Job ID = 1293334 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T14:14:20 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 ) 2019-06-02T14:14:20 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 : 48,686,011 reads read : 97,372,022 reads written : 97,372,022 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: 00:45:42 48686011 reads; of these: 48686011 (100.00%) were paired; of these: 27806059 (57.11%) aligned concordantly 0 times 17234312 (35.40%) aligned concordantly exactly 1 time 3645640 (7.49%) aligned concordantly >1 times ---- 27806059 pairs aligned concordantly 0 times; of these: 574528 (2.07%) aligned discordantly 1 time ---- 27231531 pairs aligned 0 times concordantly or discordantly; of these: 54463062 mates make up the pairs; of these: 53375964 (98.00%) aligned 0 times 725100 (1.33%) aligned exactly 1 time 361998 (0.66%) aligned >1 times 45.18% overall alignment rate Time searching: 00:45:42 Overall time: 00:45:42 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 19285635 / 21444644 = 0.8993 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 00:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.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 00:26:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:26:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.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 00:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.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 00:26:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:26:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:26:07: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:26:07: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:26:14: 1000000 INFO @ Mon, 03 Jun 2019 00:26:14: 1000000 INFO @ Mon, 03 Jun 2019 00:26:16: 1000000 INFO @ Mon, 03 Jun 2019 00:26:21: 2000000 INFO @ Mon, 03 Jun 2019 00:26:22: 2000000 INFO @ Mon, 03 Jun 2019 00:26:26: 2000000 INFO @ Mon, 03 Jun 2019 00:26:28: 3000000 INFO @ Mon, 03 Jun 2019 00:26:30: 3000000 INFO @ Mon, 03 Jun 2019 00:26:35: 4000000 INFO @ Mon, 03 Jun 2019 00:26:35: 3000000 INFO @ Mon, 03 Jun 2019 00:26:37: 4000000 INFO @ Mon, 03 Jun 2019 00:26:42: 5000000 INFO @ Mon, 03 Jun 2019 00:26:45: 4000000 INFO @ Mon, 03 Jun 2019 00:26:45: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:26:45: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:26:45: #1 total tags in treatment: 2101259 INFO @ Mon, 03 Jun 2019 00:26:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:26:45: #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 00:26:45: #1 tags after filtering in treatment: 2028107 INFO @ Mon, 03 Jun 2019 00:26:45: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 00:26:45: #1 finished! INFO @ Mon, 03 Jun 2019 00:26:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:26:45: 5000000 INFO @ Mon, 03 Jun 2019 00:26:45: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 00:26:45: start model_add_line... INFO @ Mon, 03 Jun 2019 00:26:45: start X-correlation... INFO @ Mon, 03 Jun 2019 00:26:45: end of X-cor INFO @ Mon, 03 Jun 2019 00:26:45: #2 finished! INFO @ Mon, 03 Jun 2019 00:26:45: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 00:26:45: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 00:26:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05_model.r INFO @ Mon, 03 Jun 2019 00:26:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:26:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:26:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:26:48: #1 total tags in treatment: 2101259 INFO @ Mon, 03 Jun 2019 00:26:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:26:48: #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 00:26:48: #1 tags after filtering in treatment: 2028107 INFO @ Mon, 03 Jun 2019 00:26:48: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 00:26:48: #1 finished! INFO @ Mon, 03 Jun 2019 00:26:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:26:49: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 00:26:49: start model_add_line... INFO @ Mon, 03 Jun 2019 00:26:49: start X-correlation... INFO @ Mon, 03 Jun 2019 00:26:49: end of X-cor INFO @ Mon, 03 Jun 2019 00:26:49: #2 finished! INFO @ Mon, 03 Jun 2019 00:26:49: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 00:26:49: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 00:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10_model.r INFO @ Mon, 03 Jun 2019 00:26:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:26:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:26:54: 5000000 INFO @ Mon, 03 Jun 2019 00:26:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.05_summits.bed INFO @ Mon, 03 Jun 2019 00:26:56: Done! INFO @ Mon, 03 Jun 2019 00:26:56: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3575 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:26:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 00:26:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 00:26:57: #1 total tags in treatment: 2101259 INFO @ Mon, 03 Jun 2019 00:26:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:26:57: #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 00:26:57: #1 tags after filtering in treatment: 2028107 INFO @ Mon, 03 Jun 2019 00:26:57: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 00:26:57: #1 finished! INFO @ Mon, 03 Jun 2019 00:26:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:26:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:26:58: #2 number of paired peaks: 3865 INFO @ Mon, 03 Jun 2019 00:26:58: start model_add_line... INFO @ Mon, 03 Jun 2019 00:26:58: start X-correlation... INFO @ Mon, 03 Jun 2019 00:26:58: end of X-cor INFO @ Mon, 03 Jun 2019 00:26:58: #2 finished! INFO @ Mon, 03 Jun 2019 00:26:58: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 00:26:58: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 00:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20_model.r INFO @ Mon, 03 Jun 2019 00:26:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.10_summits.bed INFO @ Mon, 03 Jun 2019 00:26:59: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (1467 records, 4 fields): 97 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:27:05: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818264/ERX1818264.20_summits.bed INFO @ Mon, 03 Jun 2019 00:27:09: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (319 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。