Job ID = 1292423 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,127,036 reads read : 12,254,072 reads written : 6,127,036 reads 0-length : 6,127,036 spots read : 5,986,440 reads read : 11,972,880 reads written : 5,986,440 reads 0-length : 5,986,440 2019-06-02T09:30:27 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' 2019-06-02T09:30:27 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/sra64/SRR/007120/SRR7291523' 2019-06-02T09:30:27 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291523' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:30:27 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 6,132,269 reads read : 12,264,538 reads written : 6,132,269 reads 0-length : 6,132,269 spots read : 5,930,194 reads read : 11,860,388 reads written : 5,930,194 reads 0-length : 5,930,194 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: 00:09:25 24175939 reads; of these: 24175939 (100.00%) were unpaired; of these: 333021 (1.38%) aligned 0 times 20138698 (83.30%) aligned exactly 1 time 3704220 (15.32%) aligned >1 times 98.62% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3726830 / 23842918 = 0.1563 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 @ Sun, 02 Jun 2019 19:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.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 @ Sun, 02 Jun 2019 19:00:02: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:02: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.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 @ Sun, 02 Jun 2019 19:00:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.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 @ Sun, 02 Jun 2019 19:00:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:13: 1000000 INFO @ Sun, 02 Jun 2019 19:00:14: 1000000 INFO @ Sun, 02 Jun 2019 19:00:14: 1000000 INFO @ Sun, 02 Jun 2019 19:00:22: 2000000 INFO @ Sun, 02 Jun 2019 19:00:24: 2000000 INFO @ Sun, 02 Jun 2019 19:00:24: 2000000 INFO @ Sun, 02 Jun 2019 19:00:30: 3000000 INFO @ Sun, 02 Jun 2019 19:00:34: 3000000 INFO @ Sun, 02 Jun 2019 19:00:34: 3000000 INFO @ Sun, 02 Jun 2019 19:00:40: 4000000 INFO @ Sun, 02 Jun 2019 19:00:45: 4000000 INFO @ Sun, 02 Jun 2019 19:00:45: 4000000 INFO @ Sun, 02 Jun 2019 19:00:49: 5000000 INFO @ Sun, 02 Jun 2019 19:00:55: 5000000 INFO @ Sun, 02 Jun 2019 19:00:55: 5000000 INFO @ Sun, 02 Jun 2019 19:00:58: 6000000 INFO @ Sun, 02 Jun 2019 19:01:05: 6000000 INFO @ Sun, 02 Jun 2019 19:01:05: 6000000 INFO @ Sun, 02 Jun 2019 19:01:07: 7000000 INFO @ Sun, 02 Jun 2019 19:01:15: 7000000 INFO @ Sun, 02 Jun 2019 19:01:15: 7000000 INFO @ Sun, 02 Jun 2019 19:01:15: 8000000 INFO @ Sun, 02 Jun 2019 19:01:24: 9000000 INFO @ Sun, 02 Jun 2019 19:01:25: 8000000 INFO @ Sun, 02 Jun 2019 19:01:25: 8000000 INFO @ Sun, 02 Jun 2019 19:01:33: 10000000 INFO @ Sun, 02 Jun 2019 19:01:35: 9000000 INFO @ Sun, 02 Jun 2019 19:01:35: 9000000 INFO @ Sun, 02 Jun 2019 19:01:42: 11000000 INFO @ Sun, 02 Jun 2019 19:01:45: 10000000 INFO @ Sun, 02 Jun 2019 19:01:45: 10000000 INFO @ Sun, 02 Jun 2019 19:01:51: 12000000 INFO @ Sun, 02 Jun 2019 19:01:54: 11000000 INFO @ Sun, 02 Jun 2019 19:01:55: 11000000 INFO @ Sun, 02 Jun 2019 19:02:00: 13000000 INFO @ Sun, 02 Jun 2019 19:02:04: 12000000 INFO @ Sun, 02 Jun 2019 19:02:05: 12000000 INFO @ Sun, 02 Jun 2019 19:02:09: 14000000 INFO @ Sun, 02 Jun 2019 19:02:14: 13000000 INFO @ Sun, 02 Jun 2019 19:02:15: 13000000 INFO @ Sun, 02 Jun 2019 19:02:18: 15000000 INFO @ Sun, 02 Jun 2019 19:02:25: 14000000 INFO @ Sun, 02 Jun 2019 19:02:25: 14000000 INFO @ Sun, 02 Jun 2019 19:02:27: 16000000 INFO @ Sun, 02 Jun 2019 19:02:35: 15000000 INFO @ Sun, 02 Jun 2019 19:02:36: 15000000 INFO @ Sun, 02 Jun 2019 19:02:36: 17000000 INFO @ Sun, 02 Jun 2019 19:02:44: 18000000 INFO @ Sun, 02 Jun 2019 19:02:45: 16000000 INFO @ Sun, 02 Jun 2019 19:02:46: 16000000 INFO @ Sun, 02 Jun 2019 19:02:53: 19000000 INFO @ Sun, 02 Jun 2019 19:02:54: 17000000 INFO @ Sun, 02 Jun 2019 19:02:55: 17000000 INFO @ Sun, 02 Jun 2019 19:03:02: 20000000 INFO @ Sun, 02 Jun 2019 19:03:03: #1 tag size is determined as 74 bps INFO @ Sun, 02 Jun 2019 19:03:03: #1 tag size = 74 INFO @ Sun, 02 Jun 2019 19:03:03: #1 total tags in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:03: #1 tags after filtering in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:03: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:04: 18000000 INFO @ Sun, 02 Jun 2019 19:03:05: 18000000 INFO @ Sun, 02 Jun 2019 19:03:05: #2 number of paired peaks: 182 WARNING @ Sun, 02 Jun 2019 19:03:05: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:05: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:05: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:05: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:05: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:05: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:03:05: #2 alternative fragment length(s) may be 2,51,530,556,578 bps INFO @ Sun, 02 Jun 2019 19:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10_model.r WARNING @ Sun, 02 Jun 2019 19:03:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:05: #2 You may need to consider one of the other alternative d(s): 2,51,530,556,578 WARNING @ Sun, 02 Jun 2019 19:03:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:14: 19000000 INFO @ Sun, 02 Jun 2019 19:03:15: 19000000 INFO @ Sun, 02 Jun 2019 19:03:24: 20000000 INFO @ Sun, 02 Jun 2019 19:03:25: 20000000 INFO @ Sun, 02 Jun 2019 19:03:25: #1 tag size is determined as 74 bps INFO @ Sun, 02 Jun 2019 19:03:25: #1 tag size = 74 INFO @ Sun, 02 Jun 2019 19:03:25: #1 total tags in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:26: #1 tags after filtering in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:26: #1 tag size is determined as 74 bps INFO @ Sun, 02 Jun 2019 19:03:26: #1 tag size = 74 INFO @ Sun, 02 Jun 2019 19:03:26: #1 total tags in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:03:26: #1 tags after filtering in treatment: 20116088 INFO @ Sun, 02 Jun 2019 19:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:26: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:27: #2 number of paired peaks: 182 WARNING @ Sun, 02 Jun 2019 19:03:27: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:28: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:03:28: #2 alternative fragment length(s) may be 2,51,530,556,578 bps INFO @ Sun, 02 Jun 2019 19:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20_model.r WARNING @ Sun, 02 Jun 2019 19:03:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:28: #2 You may need to consider one of the other alternative d(s): 2,51,530,556,578 WARNING @ Sun, 02 Jun 2019 19:03:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:28: #2 number of paired peaks: 182 WARNING @ Sun, 02 Jun 2019 19:03:28: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:28: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:28: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 19:03:28: #2 alternative fragment length(s) may be 2,51,530,556,578 bps INFO @ Sun, 02 Jun 2019 19:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05_model.r WARNING @ Sun, 02 Jun 2019 19:03:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:28: #2 You may need to consider one of the other alternative d(s): 2,51,530,556,578 WARNING @ Sun, 02 Jun 2019 19:03:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.10_summits.bed INFO @ Sun, 02 Jun 2019 19:04:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.20_summits.bed INFO @ Sun, 02 Jun 2019 19:04:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (170 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194209/SRX4194209.05_summits.bed INFO @ Sun, 02 Jun 2019 19:04:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (713 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。