Job ID = 1293223 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T13:20:47 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' 2019-06-02T13:20:47 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/sra77/SRR/008401/SRR8603006' 2019-06-02T13:20:52 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' 2019-06-02T13:20:52 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/sra77/SRR/008401/SRR8603006' 2019-06-02T13:20:52 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR8603006', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 19,673,243 reads read : 19,673,243 reads written : 19,673,243 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:04:15 19673243 reads; of these: 19673243 (100.00%) were unpaired; of these: 3956854 (20.11%) aligned 0 times 12932875 (65.74%) aligned exactly 1 time 2783514 (14.15%) aligned >1 times 79.89% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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 8 files... [bam_rmdupse_core] 1437976 / 15716389 = 0.0915 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 22:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.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 22:43:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.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 22:43:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.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 22:43:05: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:43:05: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:43:13: 1000000 INFO @ Sun, 02 Jun 2019 22:43:13: 1000000 INFO @ Sun, 02 Jun 2019 22:43:14: 1000000 INFO @ Sun, 02 Jun 2019 22:43:20: 2000000 INFO @ Sun, 02 Jun 2019 22:43:21: 2000000 INFO @ Sun, 02 Jun 2019 22:43:22: 2000000 INFO @ Sun, 02 Jun 2019 22:43:28: 3000000 INFO @ Sun, 02 Jun 2019 22:43:28: 3000000 INFO @ Sun, 02 Jun 2019 22:43:30: 3000000 INFO @ Sun, 02 Jun 2019 22:43:35: 4000000 INFO @ Sun, 02 Jun 2019 22:43:35: 4000000 INFO @ Sun, 02 Jun 2019 22:43:39: 4000000 INFO @ Sun, 02 Jun 2019 22:43:42: 5000000 INFO @ Sun, 02 Jun 2019 22:43:43: 5000000 INFO @ Sun, 02 Jun 2019 22:43:46: 5000000 INFO @ Sun, 02 Jun 2019 22:43:49: 6000000 INFO @ Sun, 02 Jun 2019 22:43:50: 6000000 INFO @ Sun, 02 Jun 2019 22:43:54: 6000000 INFO @ Sun, 02 Jun 2019 22:43:56: 7000000 INFO @ Sun, 02 Jun 2019 22:43:57: 7000000 INFO @ Sun, 02 Jun 2019 22:44:02: 7000000 INFO @ Sun, 02 Jun 2019 22:44:03: 8000000 INFO @ Sun, 02 Jun 2019 22:44:04: 8000000 INFO @ Sun, 02 Jun 2019 22:44:10: 9000000 INFO @ Sun, 02 Jun 2019 22:44:10: 8000000 INFO @ Sun, 02 Jun 2019 22:44:11: 9000000 INFO @ Sun, 02 Jun 2019 22:44:17: 10000000 INFO @ Sun, 02 Jun 2019 22:44:18: 10000000 INFO @ Sun, 02 Jun 2019 22:44:18: 9000000 INFO @ Sun, 02 Jun 2019 22:44:23: 11000000 INFO @ Sun, 02 Jun 2019 22:44:25: 11000000 INFO @ Sun, 02 Jun 2019 22:44:26: 10000000 INFO @ Sun, 02 Jun 2019 22:44:30: 12000000 INFO @ Sun, 02 Jun 2019 22:44:32: 12000000 INFO @ Sun, 02 Jun 2019 22:44:34: 11000000 INFO @ Sun, 02 Jun 2019 22:44:37: 13000000 INFO @ Sun, 02 Jun 2019 22:44:39: 13000000 INFO @ Sun, 02 Jun 2019 22:44:42: 12000000 INFO @ Sun, 02 Jun 2019 22:44:44: 14000000 INFO @ Sun, 02 Jun 2019 22:44:46: 14000000 INFO @ Sun, 02 Jun 2019 22:44:46: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:44:46: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:44:46: #1 total tags in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:44:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:44:46: #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 22:44:47: #1 tags after filtering in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:44:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:44:47: #1 finished! INFO @ Sun, 02 Jun 2019 22:44:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:44:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:44:48: #2 number of paired peaks: 301 WARNING @ Sun, 02 Jun 2019 22:44:48: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sun, 02 Jun 2019 22:44:48: start model_add_line... INFO @ Sun, 02 Jun 2019 22:44:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:44:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:44:48: #1 total tags in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:44:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:44:48: #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 22:44:48: start X-correlation... INFO @ Sun, 02 Jun 2019 22:44:48: end of X-cor INFO @ Sun, 02 Jun 2019 22:44:48: #2 finished! INFO @ Sun, 02 Jun 2019 22:44:48: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 22:44:48: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 22:44:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10_model.r WARNING @ Sun, 02 Jun 2019 22:44:48: #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 22:44:48: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 22:44:48: #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 22:44:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:44:48: #1 tags after filtering in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:44:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:44:48: #1 finished! INFO @ Sun, 02 Jun 2019 22:44:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:44:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:44:49: 13000000 INFO @ Sun, 02 Jun 2019 22:44:50: #2 number of paired peaks: 301 WARNING @ Sun, 02 Jun 2019 22:44:50: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sun, 02 Jun 2019 22:44:50: start model_add_line... INFO @ Sun, 02 Jun 2019 22:44:50: start X-correlation... INFO @ Sun, 02 Jun 2019 22:44:50: end of X-cor INFO @ Sun, 02 Jun 2019 22:44:50: #2 finished! INFO @ Sun, 02 Jun 2019 22:44:50: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 22:44:50: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 22:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05_model.r WARNING @ Sun, 02 Jun 2019 22:44:50: #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 22:44:50: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 22:44:50: #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 22:44:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:44:57: 14000000 INFO @ Sun, 02 Jun 2019 22:44:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:44:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:44:59: #1 total tags in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:44:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:44:59: #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 22:45:00: #1 tags after filtering in treatment: 14278413 INFO @ Sun, 02 Jun 2019 22:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:45:00: #1 finished! INFO @ Sun, 02 Jun 2019 22:45:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:45:01: #2 number of paired peaks: 301 WARNING @ Sun, 02 Jun 2019 22:45:01: Fewer paired peaks (301) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 301 pairs to build model! INFO @ Sun, 02 Jun 2019 22:45:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:45:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:45:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:45:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:45:01: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 22:45:01: #2 alternative fragment length(s) may be 2,48 bps INFO @ Sun, 02 Jun 2019 22:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20_model.r WARNING @ Sun, 02 Jun 2019 22:45:01: #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 22:45:01: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Sun, 02 Jun 2019 22:45:01: #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 22:45:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:45:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:45:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:45:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.10_summits.bed INFO @ Sun, 02 Jun 2019 22:45:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:45:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:45:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:45:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.05_summits.bed INFO @ Sun, 02 Jun 2019 22:45:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (718 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:45:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:45:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:45:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402772/SRX5402772.20_summits.bed INFO @ Sun, 02 Jun 2019 22:45:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 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。