Job ID = 1298109 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:14:32 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 : 41,573,194 reads read : 83,146,388 reads written : 83,146,388 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: 00:12:30 41573194 reads; of these: 41573194 (100.00%) were paired; of these: 38681655 (93.04%) aligned concordantly 0 times 2296773 (5.52%) aligned concordantly exactly 1 time 594766 (1.43%) aligned concordantly >1 times ---- 38681655 pairs aligned concordantly 0 times; of these: 11878 (0.03%) aligned discordantly 1 time ---- 38669777 pairs aligned 0 times concordantly or discordantly; of these: 77339554 mates make up the pairs; of these: 76197101 (98.52%) aligned 0 times 471186 (0.61%) aligned exactly 1 time 671267 (0.87%) aligned >1 times 8.36% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 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] 155091 / 2894754 = 0.0536 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 17:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.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 17:41:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.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 17:41:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.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 17:41:59: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:41:59: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:42:08: 1000000 INFO @ Mon, 03 Jun 2019 17:42:10: 1000000 INFO @ Mon, 03 Jun 2019 17:42:11: 1000000 INFO @ Mon, 03 Jun 2019 17:42:17: 2000000 INFO @ Mon, 03 Jun 2019 17:42:21: 2000000 INFO @ Mon, 03 Jun 2019 17:42:21: 2000000 INFO @ Mon, 03 Jun 2019 17:42:26: 3000000 INFO @ Mon, 03 Jun 2019 17:42:31: 3000000 INFO @ Mon, 03 Jun 2019 17:42:33: 3000000 INFO @ Mon, 03 Jun 2019 17:42:34: 4000000 INFO @ Mon, 03 Jun 2019 17:42:42: 4000000 INFO @ Mon, 03 Jun 2019 17:42:43: 5000000 INFO @ Mon, 03 Jun 2019 17:42:43: 4000000 INFO @ Mon, 03 Jun 2019 17:42:51: 6000000 INFO @ Mon, 03 Jun 2019 17:42:52: 5000000 INFO @ Mon, 03 Jun 2019 17:42:54: 5000000 INFO @ Mon, 03 Jun 2019 17:42:56: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:42:56: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:42:56: #1 total tags in treatment: 2736610 INFO @ Mon, 03 Jun 2019 17:42:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:42:56: #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 17:42:56: #1 tags after filtering in treatment: 2597200 INFO @ Mon, 03 Jun 2019 17:42:56: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:42:56: #1 finished! INFO @ Mon, 03 Jun 2019 17:42:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:42:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:42:56: #2 number of paired peaks: 2182 INFO @ Mon, 03 Jun 2019 17:42:56: start model_add_line... INFO @ Mon, 03 Jun 2019 17:42:56: start X-correlation... INFO @ Mon, 03 Jun 2019 17:42:56: end of X-cor INFO @ Mon, 03 Jun 2019 17:42:56: #2 finished! INFO @ Mon, 03 Jun 2019 17:42:56: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:42:56: #2 alternative fragment length(s) may be 3,147 bps INFO @ Mon, 03 Jun 2019 17:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20_model.r INFO @ Mon, 03 Jun 2019 17:42:56: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:43:02: 6000000 INFO @ Mon, 03 Jun 2019 17:43:04: 6000000 INFO @ Mon, 03 Jun 2019 17:43:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:43:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:43:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:43:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.20_summits.bed INFO @ Mon, 03 Jun 2019 17:43:09: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:43:09: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:43:09: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:43:09: #1 total tags in treatment: 2736610 INFO @ Mon, 03 Jun 2019 17:43:09: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:43:09: #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 17:43:09: #1 tags after filtering in treatment: 2597200 INFO @ Mon, 03 Jun 2019 17:43:09: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:43:09: #1 finished! INFO @ Mon, 03 Jun 2019 17:43:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:43:09: #2 number of paired peaks: 2182 INFO @ Mon, 03 Jun 2019 17:43:09: start model_add_line... INFO @ Mon, 03 Jun 2019 17:43:09: start X-correlation... INFO @ Mon, 03 Jun 2019 17:43:09: end of X-cor INFO @ Mon, 03 Jun 2019 17:43:09: #2 finished! INFO @ Mon, 03 Jun 2019 17:43:09: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:43:09: #2 alternative fragment length(s) may be 3,147 bps INFO @ Mon, 03 Jun 2019 17:43:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10_model.r INFO @ Mon, 03 Jun 2019 17:43:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:43:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:43:11: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:43:11: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:43:11: #1 total tags in treatment: 2736610 INFO @ Mon, 03 Jun 2019 17:43:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:43:11: #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 17:43:11: #1 tags after filtering in treatment: 2597200 INFO @ Mon, 03 Jun 2019 17:43:11: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:43:11: #1 finished! INFO @ Mon, 03 Jun 2019 17:43:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:43:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:43:11: #2 number of paired peaks: 2182 INFO @ Mon, 03 Jun 2019 17:43:11: start model_add_line... INFO @ Mon, 03 Jun 2019 17:43:11: start X-correlation... INFO @ Mon, 03 Jun 2019 17:43:11: end of X-cor INFO @ Mon, 03 Jun 2019 17:43:11: #2 finished! INFO @ Mon, 03 Jun 2019 17:43:11: #2 predicted fragment length is 147 bps INFO @ Mon, 03 Jun 2019 17:43:11: #2 alternative fragment length(s) may be 3,147 bps INFO @ Mon, 03 Jun 2019 17:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05_model.r INFO @ Mon, 03 Jun 2019 17:43:11: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:43:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:43:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.10_summits.bed INFO @ Mon, 03 Jun 2019 17:43:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:43:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:43:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:43:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650885/SRX4650885.05_summits.bed INFO @ Mon, 03 Jun 2019 17:43:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (477 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。