Job ID = 1294245 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-02T20:46:15 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 ) 2019-06-02T20:50:35 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 : 25,845,627 reads read : 51,691,254 reads written : 25,845,627 reads 0-length : 25,845,627 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: 00:09:40 25845627 reads; of these: 25845627 (100.00%) were unpaired; of these: 776013 (3.00%) aligned 0 times 19788513 (76.56%) aligned exactly 1 time 5281101 (20.43%) aligned >1 times 97.00% overall alignment rate Time searching: 00:09:40 Overall time: 00:09:40 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 12 files... [bam_rmdupse_core] 5654273 / 25069614 = 0.2255 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 06:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.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 06:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.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 06:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.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 06:11:26: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:11:26: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:11:35: 1000000 INFO @ Mon, 03 Jun 2019 06:11:35: 1000000 INFO @ Mon, 03 Jun 2019 06:11:35: 1000000 INFO @ Mon, 03 Jun 2019 06:11:43: 2000000 INFO @ Mon, 03 Jun 2019 06:11:44: 2000000 INFO @ Mon, 03 Jun 2019 06:11:44: 2000000 INFO @ Mon, 03 Jun 2019 06:11:50: 3000000 INFO @ Mon, 03 Jun 2019 06:11:53: 3000000 INFO @ Mon, 03 Jun 2019 06:11:53: 3000000 INFO @ Mon, 03 Jun 2019 06:11:58: 4000000 INFO @ Mon, 03 Jun 2019 06:12:02: 4000000 INFO @ Mon, 03 Jun 2019 06:12:02: 4000000 INFO @ Mon, 03 Jun 2019 06:12:06: 5000000 INFO @ Mon, 03 Jun 2019 06:12:10: 5000000 INFO @ Mon, 03 Jun 2019 06:12:11: 5000000 INFO @ Mon, 03 Jun 2019 06:12:14: 6000000 INFO @ Mon, 03 Jun 2019 06:12:19: 6000000 INFO @ Mon, 03 Jun 2019 06:12:21: 6000000 INFO @ Mon, 03 Jun 2019 06:12:23: 7000000 INFO @ Mon, 03 Jun 2019 06:12:29: 7000000 INFO @ Mon, 03 Jun 2019 06:12:30: 7000000 INFO @ Mon, 03 Jun 2019 06:12:32: 8000000 INFO @ Mon, 03 Jun 2019 06:12:38: 8000000 INFO @ Mon, 03 Jun 2019 06:12:40: 8000000 INFO @ Mon, 03 Jun 2019 06:12:41: 9000000 INFO @ Mon, 03 Jun 2019 06:12:46: 9000000 INFO @ Mon, 03 Jun 2019 06:12:48: 9000000 INFO @ Mon, 03 Jun 2019 06:12:49: 10000000 INFO @ Mon, 03 Jun 2019 06:12:55: 10000000 INFO @ Mon, 03 Jun 2019 06:12:56: 11000000 INFO @ Mon, 03 Jun 2019 06:12:57: 10000000 INFO @ Mon, 03 Jun 2019 06:13:03: 11000000 INFO @ Mon, 03 Jun 2019 06:13:04: 12000000 INFO @ Mon, 03 Jun 2019 06:13:06: 11000000 INFO @ Mon, 03 Jun 2019 06:13:11: 12000000 INFO @ Mon, 03 Jun 2019 06:13:12: 13000000 INFO @ Mon, 03 Jun 2019 06:13:14: 12000000 INFO @ Mon, 03 Jun 2019 06:13:19: 14000000 INFO @ Mon, 03 Jun 2019 06:13:20: 13000000 INFO @ Mon, 03 Jun 2019 06:13:23: 13000000 INFO @ Mon, 03 Jun 2019 06:13:27: 15000000 INFO @ Mon, 03 Jun 2019 06:13:28: 14000000 INFO @ Mon, 03 Jun 2019 06:13:32: 14000000 INFO @ Mon, 03 Jun 2019 06:13:34: 16000000 INFO @ Mon, 03 Jun 2019 06:13:36: 15000000 INFO @ Mon, 03 Jun 2019 06:13:41: 15000000 INFO @ Mon, 03 Jun 2019 06:13:42: 17000000 INFO @ Mon, 03 Jun 2019 06:13:45: 16000000 INFO @ Mon, 03 Jun 2019 06:13:50: 16000000 INFO @ Mon, 03 Jun 2019 06:13:50: 18000000 INFO @ Mon, 03 Jun 2019 06:13:53: 17000000 INFO @ Mon, 03 Jun 2019 06:13:57: 19000000 INFO @ Mon, 03 Jun 2019 06:13:58: 17000000 INFO @ Mon, 03 Jun 2019 06:14:01: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:14:01: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:14:01: #1 total tags in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:14:01: #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 06:14:01: #1 tags after filtering in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:14:01: #1 finished! INFO @ Mon, 03 Jun 2019 06:14:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:14:02: 18000000 INFO @ Mon, 03 Jun 2019 06:14:03: #2 number of paired peaks: 1277 INFO @ Mon, 03 Jun 2019 06:14:03: start model_add_line... INFO @ Mon, 03 Jun 2019 06:14:03: start X-correlation... INFO @ Mon, 03 Jun 2019 06:14:03: end of X-cor INFO @ Mon, 03 Jun 2019 06:14:03: #2 finished! INFO @ Mon, 03 Jun 2019 06:14:03: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:14:03: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20_model.r INFO @ Mon, 03 Jun 2019 06:14:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:14:07: 18000000 INFO @ Mon, 03 Jun 2019 06:14:10: 19000000 INFO @ Mon, 03 Jun 2019 06:14:14: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:14:14: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:14:14: #1 total tags in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:14:14: #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 06:14:14: #1 tags after filtering in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:14:14: #1 finished! INFO @ Mon, 03 Jun 2019 06:14:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:14:15: 19000000 INFO @ Mon, 03 Jun 2019 06:14:16: #2 number of paired peaks: 1277 INFO @ Mon, 03 Jun 2019 06:14:16: start model_add_line... INFO @ Mon, 03 Jun 2019 06:14:16: start X-correlation... INFO @ Mon, 03 Jun 2019 06:14:16: end of X-cor INFO @ Mon, 03 Jun 2019 06:14:16: #2 finished! INFO @ Mon, 03 Jun 2019 06:14:16: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:14:16: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10_model.r INFO @ Mon, 03 Jun 2019 06:14:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:14:19: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 06:14:19: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 06:14:19: #1 total tags in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:14:19: #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 06:14:19: #1 tags after filtering in treatment: 19415341 INFO @ Mon, 03 Jun 2019 06:14:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:14:19: #1 finished! INFO @ Mon, 03 Jun 2019 06:14:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:14:21: #2 number of paired peaks: 1277 INFO @ Mon, 03 Jun 2019 06:14:21: start model_add_line... INFO @ Mon, 03 Jun 2019 06:14:21: start X-correlation... INFO @ Mon, 03 Jun 2019 06:14:21: end of X-cor INFO @ Mon, 03 Jun 2019 06:14:21: #2 finished! INFO @ Mon, 03 Jun 2019 06:14:21: #2 predicted fragment length is 119 bps INFO @ Mon, 03 Jun 2019 06:14:21: #2 alternative fragment length(s) may be 119 bps INFO @ Mon, 03 Jun 2019 06:14:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05_model.r INFO @ Mon, 03 Jun 2019 06:14:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:14:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:15:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:15:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.20_summits.bed INFO @ Mon, 03 Jun 2019 06:15:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5004 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:15:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:15:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:15:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.10_summits.bed INFO @ Mon, 03 Jun 2019 06:15:36: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8577 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2035277/SRX2035277.05_summits.bed INFO @ Mon, 03 Jun 2019 06:15:41: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12515 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。