Job ID = 1292410 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,289,513 reads read : 12,579,026 reads written : 6,289,513 reads 0-length : 6,289,513 spots read : 6,164,909 reads read : 12,329,818 reads written : 6,164,909 reads 0-length : 6,164,909 2019-06-02T09:25:53 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' 2019-06-02T09:25:53 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/SRR7291468' 2019-06-02T09:25:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7291468' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T09:25:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 6,287,384 reads read : 12,574,768 reads written : 6,287,384 reads 0-length : 6,287,384 spots read : 6,101,238 reads read : 12,202,476 reads written : 6,101,238 reads 0-length : 6,101,238 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:31 24843044 reads; of these: 24843044 (100.00%) were unpaired; of these: 1312437 (5.28%) aligned 0 times 18979050 (76.40%) aligned exactly 1 time 4551557 (18.32%) aligned >1 times 94.72% overall alignment rate Time searching: 00:10:32 Overall time: 00:10:32 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] 7718731 / 23530607 = 0.3280 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 18:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.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 18:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.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 18:55:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.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 18:55:58: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:55:58: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:56:06: 1000000 INFO @ Sun, 02 Jun 2019 18:56:06: 1000000 INFO @ Sun, 02 Jun 2019 18:56:06: 1000000 INFO @ Sun, 02 Jun 2019 18:56:15: 2000000 INFO @ Sun, 02 Jun 2019 18:56:15: 2000000 INFO @ Sun, 02 Jun 2019 18:56:15: 2000000 INFO @ Sun, 02 Jun 2019 18:56:23: 3000000 INFO @ Sun, 02 Jun 2019 18:56:23: 3000000 INFO @ Sun, 02 Jun 2019 18:56:23: 3000000 INFO @ Sun, 02 Jun 2019 18:56:31: 4000000 INFO @ Sun, 02 Jun 2019 18:56:31: 4000000 INFO @ Sun, 02 Jun 2019 18:56:31: 4000000 INFO @ Sun, 02 Jun 2019 18:56:39: 5000000 INFO @ Sun, 02 Jun 2019 18:56:40: 5000000 INFO @ Sun, 02 Jun 2019 18:56:40: 5000000 INFO @ Sun, 02 Jun 2019 18:56:48: 6000000 INFO @ Sun, 02 Jun 2019 18:56:48: 6000000 INFO @ Sun, 02 Jun 2019 18:56:48: 6000000 INFO @ Sun, 02 Jun 2019 18:56:56: 7000000 INFO @ Sun, 02 Jun 2019 18:56:56: 7000000 INFO @ Sun, 02 Jun 2019 18:56:56: 7000000 INFO @ Sun, 02 Jun 2019 18:57:04: 8000000 INFO @ Sun, 02 Jun 2019 18:57:05: 8000000 INFO @ Sun, 02 Jun 2019 18:57:05: 8000000 INFO @ Sun, 02 Jun 2019 18:57:12: 9000000 INFO @ Sun, 02 Jun 2019 18:57:13: 9000000 INFO @ Sun, 02 Jun 2019 18:57:13: 9000000 INFO @ Sun, 02 Jun 2019 18:57:20: 10000000 INFO @ Sun, 02 Jun 2019 18:57:21: 10000000 INFO @ Sun, 02 Jun 2019 18:57:21: 10000000 INFO @ Sun, 02 Jun 2019 18:57:29: 11000000 INFO @ Sun, 02 Jun 2019 18:57:30: 11000000 INFO @ Sun, 02 Jun 2019 18:57:30: 11000000 INFO @ Sun, 02 Jun 2019 18:57:37: 12000000 INFO @ Sun, 02 Jun 2019 18:57:38: 12000000 INFO @ Sun, 02 Jun 2019 18:57:38: 12000000 INFO @ Sun, 02 Jun 2019 18:57:45: 13000000 INFO @ Sun, 02 Jun 2019 18:57:46: 13000000 INFO @ Sun, 02 Jun 2019 18:57:47: 13000000 INFO @ Sun, 02 Jun 2019 18:57:53: 14000000 INFO @ Sun, 02 Jun 2019 18:57:55: 14000000 INFO @ Sun, 02 Jun 2019 18:57:55: 14000000 INFO @ Sun, 02 Jun 2019 18:58:01: 15000000 INFO @ Sun, 02 Jun 2019 18:58:03: 15000000 INFO @ Sun, 02 Jun 2019 18:58:03: 15000000 INFO @ Sun, 02 Jun 2019 18:58:07: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:58:07: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:58:07: #1 total tags in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:07: #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 18:58:08: #1 tags after filtering in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:08: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:09: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 18:58:09: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:09: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:09: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:09: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:09: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:09: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:58:09: #2 alternative fragment length(s) may be 2,44,561 bps INFO @ Sun, 02 Jun 2019 18:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10_model.r WARNING @ Sun, 02 Jun 2019 18:58:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:09: #2 You may need to consider one of the other alternative d(s): 2,44,561 WARNING @ Sun, 02 Jun 2019 18:58:09: #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 18:58:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:09: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:58:09: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:58:09: #1 total tags in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:09: #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 18:58:10: #1 tags after filtering in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:10: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:10: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 18:58:10: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 18:58:10: #1 total tags in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:58:10: #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 18:58:10: #1 tags after filtering in treatment: 15811876 INFO @ Sun, 02 Jun 2019 18:58:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:58:10: #1 finished! INFO @ Sun, 02 Jun 2019 18:58:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:58:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:58:11: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 18:58:11: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:11: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:11: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:11: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:11: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:11: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:58:11: #2 alternative fragment length(s) may be 2,44,561 bps INFO @ Sun, 02 Jun 2019 18:58:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05_model.r WARNING @ Sun, 02 Jun 2019 18:58:11: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:11: #2 You may need to consider one of the other alternative d(s): 2,44,561 WARNING @ Sun, 02 Jun 2019 18:58:11: #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 18:58:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:12: #2 number of paired peaks: 386 WARNING @ Sun, 02 Jun 2019 18:58:12: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Sun, 02 Jun 2019 18:58:12: start model_add_line... INFO @ Sun, 02 Jun 2019 18:58:12: start X-correlation... INFO @ Sun, 02 Jun 2019 18:58:12: end of X-cor INFO @ Sun, 02 Jun 2019 18:58:12: #2 finished! INFO @ Sun, 02 Jun 2019 18:58:12: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 18:58:12: #2 alternative fragment length(s) may be 2,44,561 bps INFO @ Sun, 02 Jun 2019 18:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20_model.r WARNING @ Sun, 02 Jun 2019 18:58:12: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:58:12: #2 You may need to consider one of the other alternative d(s): 2,44,561 WARNING @ Sun, 02 Jun 2019 18:58:12: #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 18:58:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:58:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:58:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.10_summits.bed INFO @ Sun, 02 Jun 2019 18:59:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.05_summits.bed INFO @ Sun, 02 Jun 2019 18:59:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4194194/SRX4194194.20_summits.bed INFO @ Sun, 02 Jun 2019 18:59:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 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。