Job ID = 1292413 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,427,827 reads read : 12,855,654 reads written : 6,427,827 reads 0-length : 6,427,827 spots read : 6,256,271 reads read : 12,512,542 reads written : 6,256,271 reads 0-length : 6,256,271 2019-06-02T09:26:12 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' 2019-06-02T09:26:12 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/SRR7291481' 2019-06-02T09:26:12 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291481' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:26:12 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 6,450,099 reads read : 12,900,198 reads written : 6,450,099 reads 0-length : 6,450,099 spots read : 6,218,328 reads read : 12,436,656 reads written : 6,218,328 reads 0-length : 6,218,328 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: 00:10:05 25352525 reads; of these: 25352525 (100.00%) were unpaired; of these: 591578 (2.33%) aligned 0 times 20124010 (79.38%) aligned exactly 1 time 4636937 (18.29%) aligned >1 times 97.67% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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] 11262853 / 24760947 = 0.4549 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 18:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.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 18:55:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.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 18:55:51: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:51: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.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 18:55:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:01: 1000000 INFO @ Sun, 02 Jun 2019 18:56:03: 1000000 INFO @ Sun, 02 Jun 2019 18:56:03: 1000000 INFO @ Sun, 02 Jun 2019 18:56:10: 2000000 INFO @ Sun, 02 Jun 2019 18:56:13: 2000000 INFO @ Sun, 02 Jun 2019 18:56:14: 2000000 INFO @ Sun, 02 Jun 2019 18:56:19: 3000000 INFO @ Sun, 02 Jun 2019 18:56:24: 3000000 INFO @ Sun, 02 Jun 2019 18:56:24: 3000000 INFO @ Sun, 02 Jun 2019 18:56:28: 4000000 INFO @ Sun, 02 Jun 2019 18:56:34: 4000000 INFO @ Sun, 02 Jun 2019 18:56:34: 4000000 INFO @ Sun, 02 Jun 2019 18:56:36: 5000000 INFO @ Sun, 02 Jun 2019 18:56:44: 5000000 INFO @ Sun, 02 Jun 2019 18:56:44: 5000000 INFO @ Sun, 02 Jun 2019 18:56:45: 6000000 INFO @ Sun, 02 Jun 2019 18:56:53: 7000000 INFO @ Sun, 02 Jun 2019 18:56:53: 6000000 INFO @ Sun, 02 Jun 2019 18:56:54: 6000000 INFO @ Sun, 02 Jun 2019 18:57:01: 8000000 INFO @ Sun, 02 Jun 2019 18:57:03: 7000000 INFO @ Sun, 02 Jun 2019 18:57:04: 7000000 INFO @ Sun, 02 Jun 2019 18:57:10: 9000000 INFO @ Sun, 02 Jun 2019 18:57:12: 8000000 INFO @ Sun, 02 Jun 2019 18:57:14: 8000000 INFO @ Sun, 02 Jun 2019 18:57:18: 10000000 INFO @ Sun, 02 Jun 2019 18:57:20: 9000000 INFO @ Sun, 02 Jun 2019 18:57:24: 9000000 INFO @ Sun, 02 Jun 2019 18:57:26: 11000000 INFO @ Sun, 02 Jun 2019 18:57:28: 10000000 INFO @ Sun, 02 Jun 2019 18:57:33: 10000000 INFO @ Sun, 02 Jun 2019 18:57:35: 12000000 INFO @ Sun, 02 Jun 2019 18:57:35: 11000000 INFO @ Sun, 02 Jun 2019 18:57:43: 13000000 INFO @ Sun, 02 Jun 2019 18:57:43: 12000000 INFO @ Sun, 02 Jun 2019 18:57:43: 11000000 INFO @ Sun, 02 Jun 2019 18:57:47: #1 tag size is determined as 57 bps INFO @ Sun, 02 Jun 2019 18:57:47: #1 tag size = 57 INFO @ Sun, 02 Jun 2019 18:57:47: #1 total tags in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:57:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:47: #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 18:57:47: #1 tags after filtering in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:47: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:49: #2 number of paired peaks: 482 WARNING @ Sun, 02 Jun 2019 18:57:49: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:49: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:49: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:49: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:49: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:49: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 18:57:49: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 18:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05_model.r WARNING @ Sun, 02 Jun 2019 18:57:49: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:49: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 18:57:49: #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 18:57:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:51: 13000000 INFO @ Sun, 02 Jun 2019 18:57:53: 12000000 INFO @ Sun, 02 Jun 2019 18:57:55: #1 tag size is determined as 57 bps INFO @ Sun, 02 Jun 2019 18:57:55: #1 tag size = 57 INFO @ Sun, 02 Jun 2019 18:57:55: #1 total tags in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:57:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:55: #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 18:57:55: #1 tags after filtering in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:55: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:56: #2 number of paired peaks: 482 WARNING @ Sun, 02 Jun 2019 18:57:56: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:56: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:56: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:56: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:56: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:56: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 18:57:56: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 18:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20_model.r WARNING @ Sun, 02 Jun 2019 18:57:56: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:56: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 18:57:56: #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 18:57:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:03: 13000000 INFO @ Sun, 02 Jun 2019 18:58:08: #1 tag size is determined as 57 bps INFO @ Sun, 02 Jun 2019 18:58:08: #1 tag size = 57 INFO @ Sun, 02 Jun 2019 18:58:08: #1 total tags in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:58:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:08: #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 18:58:08: #1 tags after filtering in treatment: 13498094 INFO @ Sun, 02 Jun 2019 18:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:08: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:09: #2 number of paired peaks: 482 WARNING @ Sun, 02 Jun 2019 18:58:09: Fewer paired peaks (482) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 482 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:09: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:09: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:09: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:09: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:09: #2 predicted fragment length is 68 bps INFO @ Sun, 02 Jun 2019 18:58:09: #2 alternative fragment length(s) may be 4,68 bps INFO @ Sun, 02 Jun 2019 18:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10_model.r WARNING @ Sun, 02 Jun 2019 18:58:09: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:09: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Sun, 02 Jun 2019 18:58:09: #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 18:58:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.05_summits.bed INFO @ Sun, 02 Jun 2019 18:58:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1527 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:58:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.20_summits.bed INFO @ Sun, 02 Jun 2019 18:58:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194198/SRX4194198.10_summits.bed INFO @ Sun, 02 Jun 2019 18:59:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (841 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。