Job ID = 1292412 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,903,405 reads read : 11,806,810 reads written : 5,903,405 reads 0-length : 5,903,405 2019-06-02T09:21:06 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' 2019-06-02T09:21:06 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/SRR7291476' 2019-06-02T09:21:06 fasterq-dump.2.9.6 err: invalid accession 'SRR7291476' 2019-06-02T09:21:11 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' 2019-06-02T09:21:11 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/SRR7291476' 2019-06-02T09:21:11 fasterq-dump.2.9.6 err: invalid accession 'SRR7291476' spots read : 5,778,026 reads read : 11,556,052 reads written : 5,778,026 reads 0-length : 5,778,026 2019-06-02T09:26:00 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' 2019-06-02T09:26:00 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/SRR7291477' 2019-06-02T09:26:00 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291477' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:26:00 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 5,900,969 reads read : 11,801,938 reads written : 5,900,969 reads 0-length : 5,900,969 2019-06-02T09:33:40 fasterq-dump.2.9.6 fatal: SIGNAL - Segmentation fault spots read : 5,720,230 reads read : 11,440,460 reads written : 5,720,230 reads 0-length : 5,720,230 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: 00:09:29 23302630 reads; of these: 23302630 (100.00%) were unpaired; of these: 497749 (2.14%) aligned 0 times 18368027 (78.82%) aligned exactly 1 time 4436854 (19.04%) aligned >1 times 97.86% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 8094544 / 22804881 = 0.3549 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 18:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.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 18:55:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.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 18:55:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.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 18:55:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:14: 1000000 INFO @ Sun, 02 Jun 2019 18:55:15: 1000000 INFO @ Sun, 02 Jun 2019 18:55:16: 1000000 INFO @ Sun, 02 Jun 2019 18:55:21: 2000000 INFO @ Sun, 02 Jun 2019 18:55:24: 2000000 INFO @ Sun, 02 Jun 2019 18:55:26: 2000000 INFO @ Sun, 02 Jun 2019 18:55:29: 3000000 INFO @ Sun, 02 Jun 2019 18:55:32: 3000000 INFO @ Sun, 02 Jun 2019 18:55:36: 3000000 INFO @ Sun, 02 Jun 2019 18:55:36: 4000000 INFO @ Sun, 02 Jun 2019 18:55:41: 4000000 INFO @ Sun, 02 Jun 2019 18:55:44: 5000000 INFO @ Sun, 02 Jun 2019 18:55:46: 4000000 INFO @ Sun, 02 Jun 2019 18:55:49: 5000000 INFO @ Sun, 02 Jun 2019 18:55:52: 6000000 INFO @ Sun, 02 Jun 2019 18:55:56: 5000000 INFO @ Sun, 02 Jun 2019 18:55:58: 6000000 INFO @ Sun, 02 Jun 2019 18:56:00: 7000000 INFO @ Sun, 02 Jun 2019 18:56:07: 6000000 INFO @ Sun, 02 Jun 2019 18:56:08: 8000000 INFO @ Sun, 02 Jun 2019 18:56:08: 7000000 INFO @ Sun, 02 Jun 2019 18:56:15: 9000000 INFO @ Sun, 02 Jun 2019 18:56:16: 8000000 INFO @ Sun, 02 Jun 2019 18:56:18: 7000000 INFO @ Sun, 02 Jun 2019 18:56:23: 10000000 INFO @ Sun, 02 Jun 2019 18:56:25: 9000000 INFO @ Sun, 02 Jun 2019 18:56:28: 8000000 INFO @ Sun, 02 Jun 2019 18:56:30: 11000000 INFO @ Sun, 02 Jun 2019 18:56:34: 10000000 INFO @ Sun, 02 Jun 2019 18:56:38: 12000000 INFO @ Sun, 02 Jun 2019 18:56:38: 9000000 INFO @ Sun, 02 Jun 2019 18:56:43: 11000000 INFO @ Sun, 02 Jun 2019 18:56:46: 13000000 INFO @ Sun, 02 Jun 2019 18:56:48: 10000000 INFO @ Sun, 02 Jun 2019 18:56:51: 12000000 INFO @ Sun, 02 Jun 2019 18:56:53: 14000000 INFO @ Sun, 02 Jun 2019 18:56:58: 11000000 INFO @ Sun, 02 Jun 2019 18:56:59: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:56:59: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:56:59: #1 total tags in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:56:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:59: #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 18:56:59: #1 tags after filtering in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:00: 13000000 INFO @ Sun, 02 Jun 2019 18:57:00: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 18:57:00: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:00: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:00: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:00: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:00: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:00: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:57:00: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 18:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20_model.r WARNING @ Sun, 02 Jun 2019 18:57:00: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:00: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 18:57:00: #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 18:57:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:09: 14000000 INFO @ Sun, 02 Jun 2019 18:57:09: 12000000 INFO @ Sun, 02 Jun 2019 18:57:15: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:57:15: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:57:15: #1 total tags in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:57:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:15: #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 18:57:15: #1 tags after filtering in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:15: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:16: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 18:57:16: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:17: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:17: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:17: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:17: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:57:17: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 18:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05_model.r WARNING @ Sun, 02 Jun 2019 18:57:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:17: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 18:57:17: #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 18:57:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:19: 13000000 INFO @ Sun, 02 Jun 2019 18:57:28: 14000000 INFO @ Sun, 02 Jun 2019 18:57:35: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:57:35: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:57:35: #1 total tags in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:57:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:35: #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 18:57:35: #1 tags after filtering in treatment: 14710337 INFO @ Sun, 02 Jun 2019 18:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:35: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:37: #2 number of paired peaks: 415 WARNING @ Sun, 02 Jun 2019 18:57:37: Fewer paired peaks (415) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 415 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:37: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:37: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:37: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:37: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:37: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:57:37: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 18:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10_model.r WARNING @ Sun, 02 Jun 2019 18:57:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:37: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 18:57:37: #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 18:57:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.20_summits.bed INFO @ Sun, 02 Jun 2019 18:57:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.05_summits.bed INFO @ Sun, 02 Jun 2019 18:58:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (748 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:58:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194197/SRX4194197.10_summits.bed INFO @ Sun, 02 Jun 2019 18:58:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。