Job ID = 1294192 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:21:12 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' 2019-06-02T20:21:12 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/sos/sra-pub-run-1/SRR597005/SRR597005.1' 2019-06-02T20:21:17 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' 2019-06-02T20:21:17 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/sos/sra-pub-run-1/SRR597005/SRR597005.1' 2019-06-02T20:21:17 fasterq-dump.2.9.6 err: cmn_iter.c cmn_get_acc_type( 'SRR597005', 'NAME' ).VDBManagerOpenTableRead() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) spots read : 1,212,701 reads read : 1,212,701 reads written : 1,212,701 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: 00:00:23 1212701 reads; of these: 1212701 (100.00%) were unpaired; of these: 514030 (42.39%) aligned 0 times 471503 (38.88%) aligned exactly 1 time 227168 (18.73%) aligned >1 times 57.61% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 240493 / 698671 = 0.3442 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 @ Mon, 03 Jun 2019 05:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 05:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 05:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 03 Jun 2019 05:22:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:22:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:23:02: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:23:02: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:23:02: #1 total tags in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:23:02: #1 tags after filtering in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:02: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:02: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:02: #2 number of paired peaks: 690 WARNING @ Mon, 03 Jun 2019 05:23:02: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:02: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:02: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:02: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:02: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:02: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 05:23:02: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 05:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10_model.r WARNING @ Mon, 03 Jun 2019 05:23:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:02: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 05:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:23:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:23:03: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:23:03: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:23:03: #1 total tags in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:23:03: #1 tags after filtering in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:03: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:03: #2 number of paired peaks: 690 WARNING @ Mon, 03 Jun 2019 05:23:03: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:03: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:03: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:03: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:03: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 05:23:03: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 05:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20_model.r WARNING @ Mon, 03 Jun 2019 05:23:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 05:23:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:23:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:23:03: #1 tag size is determined as 45 bps INFO @ Mon, 03 Jun 2019 05:23:03: #1 tag size = 45 INFO @ Mon, 03 Jun 2019 05:23:03: #1 total tags in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:23:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:23:03: #1 tags after filtering in treatment: 458178 INFO @ Mon, 03 Jun 2019 05:23:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:23:03: #1 finished! INFO @ Mon, 03 Jun 2019 05:23:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:23:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:23:03: #2 number of paired peaks: 690 WARNING @ Mon, 03 Jun 2019 05:23:03: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Mon, 03 Jun 2019 05:23:03: start model_add_line... INFO @ Mon, 03 Jun 2019 05:23:03: start X-correlation... INFO @ Mon, 03 Jun 2019 05:23:03: end of X-cor INFO @ Mon, 03 Jun 2019 05:23:03: #2 finished! INFO @ Mon, 03 Jun 2019 05:23:03: #2 predicted fragment length is 51 bps INFO @ Mon, 03 Jun 2019 05:23:03: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 03 Jun 2019 05:23:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05_model.r WARNING @ Mon, 03 Jun 2019 05:23:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:23:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 03 Jun 2019 05:23:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:23:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:23:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 05:23:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:23:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:23:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.10_summits.bed INFO @ Mon, 03 Jun 2019 05:23:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:23:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.20_summits.bed INFO @ Mon, 03 Jun 2019 05:23:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:23:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX197577/SRX197577.05_summits.bed INFO @ Mon, 03 Jun 2019 05:23:05: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 2 millis CompletedMACS2peakCalling