Job ID = 1293684 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T16:30:58 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' 2019-06-02T16:30:58 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/sra31/SRR/002047/SRR2096478' 2019-06-02T16:30:58 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR2096478' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T16:30:58 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-02T16:54:14 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 7,803,879 reads read : 15,607,758 reads written : 7,803,879 reads 0-length : 7,803,879 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: 00:06:28 7803879 reads; of these: 7803879 (100.00%) were unpaired; of these: 364359 (4.67%) aligned 0 times 6798977 (87.12%) aligned exactly 1 time 640543 (8.21%) aligned >1 times 95.33% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2271881 / 7439520 = 0.3054 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 02:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.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 02:06:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.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 02:06:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:06:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.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 02:06:55: #1 read tag files... INFO @ Mon, 03 Jun 2019 02:06:55: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 02:07:08: 1000000 INFO @ Mon, 03 Jun 2019 02:07:09: 1000000 INFO @ Mon, 03 Jun 2019 02:07:14: 1000000 INFO @ Mon, 03 Jun 2019 02:07:20: 2000000 INFO @ Mon, 03 Jun 2019 02:07:23: 2000000 INFO @ Mon, 03 Jun 2019 02:07:30: 2000000 INFO @ Mon, 03 Jun 2019 02:07:32: 3000000 INFO @ Mon, 03 Jun 2019 02:07:36: 3000000 INFO @ Mon, 03 Jun 2019 02:07:44: 4000000 INFO @ Mon, 03 Jun 2019 02:07:48: 3000000 INFO @ Mon, 03 Jun 2019 02:07:50: 4000000 INFO @ Mon, 03 Jun 2019 02:07:56: 5000000 INFO @ Mon, 03 Jun 2019 02:07:58: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 02:07:58: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 02:07:58: #1 total tags in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:07:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:07:58: #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 02:07:59: #1 tags after filtering in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:07:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:07:59: #1 finished! INFO @ Mon, 03 Jun 2019 02:07:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:07:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:07:59: #2 number of paired peaks: 2673 INFO @ Mon, 03 Jun 2019 02:07:59: start model_add_line... INFO @ Mon, 03 Jun 2019 02:07:59: start X-correlation... INFO @ Mon, 03 Jun 2019 02:07:59: end of X-cor INFO @ Mon, 03 Jun 2019 02:07:59: #2 finished! INFO @ Mon, 03 Jun 2019 02:07:59: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 02:07:59: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 02:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05_model.r WARNING @ Mon, 03 Jun 2019 02:07:59: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:07:59: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Mon, 03 Jun 2019 02:07:59: #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 02:07:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:08:04: 5000000 INFO @ Mon, 03 Jun 2019 02:08:06: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 02:08:06: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 02:08:06: #1 total tags in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:08:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:08:06: #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 02:08:06: #1 tags after filtering in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:08:06: #1 finished! INFO @ Mon, 03 Jun 2019 02:08:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:08:07: 4000000 INFO @ Mon, 03 Jun 2019 02:08:07: #2 number of paired peaks: 2673 INFO @ Mon, 03 Jun 2019 02:08:07: start model_add_line... INFO @ Mon, 03 Jun 2019 02:08:07: start X-correlation... INFO @ Mon, 03 Jun 2019 02:08:07: end of X-cor INFO @ Mon, 03 Jun 2019 02:08:07: #2 finished! INFO @ Mon, 03 Jun 2019 02:08:07: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 02:08:07: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 02:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10_model.r WARNING @ Mon, 03 Jun 2019 02:08:07: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:08:07: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Mon, 03 Jun 2019 02:08:07: #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 02:08:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:08:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:08:24: 5000000 INFO @ Mon, 03 Jun 2019 02:08:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 02:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05_peaks.xls INFO @ Mon, 03 Jun 2019 02:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.05_summits.bed INFO @ Mon, 03 Jun 2019 02:08:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8865 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:08:26: #1 tag size is determined as 148 bps INFO @ Mon, 03 Jun 2019 02:08:26: #1 tag size = 148 INFO @ Mon, 03 Jun 2019 02:08:26: #1 total tags in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:08:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 02:08:26: #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 02:08:26: #1 tags after filtering in treatment: 5167639 INFO @ Mon, 03 Jun 2019 02:08:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 02:08:26: #1 finished! INFO @ Mon, 03 Jun 2019 02:08:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 02:08:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 02:08:27: #2 number of paired peaks: 2673 INFO @ Mon, 03 Jun 2019 02:08:27: start model_add_line... INFO @ Mon, 03 Jun 2019 02:08:27: start X-correlation... INFO @ Mon, 03 Jun 2019 02:08:27: end of X-cor INFO @ Mon, 03 Jun 2019 02:08:27: #2 finished! INFO @ Mon, 03 Jun 2019 02:08:27: #2 predicted fragment length is 161 bps INFO @ Mon, 03 Jun 2019 02:08:27: #2 alternative fragment length(s) may be 161 bps INFO @ Mon, 03 Jun 2019 02:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20_model.r WARNING @ Mon, 03 Jun 2019 02:08:27: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 02:08:27: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Mon, 03 Jun 2019 02:08:27: #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 02:08:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 02:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 02:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10_peaks.xls INFO @ Mon, 03 Jun 2019 02:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.10_summits.bed INFO @ Mon, 03 Jun 2019 02:08:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4158 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 02:08:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 02:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20_peaks.xls INFO @ Mon, 03 Jun 2019 02:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 02:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1091594/SRX1091594.20_summits.bed INFO @ Mon, 03 Jun 2019 02:08:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1826 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。