Job ID = 1296437 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:15:49 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 ) 2019-06-03T07:23:58 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 : 35,271,827 reads read : 70,543,654 reads written : 70,543,654 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: 00:06:39 35271827 reads; of these: 35271827 (100.00%) were paired; of these: 34959128 (99.11%) aligned concordantly 0 times 247253 (0.70%) aligned concordantly exactly 1 time 65446 (0.19%) aligned concordantly >1 times ---- 34959128 pairs aligned concordantly 0 times; of these: 1273 (0.00%) aligned discordantly 1 time ---- 34957855 pairs aligned 0 times concordantly or discordantly; of these: 69915710 mates make up the pairs; of these: 69215665 (99.00%) aligned 0 times 161408 (0.23%) aligned exactly 1 time 538637 (0.77%) aligned >1 times 1.88% overall alignment rate Time searching: 00:06:39 Overall time: 00:06:39 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_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] 9880 / 312531 = 0.0316 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 16:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.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 16:39:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:39:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.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 16:39:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:39:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.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 16:39:57: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:39:57: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:40:04: 1000000 INFO @ Mon, 03 Jun 2019 16:40:04: 1000000 INFO @ Mon, 03 Jun 2019 16:40:04: 1000000 INFO @ Mon, 03 Jun 2019 16:40:05: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:40:05: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:40:05: #1 total tags in treatment: 302850 INFO @ Mon, 03 Jun 2019 16:40:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:40:05: #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 16:40:05: #1 tags after filtering in treatment: 298288 INFO @ Mon, 03 Jun 2019 16:40:05: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:40:05: #1 finished! INFO @ Mon, 03 Jun 2019 16:40:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:40:05: #2 number of paired peaks: 1585 INFO @ Mon, 03 Jun 2019 16:40:05: start model_add_line... INFO @ Mon, 03 Jun 2019 16:40:05: start X-correlation... INFO @ Mon, 03 Jun 2019 16:40:05: end of X-cor INFO @ Mon, 03 Jun 2019 16:40:05: #2 finished! INFO @ Mon, 03 Jun 2019 16:40:05: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 16:40:05: #2 alternative fragment length(s) may be 93,126 bps INFO @ Mon, 03 Jun 2019 16:40:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20_model.r INFO @ Mon, 03 Jun 2019 16:40:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:40:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:40:06: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:40:06: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:40:06: #1 total tags in treatment: 302850 INFO @ Mon, 03 Jun 2019 16:40:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:40:06: #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 16:40:06: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 16:40:06: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 16:40:06: #1 total tags in treatment: 302850 INFO @ Mon, 03 Jun 2019 16:40:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:40:06: #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 16:40:06: #1 tags after filtering in treatment: 298288 INFO @ Mon, 03 Jun 2019 16:40:06: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:40:06: #1 finished! INFO @ Mon, 03 Jun 2019 16:40:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:40:06: #1 tags after filtering in treatment: 298288 INFO @ Mon, 03 Jun 2019 16:40:06: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 16:40:06: #1 finished! INFO @ Mon, 03 Jun 2019 16:40:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:40:06: #2 number of paired peaks: 1585 INFO @ Mon, 03 Jun 2019 16:40:06: start model_add_line... INFO @ Mon, 03 Jun 2019 16:40:06: start X-correlation... INFO @ Mon, 03 Jun 2019 16:40:06: #2 number of paired peaks: 1585 INFO @ Mon, 03 Jun 2019 16:40:06: start model_add_line... INFO @ Mon, 03 Jun 2019 16:40:06: start X-correlation... INFO @ Mon, 03 Jun 2019 16:40:06: end of X-cor INFO @ Mon, 03 Jun 2019 16:40:06: #2 finished! INFO @ Mon, 03 Jun 2019 16:40:06: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 16:40:06: #2 alternative fragment length(s) may be 93,126 bps INFO @ Mon, 03 Jun 2019 16:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10_model.r INFO @ Mon, 03 Jun 2019 16:40:06: end of X-cor INFO @ Mon, 03 Jun 2019 16:40:06: #2 finished! INFO @ Mon, 03 Jun 2019 16:40:06: #2 predicted fragment length is 93 bps INFO @ Mon, 03 Jun 2019 16:40:06: #2 alternative fragment length(s) may be 93,126 bps INFO @ Mon, 03 Jun 2019 16:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05_model.r INFO @ Mon, 03 Jun 2019 16:40:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:40:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:40:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:40:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:40:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.20_summits.bed INFO @ Mon, 03 Jun 2019 16:40:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:40:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:40:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.05_summits.bed INFO @ Mon, 03 Jun 2019 16:40:08: Done! INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650771/SRX4650771.10_summits.bed INFO @ Mon, 03 Jun 2019 16:40:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 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。