Job ID = 1292409 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,767,727 reads read : 11,535,454 reads written : 5,767,727 reads 0-length : 5,767,727 spots read : 5,628,088 reads read : 11,256,176 reads written : 5,628,088 reads 0-length : 5,628,088 2019-06-02T09:25:30 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' 2019-06-02T09:25:30 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/SRR7291464' 2019-06-02T09:25:30 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291464' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:25:30 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 5,766,137 reads read : 11,532,274 reads written : 5,766,137 reads 0-length : 5,766,137 spots read : 5,566,012 reads read : 11,132,024 reads written : 5,566,012 reads 0-length : 5,566,012 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: 00:09:37 22727964 reads; of these: 22727964 (100.00%) were unpaired; of these: 528322 (2.32%) aligned 0 times 17960809 (79.03%) aligned exactly 1 time 4238833 (18.65%) aligned >1 times 97.68% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 5774390 / 22199642 = 0.2601 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 18:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.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 18:53:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.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 18:53:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.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 18:53:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:53:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:54:01: 1000000 INFO @ Sun, 02 Jun 2019 18:54:02: 1000000 INFO @ Sun, 02 Jun 2019 18:54:03: 1000000 INFO @ Sun, 02 Jun 2019 18:54:10: 2000000 INFO @ Sun, 02 Jun 2019 18:54:12: 2000000 INFO @ Sun, 02 Jun 2019 18:54:14: 2000000 INFO @ Sun, 02 Jun 2019 18:54:18: 3000000 INFO @ Sun, 02 Jun 2019 18:54:22: 3000000 INFO @ Sun, 02 Jun 2019 18:54:25: 3000000 INFO @ Sun, 02 Jun 2019 18:54:27: 4000000 INFO @ Sun, 02 Jun 2019 18:54:31: 4000000 INFO @ Sun, 02 Jun 2019 18:54:35: 5000000 INFO @ Sun, 02 Jun 2019 18:54:36: 4000000 INFO @ Sun, 02 Jun 2019 18:54:40: 5000000 INFO @ Sun, 02 Jun 2019 18:54:44: 6000000 INFO @ Sun, 02 Jun 2019 18:54:47: 5000000 INFO @ Sun, 02 Jun 2019 18:54:50: 6000000 INFO @ Sun, 02 Jun 2019 18:54:53: 7000000 INFO @ Sun, 02 Jun 2019 18:54:57: 6000000 INFO @ Sun, 02 Jun 2019 18:54:59: 7000000 INFO @ Sun, 02 Jun 2019 18:55:01: 8000000 INFO @ Sun, 02 Jun 2019 18:55:08: 7000000 INFO @ Sun, 02 Jun 2019 18:55:09: 8000000 INFO @ Sun, 02 Jun 2019 18:55:10: 9000000 INFO @ Sun, 02 Jun 2019 18:55:18: 8000000 INFO @ Sun, 02 Jun 2019 18:55:19: 9000000 INFO @ Sun, 02 Jun 2019 18:55:19: 10000000 INFO @ Sun, 02 Jun 2019 18:55:27: 11000000 INFO @ Sun, 02 Jun 2019 18:55:28: 10000000 INFO @ Sun, 02 Jun 2019 18:55:29: 9000000 INFO @ Sun, 02 Jun 2019 18:55:36: 12000000 INFO @ Sun, 02 Jun 2019 18:55:38: 11000000 INFO @ Sun, 02 Jun 2019 18:55:39: 10000000 INFO @ Sun, 02 Jun 2019 18:55:45: 13000000 INFO @ Sun, 02 Jun 2019 18:55:48: 12000000 INFO @ Sun, 02 Jun 2019 18:55:49: 11000000 INFO @ Sun, 02 Jun 2019 18:55:54: 14000000 INFO @ Sun, 02 Jun 2019 18:55:57: 13000000 INFO @ Sun, 02 Jun 2019 18:56:00: 12000000 INFO @ Sun, 02 Jun 2019 18:56:03: 15000000 INFO @ Sun, 02 Jun 2019 18:56:07: 14000000 INFO @ Sun, 02 Jun 2019 18:56:10: 13000000 INFO @ Sun, 02 Jun 2019 18:56:12: 16000000 INFO @ Sun, 02 Jun 2019 18:56:15: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 18:56:15: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 18:56:15: #1 total tags in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:15: #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 18:56:16: #1 tags after filtering in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:16: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:17: #2 number of paired peaks: 372 WARNING @ Sun, 02 Jun 2019 18:56:17: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 02 Jun 2019 18:56:17: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:17: 15000000 INFO @ Sun, 02 Jun 2019 18:56:17: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:17: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:17: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:17: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:56:17: #2 alternative fragment length(s) may be 2,50,566 bps INFO @ Sun, 02 Jun 2019 18:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20_model.r WARNING @ Sun, 02 Jun 2019 18:56:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:17: #2 You may need to consider one of the other alternative d(s): 2,50,566 WARNING @ Sun, 02 Jun 2019 18:56:17: #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 18:56:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:21: 14000000 INFO @ Sun, 02 Jun 2019 18:56:27: 16000000 INFO @ Sun, 02 Jun 2019 18:56:31: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 18:56:31: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 18:56:31: #1 total tags in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:31: #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 18:56:31: 15000000 INFO @ Sun, 02 Jun 2019 18:56:32: #1 tags after filtering in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:32: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:33: #2 number of paired peaks: 372 WARNING @ Sun, 02 Jun 2019 18:56:33: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 02 Jun 2019 18:56:33: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:33: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:33: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:33: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:33: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:56:33: #2 alternative fragment length(s) may be 2,50,566 bps INFO @ Sun, 02 Jun 2019 18:56:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10_model.r WARNING @ Sun, 02 Jun 2019 18:56:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:33: #2 You may need to consider one of the other alternative d(s): 2,50,566 WARNING @ Sun, 02 Jun 2019 18:56:33: #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 18:56:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:42: 16000000 INFO @ Sun, 02 Jun 2019 18:56:46: #1 tag size is determined as 67 bps INFO @ Sun, 02 Jun 2019 18:56:46: #1 tag size = 67 INFO @ Sun, 02 Jun 2019 18:56:46: #1 total tags in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:56:46: #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 18:56:46: #1 tags after filtering in treatment: 16425252 INFO @ Sun, 02 Jun 2019 18:56:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:56:46: #1 finished! INFO @ Sun, 02 Jun 2019 18:56:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:56:48: #2 number of paired peaks: 372 WARNING @ Sun, 02 Jun 2019 18:56:48: Fewer paired peaks (372) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 372 pairs to build model! INFO @ Sun, 02 Jun 2019 18:56:48: start model_add_line... INFO @ Sun, 02 Jun 2019 18:56:48: start X-correlation... INFO @ Sun, 02 Jun 2019 18:56:48: end of X-cor INFO @ Sun, 02 Jun 2019 18:56:48: #2 finished! INFO @ Sun, 02 Jun 2019 18:56:48: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:56:48: #2 alternative fragment length(s) may be 2,50,566 bps INFO @ Sun, 02 Jun 2019 18:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05_model.r WARNING @ Sun, 02 Jun 2019 18:56:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:56:48: #2 You may need to consider one of the other alternative d(s): 2,50,566 WARNING @ Sun, 02 Jun 2019 18:56:48: #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 18:56:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:56:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.20_summits.bed INFO @ Sun, 02 Jun 2019 18:57:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:57:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.10_summits.bed INFO @ Sun, 02 Jun 2019 18:57:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194193/SRX4194193.05_summits.bed INFO @ Sun, 02 Jun 2019 18:57:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (688 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。