Job ID = 1296905 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T07:48:51 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 : 41,571,708 reads read : 83,143,416 reads written : 83,143,416 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: 00:00:01 Multiseed full-index search: 00:11:23 41571708 reads; of these: 41571708 (100.00%) were paired; of these: 40647372 (97.78%) aligned concordantly 0 times 750876 (1.81%) aligned concordantly exactly 1 time 173460 (0.42%) aligned concordantly >1 times ---- 40647372 pairs aligned concordantly 0 times; of these: 6951 (0.02%) aligned discordantly 1 time ---- 40640421 pairs aligned 0 times concordantly or discordantly; of these: 81280842 mates make up the pairs; of these: 79838198 (98.23%) aligned 0 times 406019 (0.50%) aligned exactly 1 time 1036625 (1.28%) aligned >1 times 3.98% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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] 27522 / 927661 = 0.0297 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 17:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.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 17:09:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:09:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.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 17:09:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:09:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.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 17:09:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:09:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:09:12: 1000000 INFO @ Mon, 03 Jun 2019 17:09:13: 1000000 INFO @ Mon, 03 Jun 2019 17:09:15: 1000000 INFO @ Mon, 03 Jun 2019 17:09:19: 2000000 INFO @ Mon, 03 Jun 2019 17:09:21: 2000000 INFO @ Mon, 03 Jun 2019 17:09:24: 2000000 INFO @ Mon, 03 Jun 2019 17:09:25: 3000000 INFO @ Mon, 03 Jun 2019 17:09:27: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:27: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:27: #1 total tags in treatment: 896891 INFO @ Mon, 03 Jun 2019 17:09:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:27: #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 17:09:27: #1 tags after filtering in treatment: 876263 INFO @ Mon, 03 Jun 2019 17:09:27: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:09:27: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:27: #2 number of paired peaks: 1760 INFO @ Mon, 03 Jun 2019 17:09:27: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:27: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:27: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:27: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:27: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 17:09:27: #2 alternative fragment length(s) may be 163 bps INFO @ Mon, 03 Jun 2019 17:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20_model.r INFO @ Mon, 03 Jun 2019 17:09:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:27: 3000000 INFO @ Mon, 03 Jun 2019 17:09:29: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:29: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:29: #1 total tags in treatment: 896891 INFO @ Mon, 03 Jun 2019 17:09:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:29: #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 17:09:29: #1 tags after filtering in treatment: 876263 INFO @ Mon, 03 Jun 2019 17:09:29: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:09:29: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:29: #2 number of paired peaks: 1760 INFO @ Mon, 03 Jun 2019 17:09:29: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:29: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:29: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:29: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:29: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 17:09:29: #2 alternative fragment length(s) may be 163 bps INFO @ Mon, 03 Jun 2019 17:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10_model.r INFO @ Mon, 03 Jun 2019 17:09:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.20_summits.bed INFO @ Mon, 03 Jun 2019 17:09:32: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:09:32: 3000000 INFO @ Mon, 03 Jun 2019 17:09:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.10_summits.bed INFO @ Mon, 03 Jun 2019 17:09:34: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:09:34: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:09:34: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:09:34: #1 total tags in treatment: 896891 INFO @ Mon, 03 Jun 2019 17:09:34: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:09:34: #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 17:09:34: #1 tags after filtering in treatment: 876263 INFO @ Mon, 03 Jun 2019 17:09:34: #1 Redundant rate of treatment: 0.02 INFO @ Mon, 03 Jun 2019 17:09:34: #1 finished! INFO @ Mon, 03 Jun 2019 17:09:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:09:34: #2 number of paired peaks: 1760 INFO @ Mon, 03 Jun 2019 17:09:34: start model_add_line... INFO @ Mon, 03 Jun 2019 17:09:34: start X-correlation... INFO @ Mon, 03 Jun 2019 17:09:34: end of X-cor INFO @ Mon, 03 Jun 2019 17:09:34: #2 finished! INFO @ Mon, 03 Jun 2019 17:09:34: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 17:09:34: #2 alternative fragment length(s) may be 163 bps INFO @ Mon, 03 Jun 2019 17:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05_model.r INFO @ Mon, 03 Jun 2019 17:09:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:09:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650819/SRX4650819.05_summits.bed INFO @ Mon, 03 Jun 2019 17:09:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (254 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。