Job ID = 1290666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,500,334 reads read : 2,500,334 reads written : 2,500,334 2019-06-01T12:55:32 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' 2019-06-01T12:55:32 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/SRR013611/SRR013611.3' 2019-06-01T12:55:43 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR013611' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-01T12:55:43 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) spots read : 5,439,836 reads read : 5,439,836 reads written : 5,439,836 spots read : 5,826,755 reads read : 5,826,755 reads written : 5,826,755 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:00 13766925 reads; of these: 13766925 (100.00%) were unpaired; of these: 2348253 (17.06%) aligned 0 times 9847411 (71.53%) aligned exactly 1 time 1571261 (11.41%) aligned >1 times 82.94% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1347734 / 11418672 = 0.1180 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 @ Sat, 01 Jun 2019 22:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 01 Jun 2019 22:03:16: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:03:16: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 01 Jun 2019 22:03:16: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:03:16: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:03:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sat, 01 Jun 2019 22:03:16: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:03:16: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:03:25: 1000000 INFO @ Sat, 01 Jun 2019 22:03:26: 1000000 INFO @ Sat, 01 Jun 2019 22:03:26: 1000000 INFO @ Sat, 01 Jun 2019 22:03:33: 2000000 INFO @ Sat, 01 Jun 2019 22:03:35: 2000000 INFO @ Sat, 01 Jun 2019 22:03:36: 2000000 INFO @ Sat, 01 Jun 2019 22:03:42: 3000000 INFO @ Sat, 01 Jun 2019 22:03:45: 3000000 INFO @ Sat, 01 Jun 2019 22:03:46: 3000000 INFO @ Sat, 01 Jun 2019 22:03:51: 4000000 INFO @ Sat, 01 Jun 2019 22:03:55: 4000000 INFO @ Sat, 01 Jun 2019 22:03:56: 4000000 INFO @ Sat, 01 Jun 2019 22:04:00: 5000000 INFO @ Sat, 01 Jun 2019 22:04:04: 5000000 INFO @ Sat, 01 Jun 2019 22:04:05: 5000000 INFO @ Sat, 01 Jun 2019 22:04:09: 6000000 INFO @ Sat, 01 Jun 2019 22:04:14: 6000000 INFO @ Sat, 01 Jun 2019 22:04:15: 6000000 INFO @ Sat, 01 Jun 2019 22:04:18: 7000000 INFO @ Sat, 01 Jun 2019 22:04:24: 7000000 INFO @ Sat, 01 Jun 2019 22:04:26: 7000000 INFO @ Sat, 01 Jun 2019 22:04:26: 8000000 INFO @ Sat, 01 Jun 2019 22:04:33: 8000000 INFO @ Sat, 01 Jun 2019 22:04:34: 9000000 INFO @ Sat, 01 Jun 2019 22:04:36: 8000000 INFO @ Sat, 01 Jun 2019 22:04:42: 9000000 INFO @ Sat, 01 Jun 2019 22:04:43: 10000000 INFO @ Sat, 01 Jun 2019 22:04:44: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:04:44: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:04:44: #1 total tags in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:44: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:04:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:04:44: #1 tags after filtering in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:04:44: #1 finished! INFO @ Sat, 01 Jun 2019 22:04:44: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:04:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:04:45: #2 number of paired peaks: 881 WARNING @ Sat, 01 Jun 2019 22:04:45: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 01 Jun 2019 22:04:45: start model_add_line... INFO @ Sat, 01 Jun 2019 22:04:45: start X-correlation... INFO @ Sat, 01 Jun 2019 22:04:45: end of X-cor INFO @ Sat, 01 Jun 2019 22:04:45: #2 finished! INFO @ Sat, 01 Jun 2019 22:04:45: #2 predicted fragment length is 122 bps INFO @ Sat, 01 Jun 2019 22:04:45: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 01 Jun 2019 22:04:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05_model.r INFO @ Sat, 01 Jun 2019 22:04:45: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:04:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:04:46: 9000000 INFO @ Sat, 01 Jun 2019 22:04:52: 10000000 INFO @ Sat, 01 Jun 2019 22:04:52: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:04:52: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:04:52: #1 total tags in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:52: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:04:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:04:53: #1 tags after filtering in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:04:53: #1 finished! INFO @ Sat, 01 Jun 2019 22:04:53: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:04:54: #2 number of paired peaks: 881 WARNING @ Sat, 01 Jun 2019 22:04:54: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 01 Jun 2019 22:04:54: start model_add_line... INFO @ Sat, 01 Jun 2019 22:04:54: start X-correlation... INFO @ Sat, 01 Jun 2019 22:04:54: end of X-cor INFO @ Sat, 01 Jun 2019 22:04:54: #2 finished! INFO @ Sat, 01 Jun 2019 22:04:54: #2 predicted fragment length is 122 bps INFO @ Sat, 01 Jun 2019 22:04:54: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 01 Jun 2019 22:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20_model.r INFO @ Sat, 01 Jun 2019 22:04:54: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:04:56: 10000000 INFO @ Sat, 01 Jun 2019 22:04:57: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:04:57: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:04:57: #1 total tags in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:57: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:04:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 22:04:57: #1 tags after filtering in treatment: 10070938 INFO @ Sat, 01 Jun 2019 22:04:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:04:57: #1 finished! INFO @ Sat, 01 Jun 2019 22:04:57: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:04:58: #2 number of paired peaks: 881 WARNING @ Sat, 01 Jun 2019 22:04:58: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Sat, 01 Jun 2019 22:04:58: start model_add_line... INFO @ Sat, 01 Jun 2019 22:04:58: start X-correlation... INFO @ Sat, 01 Jun 2019 22:04:58: end of X-cor INFO @ Sat, 01 Jun 2019 22:04:58: #2 finished! INFO @ Sat, 01 Jun 2019 22:04:58: #2 predicted fragment length is 122 bps INFO @ Sat, 01 Jun 2019 22:04:58: #2 alternative fragment length(s) may be 122 bps INFO @ Sat, 01 Jun 2019 22:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10_model.r INFO @ Sat, 01 Jun 2019 22:04:58: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:05:16: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:05:24: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:05:28: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:05:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:05:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.05_summits.bed INFO @ Sat, 01 Jun 2019 22:05:32: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (9129 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:05:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:05:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:05:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.20_summits.bed INFO @ Sat, 01 Jun 2019 22:05:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3983 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX002675/SRX002675.10_summits.bed INFO @ Sat, 01 Jun 2019 22:05:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6647 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。