Job ID = 1294559 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T23:50:44 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' 2019-06-02T23:50:44 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/sra12/SRR/000849/SRR869929' 2019-06-02T23:50:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_tbl().VDBManagerOpenTableRead( 'SRR869929' ) -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:50:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcDB,rcMgr,rcOpening,rcTable,rcIncorrect) 2019-06-02T23:55:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T23:55:50 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 9,189,464 reads read : 9,189,464 reads written : 9,189,464 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: 00:04:36 9189464 reads; of these: 9189464 (100.00%) were unpaired; of these: 328802 (3.58%) aligned 0 times 5904075 (64.25%) aligned exactly 1 time 2956587 (32.17%) aligned >1 times 96.42% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 1415846 / 8860662 = 0.1598 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 09:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.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 09:11:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.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 09:11:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.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 09:11:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:11:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:11:19: 1000000 INFO @ Mon, 03 Jun 2019 09:11:19: 1000000 INFO @ Mon, 03 Jun 2019 09:11:20: 1000000 INFO @ Mon, 03 Jun 2019 09:11:27: 2000000 INFO @ Mon, 03 Jun 2019 09:11:27: 2000000 INFO @ Mon, 03 Jun 2019 09:11:29: 2000000 INFO @ Mon, 03 Jun 2019 09:11:34: 3000000 INFO @ Mon, 03 Jun 2019 09:11:35: 3000000 INFO @ Mon, 03 Jun 2019 09:11:38: 3000000 INFO @ Mon, 03 Jun 2019 09:11:42: 4000000 INFO @ Mon, 03 Jun 2019 09:11:42: 4000000 INFO @ Mon, 03 Jun 2019 09:11:48: 4000000 INFO @ Mon, 03 Jun 2019 09:11:50: 5000000 INFO @ Mon, 03 Jun 2019 09:11:50: 5000000 INFO @ Mon, 03 Jun 2019 09:11:58: 5000000 INFO @ Mon, 03 Jun 2019 09:11:58: 6000000 INFO @ Mon, 03 Jun 2019 09:12:00: 6000000 INFO @ Mon, 03 Jun 2019 09:12:06: 7000000 INFO @ Mon, 03 Jun 2019 09:12:08: 7000000 INFO @ Mon, 03 Jun 2019 09:12:08: 6000000 INFO @ Mon, 03 Jun 2019 09:12:09: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:12:09: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:12:09: #1 total tags in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:12:09: #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 09:12:10: #1 tags after filtering in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:12:10: #1 finished! INFO @ Mon, 03 Jun 2019 09:12:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:12:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:12:10: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 09:12:10: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 09:12:10: start model_add_line... INFO @ Mon, 03 Jun 2019 09:12:10: start X-correlation... INFO @ Mon, 03 Jun 2019 09:12:10: end of X-cor INFO @ Mon, 03 Jun 2019 09:12:10: #2 finished! INFO @ Mon, 03 Jun 2019 09:12:10: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:12:10: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05_model.r WARNING @ Mon, 03 Jun 2019 09:12:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:12:10: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:12:10: #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 09:12:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:12:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:12:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:12:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:12:11: #1 total tags in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:12:11: #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 09:12:11: #1 tags after filtering in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:12:11: #1 finished! INFO @ Mon, 03 Jun 2019 09:12:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:12:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:12:12: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 09:12:12: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 09:12:12: start model_add_line... INFO @ Mon, 03 Jun 2019 09:12:12: start X-correlation... INFO @ Mon, 03 Jun 2019 09:12:12: end of X-cor INFO @ Mon, 03 Jun 2019 09:12:12: #2 finished! INFO @ Mon, 03 Jun 2019 09:12:12: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:12:12: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:12:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20_model.r WARNING @ Mon, 03 Jun 2019 09:12:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:12:12: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:12:12: #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 09:12:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:12:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:12:18: 7000000 INFO @ Mon, 03 Jun 2019 09:12:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:12:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:12:22: #1 total tags in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:12:22: #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 09:12:22: #1 tags after filtering in treatment: 7444816 INFO @ Mon, 03 Jun 2019 09:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:12:22: #1 finished! INFO @ Mon, 03 Jun 2019 09:12:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:12:23: #2 number of paired peaks: 678 WARNING @ Mon, 03 Jun 2019 09:12:23: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Mon, 03 Jun 2019 09:12:23: start model_add_line... INFO @ Mon, 03 Jun 2019 09:12:23: start X-correlation... INFO @ Mon, 03 Jun 2019 09:12:23: end of X-cor INFO @ Mon, 03 Jun 2019 09:12:23: #2 finished! INFO @ Mon, 03 Jun 2019 09:12:23: #2 predicted fragment length is 50 bps INFO @ Mon, 03 Jun 2019 09:12:23: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 03 Jun 2019 09:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10_model.r WARNING @ Mon, 03 Jun 2019 09:12:23: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 09:12:23: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 03 Jun 2019 09:12:23: #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 09:12:23: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:12:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:12:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.05_summits.bed INFO @ Mon, 03 Jun 2019 09:12:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2812 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:12:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:12:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:12:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:12:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.20_summits.bed INFO @ Mon, 03 Jun 2019 09:12:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1255 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:12:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:12:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287740/SRX287740.10_summits.bed INFO @ Mon, 03 Jun 2019 09:12:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1780 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。