Job ID = 1292416 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,007,671 reads read : 14,015,342 reads written : 7,007,671 reads 0-length : 7,007,671 spots read : 6,861,708 reads read : 13,723,416 reads written : 6,861,708 reads 0-length : 6,861,708 spots read : 7,003,828 reads read : 14,007,656 reads written : 7,003,828 reads 0-length : 7,003,828 2019-06-02T09:30:55 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' 2019-06-02T09:30:55 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/SRR7291495' 2019-06-02T09:30:55 fasterq-dump.2.9.6 err: invalid accession 'SRR7291495' spots read : 6,773,131 reads read : 13,546,262 reads written : 6,773,131 reads 0-length : 6,773,131 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: 00:10:09 27646338 reads; of these: 27646338 (100.00%) were unpaired; of these: 463826 (1.68%) aligned 0 times 23668689 (85.61%) aligned exactly 1 time 3513823 (12.71%) aligned >1 times 98.32% overall alignment rate Time searching: 00:10:09 Overall time: 00:10:09 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] 10157961 / 27182512 = 0.3737 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 18:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.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 18:55:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.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 18:55:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.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 18:55:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:12: 1000000 INFO @ Sun, 02 Jun 2019 18:55:15: 1000000 INFO @ Sun, 02 Jun 2019 18:55:15: 1000000 INFO @ Sun, 02 Jun 2019 18:55:21: 2000000 INFO @ Sun, 02 Jun 2019 18:55:26: 2000000 INFO @ Sun, 02 Jun 2019 18:55:26: 2000000 INFO @ Sun, 02 Jun 2019 18:55:29: 3000000 INFO @ Sun, 02 Jun 2019 18:55:36: 3000000 INFO @ Sun, 02 Jun 2019 18:55:37: 3000000 INFO @ Sun, 02 Jun 2019 18:55:37: 4000000 INFO @ Sun, 02 Jun 2019 18:55:45: 5000000 INFO @ Sun, 02 Jun 2019 18:55:47: 4000000 INFO @ Sun, 02 Jun 2019 18:55:48: 4000000 INFO @ Sun, 02 Jun 2019 18:55:55: 6000000 INFO @ Sun, 02 Jun 2019 18:55:59: 5000000 INFO @ Sun, 02 Jun 2019 18:56:00: 5000000 INFO @ Sun, 02 Jun 2019 18:56:03: 7000000 INFO @ Sun, 02 Jun 2019 18:56:09: 6000000 INFO @ Sun, 02 Jun 2019 18:56:11: 8000000 INFO @ Sun, 02 Jun 2019 18:56:11: 6000000 INFO @ Sun, 02 Jun 2019 18:56:19: 9000000 INFO @ Sun, 02 Jun 2019 18:56:20: 7000000 INFO @ Sun, 02 Jun 2019 18:56:23: 7000000 INFO @ Sun, 02 Jun 2019 18:56:27: 10000000 INFO @ Sun, 02 Jun 2019 18:56:30: 8000000 INFO @ Sun, 02 Jun 2019 18:56:34: 8000000 INFO @ Sun, 02 Jun 2019 18:56:35: 11000000 INFO @ Sun, 02 Jun 2019 18:56:41: 9000000 INFO @ Sun, 02 Jun 2019 18:56:44: 12000000 INFO @ Sun, 02 Jun 2019 18:56:45: 9000000 INFO @ Sun, 02 Jun 2019 18:56:52: 10000000 INFO @ Sun, 02 Jun 2019 18:56:52: 13000000 INFO @ Sun, 02 Jun 2019 18:56:57: 10000000 INFO @ Sun, 02 Jun 2019 18:57:00: 14000000 INFO @ Sun, 02 Jun 2019 18:57:03: 11000000 INFO @ Sun, 02 Jun 2019 18:57:08: 15000000 INFO @ Sun, 02 Jun 2019 18:57:08: 11000000 INFO @ Sun, 02 Jun 2019 18:57:13: 12000000 INFO @ Sun, 02 Jun 2019 18:57:16: 16000000 INFO @ Sun, 02 Jun 2019 18:57:20: 12000000 INFO @ Sun, 02 Jun 2019 18:57:23: 13000000 INFO @ Sun, 02 Jun 2019 18:57:24: 17000000 INFO @ Sun, 02 Jun 2019 18:57:25: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:57:25: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:57:25: #1 total tags in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:57:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:57:25: #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 18:57:25: #1 tags after filtering in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:57:25: #1 finished! INFO @ Sun, 02 Jun 2019 18:57:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:57:26: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 18:57:26: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 18:57:26: start model_add_line... INFO @ Sun, 02 Jun 2019 18:57:27: start X-correlation... INFO @ Sun, 02 Jun 2019 18:57:27: end of X-cor INFO @ Sun, 02 Jun 2019 18:57:27: #2 finished! INFO @ Sun, 02 Jun 2019 18:57:27: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:57:27: #2 alternative fragment length(s) may be 2,61,562 bps INFO @ Sun, 02 Jun 2019 18:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05_model.r WARNING @ Sun, 02 Jun 2019 18:57:27: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:57:27: #2 You may need to consider one of the other alternative d(s): 2,61,562 WARNING @ Sun, 02 Jun 2019 18:57:27: #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 18:57:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:57:30: 13000000 INFO @ Sun, 02 Jun 2019 18:57:34: 14000000 INFO @ Sun, 02 Jun 2019 18:57:41: 14000000 INFO @ Sun, 02 Jun 2019 18:57:44: 15000000 INFO @ Sun, 02 Jun 2019 18:57:53: 15000000 INFO @ Sun, 02 Jun 2019 18:57:54: 16000000 INFO @ Sun, 02 Jun 2019 18:58:04: 16000000 INFO @ Sun, 02 Jun 2019 18:58:05: 17000000 INFO @ Sun, 02 Jun 2019 18:58:05: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:58:05: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:58:05: #1 total tags in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:58:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:05: #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 18:58:06: #1 tags after filtering in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:58:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:06: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:07: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 18:58:07: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:07: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:07: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:07: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:07: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:07: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:58:07: #2 alternative fragment length(s) may be 2,61,562 bps INFO @ Sun, 02 Jun 2019 18:58:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20_model.r WARNING @ Sun, 02 Jun 2019 18:58:07: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:07: #2 You may need to consider one of the other alternative d(s): 2,61,562 WARNING @ Sun, 02 Jun 2019 18:58:07: #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 18:58:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:14: 17000000 INFO @ Sun, 02 Jun 2019 18:58:15: #1 tag size is determined as 65 bps INFO @ Sun, 02 Jun 2019 18:58:15: #1 tag size = 65 INFO @ Sun, 02 Jun 2019 18:58:15: #1 total tags in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:58:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:15: #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 18:58:15: #1 tags after filtering in treatment: 17024551 INFO @ Sun, 02 Jun 2019 18:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:15: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:16: #2 number of paired peaks: 169 WARNING @ Sun, 02 Jun 2019 18:58:16: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:16: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:16: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:16: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:16: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:16: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 18:58:16: #2 alternative fragment length(s) may be 2,61,562 bps INFO @ Sun, 02 Jun 2019 18:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10_model.r WARNING @ Sun, 02 Jun 2019 18:58:16: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:16: #2 You may need to consider one of the other alternative d(s): 2,61,562 WARNING @ Sun, 02 Jun 2019 18:58:16: #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 18:58:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.05_summits.bed INFO @ Sun, 02 Jun 2019 18:58:29: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3336 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:58:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.20_summits.bed INFO @ Sun, 02 Jun 2019 18:59:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194201/SRX4194201.10_summits.bed INFO @ Sun, 02 Jun 2019 18:59:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (607 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。