Job ID = 2640458 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-08-24T07:56:12 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 ) 2019-08-24T07:56:12 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 ) 2019-08-24T07:56:12 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 : 4,523,063 reads read : 9,046,126 reads written : 4,523,063 reads 0-length : 4,523,063 rm: cannot remove ‘[DSE]RR*’: 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:43 4523063 reads; of these: 4523063 (100.00%) were unpaired; of these: 267924 (5.92%) aligned 0 times 3136079 (69.34%) aligned exactly 1 time 1119060 (24.74%) aligned >1 times 94.08% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 208965 / 4255139 = 0.0491 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:03:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:03:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:03:12: 1000000 INFO @ Sat, 24 Aug 2019 17:03:20: 2000000 INFO @ Sat, 24 Aug 2019 17:03:27: 3000000 INFO @ Sat, 24 Aug 2019 17:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:03:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:03:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:03:35: 4000000 INFO @ Sat, 24 Aug 2019 17:03:35: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:03:35: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:03:35: #1 total tags in treatment: 4046174 INFO @ Sat, 24 Aug 2019 17:03:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:03:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:03:36: #1 tags after filtering in treatment: 4045868 INFO @ Sat, 24 Aug 2019 17:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:03:36: #1 finished! INFO @ Sat, 24 Aug 2019 17:03:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:03:38: #2 number of paired peaks: 11570 INFO @ Sat, 24 Aug 2019 17:03:38: start model_add_line... INFO @ Sat, 24 Aug 2019 17:03:38: start X-correlation... INFO @ Sat, 24 Aug 2019 17:03:38: end of X-cor INFO @ Sat, 24 Aug 2019 17:03:38: #2 finished! INFO @ Sat, 24 Aug 2019 17:03:38: #2 predicted fragment length is 239 bps INFO @ Sat, 24 Aug 2019 17:03:38: #2 alternative fragment length(s) may be 98,166,239 bps INFO @ Sat, 24 Aug 2019 17:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05_model.r INFO @ Sat, 24 Aug 2019 17:03:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:03:43: 1000000 INFO @ Sat, 24 Aug 2019 17:03:52: 2000000 INFO @ Sat, 24 Aug 2019 17:03:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:03:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:03:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:03:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.05_summits.bed INFO @ Sat, 24 Aug 2019 17:03:59: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (237 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:04:01: 3000000 INFO @ Sat, 24 Aug 2019 17:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:04:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:04:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:04:10: 4000000 INFO @ Sat, 24 Aug 2019 17:04:11: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:04:11: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:04:11: #1 total tags in treatment: 4046174 INFO @ Sat, 24 Aug 2019 17:04:11: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:04:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:04:11: #1 tags after filtering in treatment: 4045868 INFO @ Sat, 24 Aug 2019 17:04:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:04:11: #1 finished! INFO @ Sat, 24 Aug 2019 17:04:11: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:04:11: 1000000 INFO @ Sat, 24 Aug 2019 17:04:13: #2 number of paired peaks: 11570 INFO @ Sat, 24 Aug 2019 17:04:13: start model_add_line... INFO @ Sat, 24 Aug 2019 17:04:13: start X-correlation... INFO @ Sat, 24 Aug 2019 17:04:13: end of X-cor INFO @ Sat, 24 Aug 2019 17:04:13: #2 finished! INFO @ Sat, 24 Aug 2019 17:04:13: #2 predicted fragment length is 239 bps INFO @ Sat, 24 Aug 2019 17:04:13: #2 alternative fragment length(s) may be 98,166,239 bps INFO @ Sat, 24 Aug 2019 17:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10_model.r INFO @ Sat, 24 Aug 2019 17:04:13: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:04:19: 2000000 INFO @ Sat, 24 Aug 2019 17:04:26: 3000000 INFO @ Sat, 24 Aug 2019 17:04:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.10_summits.bed INFO @ Sat, 24 Aug 2019 17:04:34: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:04:34: 4000000 INFO @ Sat, 24 Aug 2019 17:04:35: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:04:35: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:04:35: #1 total tags in treatment: 4046174 INFO @ Sat, 24 Aug 2019 17:04:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:04:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:04:35: #1 tags after filtering in treatment: 4045868 INFO @ Sat, 24 Aug 2019 17:04:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:04:35: #1 finished! INFO @ Sat, 24 Aug 2019 17:04:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:04:37: #2 number of paired peaks: 11570 INFO @ Sat, 24 Aug 2019 17:04:37: start model_add_line... INFO @ Sat, 24 Aug 2019 17:04:37: start X-correlation... INFO @ Sat, 24 Aug 2019 17:04:37: end of X-cor INFO @ Sat, 24 Aug 2019 17:04:37: #2 finished! INFO @ Sat, 24 Aug 2019 17:04:37: #2 predicted fragment length is 239 bps INFO @ Sat, 24 Aug 2019 17:04:37: #2 alternative fragment length(s) may be 98,166,239 bps INFO @ Sat, 24 Aug 2019 17:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20_model.r INFO @ Sat, 24 Aug 2019 17:04:37: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:04:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5374979/SRX5374979.20_summits.bed INFO @ Sat, 24 Aug 2019 17:04:57: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (63 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。