Job ID = 1292422 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,141,047 reads read : 16,282,094 reads written : 8,141,047 reads 0-length : 8,141,047 spots read : 7,979,099 reads read : 15,958,198 reads written : 7,979,099 reads 0-length : 7,979,099 2019-06-02T09:30:59 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' 2019-06-02T09:30:59 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/SRR7291519' 2019-06-02T09:30:59 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_table_names( 'SRR7291519' ).VDBManagerOpenDBRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 8,129,009 reads read : 16,258,018 reads written : 8,129,009 reads 0-length : 8,129,009 spots read : 7,895,317 reads read : 15,790,634 reads written : 7,895,317 reads 0-length : 7,895,317 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: 00:12:43 32144472 reads; of these: 32144472 (100.00%) were unpaired; of these: 492230 (1.53%) aligned 0 times 26714829 (83.11%) aligned exactly 1 time 4937413 (15.36%) aligned >1 times 98.47% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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 16 files... [bam_rmdupse_core] 5731416 / 31652242 = 0.1811 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 19:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.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 19:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.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 19:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.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 19:05:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:05:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:05:12: 1000000 INFO @ Sun, 02 Jun 2019 19:05:14: 1000000 INFO @ Sun, 02 Jun 2019 19:05:15: 1000000 INFO @ Sun, 02 Jun 2019 19:05:19: 2000000 INFO @ Sun, 02 Jun 2019 19:05:24: 2000000 INFO @ Sun, 02 Jun 2019 19:05:25: 2000000 INFO @ Sun, 02 Jun 2019 19:05:26: 3000000 INFO @ Sun, 02 Jun 2019 19:05:33: 4000000 INFO @ Sun, 02 Jun 2019 19:05:34: 3000000 INFO @ Sun, 02 Jun 2019 19:05:35: 3000000 INFO @ Sun, 02 Jun 2019 19:05:40: 5000000 INFO @ Sun, 02 Jun 2019 19:05:43: 4000000 INFO @ Sun, 02 Jun 2019 19:05:45: 4000000 INFO @ Sun, 02 Jun 2019 19:05:48: 6000000 INFO @ Sun, 02 Jun 2019 19:05:52: 5000000 INFO @ Sun, 02 Jun 2019 19:05:55: 7000000 INFO @ Sun, 02 Jun 2019 19:05:55: 5000000 INFO @ Sun, 02 Jun 2019 19:06:02: 6000000 INFO @ Sun, 02 Jun 2019 19:06:02: 8000000 INFO @ Sun, 02 Jun 2019 19:06:05: 6000000 INFO @ Sun, 02 Jun 2019 19:06:09: 9000000 INFO @ Sun, 02 Jun 2019 19:06:11: 7000000 INFO @ Sun, 02 Jun 2019 19:06:15: 7000000 INFO @ Sun, 02 Jun 2019 19:06:16: 10000000 INFO @ Sun, 02 Jun 2019 19:06:21: 8000000 INFO @ Sun, 02 Jun 2019 19:06:24: 11000000 INFO @ Sun, 02 Jun 2019 19:06:25: 8000000 INFO @ Sun, 02 Jun 2019 19:06:30: 9000000 INFO @ Sun, 02 Jun 2019 19:06:31: 12000000 INFO @ Sun, 02 Jun 2019 19:06:35: 9000000 INFO @ Sun, 02 Jun 2019 19:06:39: 13000000 INFO @ Sun, 02 Jun 2019 19:06:40: 10000000 INFO @ Sun, 02 Jun 2019 19:06:45: 10000000 INFO @ Sun, 02 Jun 2019 19:06:47: 14000000 INFO @ Sun, 02 Jun 2019 19:06:49: 11000000 INFO @ Sun, 02 Jun 2019 19:06:55: 15000000 INFO @ Sun, 02 Jun 2019 19:06:55: 11000000 INFO @ Sun, 02 Jun 2019 19:06:58: 12000000 INFO @ Sun, 02 Jun 2019 19:07:03: 16000000 INFO @ Sun, 02 Jun 2019 19:07:05: 12000000 INFO @ Sun, 02 Jun 2019 19:07:08: 13000000 INFO @ Sun, 02 Jun 2019 19:07:10: 17000000 INFO @ Sun, 02 Jun 2019 19:07:15: 13000000 INFO @ Sun, 02 Jun 2019 19:07:17: 14000000 INFO @ Sun, 02 Jun 2019 19:07:19: 18000000 INFO @ Sun, 02 Jun 2019 19:07:25: 14000000 INFO @ Sun, 02 Jun 2019 19:07:26: 15000000 INFO @ Sun, 02 Jun 2019 19:07:26: 19000000 INFO @ Sun, 02 Jun 2019 19:07:36: 15000000 INFO @ Sun, 02 Jun 2019 19:07:37: 20000000 INFO @ Sun, 02 Jun 2019 19:07:37: 16000000 INFO @ Sun, 02 Jun 2019 19:07:46: 21000000 INFO @ Sun, 02 Jun 2019 19:07:47: 16000000 INFO @ Sun, 02 Jun 2019 19:07:48: 17000000 INFO @ Sun, 02 Jun 2019 19:07:54: 22000000 INFO @ Sun, 02 Jun 2019 19:07:57: 17000000 INFO @ Sun, 02 Jun 2019 19:07:57: 18000000 INFO @ Sun, 02 Jun 2019 19:08:01: 23000000 INFO @ Sun, 02 Jun 2019 19:08:07: 19000000 INFO @ Sun, 02 Jun 2019 19:08:08: 18000000 INFO @ Sun, 02 Jun 2019 19:08:09: 24000000 INFO @ Sun, 02 Jun 2019 19:08:17: 20000000 INFO @ Sun, 02 Jun 2019 19:08:17: 25000000 INFO @ Sun, 02 Jun 2019 19:08:18: 19000000 INFO @ Sun, 02 Jun 2019 19:08:25: #1 tag size is determined as 69 bps INFO @ Sun, 02 Jun 2019 19:08:25: #1 tag size = 69 INFO @ Sun, 02 Jun 2019 19:08:25: #1 total tags in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:08:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:08:25: #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 19:08:25: #1 tags after filtering in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:08:25: #1 finished! INFO @ Sun, 02 Jun 2019 19:08:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:08:26: 21000000 INFO @ Sun, 02 Jun 2019 19:08:27: #2 number of paired peaks: 118 WARNING @ Sun, 02 Jun 2019 19:08:27: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sun, 02 Jun 2019 19:08:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:08:28: start X-correlation... INFO @ Sun, 02 Jun 2019 19:08:28: end of X-cor INFO @ Sun, 02 Jun 2019 19:08:28: #2 finished! INFO @ Sun, 02 Jun 2019 19:08:28: #2 predicted fragment length is 60 bps INFO @ Sun, 02 Jun 2019 19:08:28: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 02 Jun 2019 19:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20_model.r WARNING @ Sun, 02 Jun 2019 19:08:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:08:28: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 02 Jun 2019 19:08:28: #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 19:08:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:08:28: 20000000 INFO @ Sun, 02 Jun 2019 19:08:35: 22000000 INFO @ Sun, 02 Jun 2019 19:08:38: 21000000 INFO @ Sun, 02 Jun 2019 19:08:44: 23000000 INFO @ Sun, 02 Jun 2019 19:08:48: 22000000 INFO @ Sun, 02 Jun 2019 19:08:53: 24000000 INFO @ Sun, 02 Jun 2019 19:08:57: 23000000 INFO @ Sun, 02 Jun 2019 19:09:02: 25000000 INFO @ Sun, 02 Jun 2019 19:09:07: 24000000 INFO @ Sun, 02 Jun 2019 19:09:10: #1 tag size is determined as 69 bps INFO @ Sun, 02 Jun 2019 19:09:10: #1 tag size = 69 INFO @ Sun, 02 Jun 2019 19:09:10: #1 total tags in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:09:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:09:10: #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 19:09:11: #1 tags after filtering in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:09:11: #1 finished! INFO @ Sun, 02 Jun 2019 19:09:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:09:13: #2 number of paired peaks: 118 WARNING @ Sun, 02 Jun 2019 19:09:13: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sun, 02 Jun 2019 19:09:13: start model_add_line... INFO @ Sun, 02 Jun 2019 19:09:13: start X-correlation... INFO @ Sun, 02 Jun 2019 19:09:13: end of X-cor INFO @ Sun, 02 Jun 2019 19:09:13: #2 finished! INFO @ Sun, 02 Jun 2019 19:09:13: #2 predicted fragment length is 60 bps INFO @ Sun, 02 Jun 2019 19:09:13: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 02 Jun 2019 19:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05_model.r WARNING @ Sun, 02 Jun 2019 19:09:13: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:09:13: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 02 Jun 2019 19:09:13: #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 19:09:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:09:17: 25000000 INFO @ Sun, 02 Jun 2019 19:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:09:26: #1 tag size is determined as 69 bps INFO @ Sun, 02 Jun 2019 19:09:26: #1 tag size = 69 INFO @ Sun, 02 Jun 2019 19:09:26: #1 total tags in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:09:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:09:26: #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 19:09:27: #1 tags after filtering in treatment: 25920826 INFO @ Sun, 02 Jun 2019 19:09:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:09:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:09:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:09:29: #2 number of paired peaks: 118 WARNING @ Sun, 02 Jun 2019 19:09:29: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Sun, 02 Jun 2019 19:09:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:09:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:09:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:09:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:09:29: #2 predicted fragment length is 60 bps INFO @ Sun, 02 Jun 2019 19:09:29: #2 alternative fragment length(s) may be 1,60 bps INFO @ Sun, 02 Jun 2019 19:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10_model.r WARNING @ Sun, 02 Jun 2019 19:09:29: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:09:29: #2 You may need to consider one of the other alternative d(s): 1,60 WARNING @ Sun, 02 Jun 2019 19:09:29: #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 19:09:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.20_summits.bed INFO @ Sun, 02 Jun 2019 19:09:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.05_summits.bed INFO @ Sun, 02 Jun 2019 19:10:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (709 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194208/SRX4194208.10_summits.bed INFO @ Sun, 02 Jun 2019 19:10:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (460 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。