Job ID = 1292421 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T09:21:04 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' 2019-06-02T09:21:04 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/SRR7291513' 2019-06-02T09:21:04 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291513' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:21:04 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 5,791,692 reads read : 11,583,384 reads written : 5,791,692 reads 0-length : 5,791,692 spots read : 5,653,337 reads read : 11,306,674 reads written : 5,653,337 reads 0-length : 5,653,337 spots read : 5,783,078 reads read : 11,566,156 reads written : 5,783,078 reads 0-length : 5,783,078 spots read : 5,595,770 reads read : 11,191,540 reads written : 5,595,770 reads 0-length : 5,595,770 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: 00:08:46 22823877 reads; of these: 22823877 (100.00%) were unpaired; of these: 359253 (1.57%) aligned 0 times 18905803 (82.83%) aligned exactly 1 time 3558821 (15.59%) aligned >1 times 98.43% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 3185489 / 22464624 = 0.1418 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 18:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.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 18:56:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.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 18:56:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.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 18:56:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:56:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:54: 1000000 INFO @ Sun, 02 Jun 2019 18:56:55: 1000000 INFO @ Sun, 02 Jun 2019 18:56:56: 1000000 INFO @ Sun, 02 Jun 2019 18:57:02: 2000000 INFO @ Sun, 02 Jun 2019 18:57:05: 2000000 INFO @ Sun, 02 Jun 2019 18:57:07: 2000000 INFO @ Sun, 02 Jun 2019 18:57:11: 3000000 INFO @ Sun, 02 Jun 2019 18:57:14: 3000000 INFO @ Sun, 02 Jun 2019 18:57:18: 3000000 INFO @ Sun, 02 Jun 2019 18:57:20: 4000000 INFO @ Sun, 02 Jun 2019 18:57:24: 4000000 INFO @ Sun, 02 Jun 2019 18:57:28: 5000000 INFO @ Sun, 02 Jun 2019 18:57:30: 4000000 INFO @ Sun, 02 Jun 2019 18:57:34: 5000000 INFO @ Sun, 02 Jun 2019 18:57:37: 6000000 INFO @ Sun, 02 Jun 2019 18:57:40: 5000000 INFO @ Sun, 02 Jun 2019 18:57:43: 6000000 INFO @ Sun, 02 Jun 2019 18:57:45: 7000000 INFO @ Sun, 02 Jun 2019 18:57:51: 6000000 INFO @ Sun, 02 Jun 2019 18:57:53: 7000000 INFO @ Sun, 02 Jun 2019 18:57:54: 8000000 INFO @ Sun, 02 Jun 2019 18:58:02: 8000000 INFO @ Sun, 02 Jun 2019 18:58:02: 7000000 INFO @ Sun, 02 Jun 2019 18:58:02: 9000000 INFO @ Sun, 02 Jun 2019 18:58:11: 10000000 INFO @ Sun, 02 Jun 2019 18:58:12: 9000000 INFO @ Sun, 02 Jun 2019 18:58:14: 8000000 INFO @ Sun, 02 Jun 2019 18:58:19: 11000000 INFO @ Sun, 02 Jun 2019 18:58:21: 10000000 INFO @ Sun, 02 Jun 2019 18:58:25: 9000000 INFO @ Sun, 02 Jun 2019 18:58:28: 12000000 INFO @ Sun, 02 Jun 2019 18:58:31: 11000000 INFO @ Sun, 02 Jun 2019 18:58:36: 10000000 INFO @ Sun, 02 Jun 2019 18:58:36: 13000000 INFO @ Sun, 02 Jun 2019 18:58:40: 12000000 INFO @ Sun, 02 Jun 2019 18:58:45: 14000000 INFO @ Sun, 02 Jun 2019 18:58:47: 11000000 INFO @ Sun, 02 Jun 2019 18:58:50: 13000000 INFO @ Sun, 02 Jun 2019 18:58:54: 15000000 INFO @ Sun, 02 Jun 2019 18:58:57: 12000000 INFO @ Sun, 02 Jun 2019 18:58:59: 14000000 INFO @ Sun, 02 Jun 2019 18:59:02: 16000000 INFO @ Sun, 02 Jun 2019 18:59:08: 13000000 INFO @ Sun, 02 Jun 2019 18:59:09: 15000000 INFO @ Sun, 02 Jun 2019 18:59:11: 17000000 INFO @ Sun, 02 Jun 2019 18:59:18: 16000000 INFO @ Sun, 02 Jun 2019 18:59:19: 18000000 INFO @ Sun, 02 Jun 2019 18:59:20: 14000000 INFO @ Sun, 02 Jun 2019 18:59:28: 19000000 INFO @ Sun, 02 Jun 2019 18:59:28: 17000000 INFO @ Sun, 02 Jun 2019 18:59:30: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 18:59:30: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 18:59:30: #1 total tags in treatment: 19279135 INFO @ Sun, 02 Jun 2019 18:59:30: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:30: #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 18:59:31: #1 tags after filtering in treatment: 19279135 INFO @ Sun, 02 Jun 2019 18:59:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:31: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:31: 15000000 INFO @ Sun, 02 Jun 2019 18:59:32: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 18:59:32: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:32: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:32: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:33: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:33: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:33: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:59:33: #2 alternative fragment length(s) may be 2,48,557 bps INFO @ Sun, 02 Jun 2019 18:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05_model.r WARNING @ Sun, 02 Jun 2019 18:59:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:33: #2 You may need to consider one of the other alternative d(s): 2,48,557 WARNING @ Sun, 02 Jun 2019 18:59:33: #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 18:59:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:38: 18000000 INFO @ Sun, 02 Jun 2019 18:59:42: 16000000 INFO @ Sun, 02 Jun 2019 18:59:47: 19000000 INFO @ Sun, 02 Jun 2019 18:59:50: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 18:59:50: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 18:59:50: #1 total tags in treatment: 19279135 INFO @ Sun, 02 Jun 2019 18:59:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:59:50: #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 18:59:50: #1 tags after filtering in treatment: 19279135 INFO @ Sun, 02 Jun 2019 18:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:59:50: #1 finished! INFO @ Sun, 02 Jun 2019 18:59:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:59:52: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 18:59:52: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 18:59:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:59:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:59:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:59:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:59:52: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 18:59:52: #2 alternative fragment length(s) may be 2,48,557 bps INFO @ Sun, 02 Jun 2019 18:59:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10_model.r WARNING @ Sun, 02 Jun 2019 18:59:52: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:59:52: #2 You may need to consider one of the other alternative d(s): 2,48,557 WARNING @ Sun, 02 Jun 2019 18:59:52: #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 18:59:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:59:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:59:53: 17000000 INFO @ Sun, 02 Jun 2019 19:00:03: 18000000 INFO @ Sun, 02 Jun 2019 19:00:14: 19000000 INFO @ Sun, 02 Jun 2019 19:00:17: #1 tag size is determined as 71 bps INFO @ Sun, 02 Jun 2019 19:00:17: #1 tag size = 71 INFO @ Sun, 02 Jun 2019 19:00:17: #1 total tags in treatment: 19279135 INFO @ Sun, 02 Jun 2019 19:00:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:17: #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 19:00:17: #1 tags after filtering in treatment: 19279135 INFO @ Sun, 02 Jun 2019 19:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:17: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:19: #2 number of paired peaks: 200 WARNING @ Sun, 02 Jun 2019 19:00:19: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:19: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:19: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:19: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:19: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:19: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 19:00:19: #2 alternative fragment length(s) may be 2,48,557 bps INFO @ Sun, 02 Jun 2019 19:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20_model.r WARNING @ Sun, 02 Jun 2019 19:00:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:00:19: #2 You may need to consider one of the other alternative d(s): 2,48,557 WARNING @ Sun, 02 Jun 2019 19:00:19: #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 19:00:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.05_summits.bed INFO @ Sun, 02 Jun 2019 19:00:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (686 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.10_summits.bed INFO @ Sun, 02 Jun 2019 19:00:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:01:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:01:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:01:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:01:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194207/SRX4194207.20_summits.bed INFO @ Sun, 02 Jun 2019 19:01:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (176 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。