 04:38:15: 21000000 INFO @ Mon, 03 Jun 2019 04:38:20: 21000000 INFO @ Mon, 03 Jun 2019 04:38:21: 22000000 INFO @ Mon, 03 Jun 2019 04:38:23: 22000000 INFO @ Mon, 03 Jun 2019 04:38:28: 22000000 INFO @ Mon, 03 Jun 2019 04:38:28: 23000000 INFO @ Mon, 03 Jun 2019 04:38:30: 23000000 INFO @ Mon, 03 Jun 2019 04:38:35: 23000000 INFO @ Mon, 03 Jun 2019 04:38:35: 24000000 INFO @ Mon, 03 Jun 2019 04:38:37: 24000000 INFO @ Mon, 03 Jun 2019 04:38:43: 25000000 INFO @ Mon, 03 Jun 2019 04:38:43: 24000000 INFO @ Mon, 03 Jun 2019 04:38:45: 25000000 INFO @ Mon, 03 Jun 2019 04:38:51: 26000000 INFO @ Mon, 03 Jun 2019 04:38:51: 25000000 INFO @ Mon, 03 Jun 2019 04:38:52: 26000000 INFO @ Mon, 03 Jun 2019 04:38:59: 27000000 INFO @ Mon, 03 Jun 2019 04:38:59: 26000000 INFO @ Mon, 03 Jun 2019 04:38:59: 27000000 INFO @ Mon, 03 Jun 2019 04:39:06: 27000000 INFO @ Mon, 03 Jun 2019 04:39:06: 28000000 INFO @ Mon, 03 Jun 2019 04:39:06: 28000000 INFO @ Mon, 03 Jun 2019 04:39:14: 29000000 INFO @ Mon, 03 Jun 2019 04:39:14: 28000000 INFO @ Mon, 03 Jun 2019 04:39:14: 29000000 INFO @ Mon, 03 Jun 2019 04:39:21: 30000000 INFO @ Mon, 03 Jun 2019 04:39:22: 29000000 INFO @ Mon, 03 Jun 2019 04:39:22: 30000000 INFO @ Mon, 03 Jun 2019 04:39:26: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:39:26: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:39:26: #1 total tags in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:26: #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 04:39:27: #1 tags after filtering in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:39:27: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:28: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:39:28: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:39:28: #1 total tags in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:28: #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 04:39:28: #1 tags after filtering in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:39:28: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:29: 30000000 INFO @ Mon, 03 Jun 2019 04:39:30: #2 number of paired peaks: 268 WARNING @ Mon, 03 Jun 2019 04:39:30: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 03 Jun 2019 04:39:30: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:30: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:30: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:30: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:30: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 04:39:30: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 04:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10_model.r INFO @ Mon, 03 Jun 2019 04:39:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:39:31: #2 number of paired peaks: 268 WARNING @ Mon, 03 Jun 2019 04:39:31: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 03 Jun 2019 04:39:31: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:31: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:31: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:31: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:31: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 04:39:31: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 04:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05_model.r INFO @ Mon, 03 Jun 2019 04:39:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:39:35: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 04:39:35: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 04:39:35: #1 total tags in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:39:35: #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 04:39:35: #1 tags after filtering in treatment: 30742734 INFO @ Mon, 03 Jun 2019 04:39:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:39:35: #1 finished! INFO @ Mon, 03 Jun 2019 04:39:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:39:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:39:38: #2 number of paired peaks: 268 WARNING @ Mon, 03 Jun 2019 04:39:38: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Mon, 03 Jun 2019 04:39:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:39:38: start X-correlation... INFO @ Mon, 03 Jun 2019 04:39:38: end of X-cor INFO @ Mon, 03 Jun 2019 04:39:38: #2 finished! INFO @ Mon, 03 Jun 2019 04:39:38: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 04:39:38: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 04:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20_model.r INFO @ Mon, 03 Jun 2019 04:39:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:39:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:40:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:40:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:40:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.10_summits.bed INFO @ Mon, 03 Jun 2019 04:41:21: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8660 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:41:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:41:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:41:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.05_summits.bed INFO @ Mon, 03 Jun 2019 04:41:22: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (12219 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1550620/SRX1550620.20_summits.bed INFO @ Mon, 03 Jun 2019 04:41:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5189 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。