Job ID = 1297391 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:01:24 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 ) 2019-06-03T08:13:01 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 ) 2019-06-03T08:13:01 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 ) 2019-06-03T08:13:01 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 ) 2019-06-03T08:13:01 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 : 54,620,815 reads read : 109,241,630 reads written : 109,241,630 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: 00:18:46 54620815 reads; of these: 54620815 (100.00%) were paired; of these: 51771335 (94.78%) aligned concordantly 0 times 2269162 (4.15%) aligned concordantly exactly 1 time 580318 (1.06%) aligned concordantly >1 times ---- 51771335 pairs aligned concordantly 0 times; of these: 5849 (0.01%) aligned discordantly 1 time ---- 51765486 pairs aligned 0 times concordantly or discordantly; of these: 103530972 mates make up the pairs; of these: 102850850 (99.34%) aligned 0 times 277631 (0.27%) aligned exactly 1 time 402491 (0.39%) aligned >1 times 5.85% overall alignment rate Time searching: 00:18:46 Overall time: 00:18:46 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] 179946 / 2850921 = 0.0631 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 17:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.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 17:39:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:39:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.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 17:39:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:39:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.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 17:39:31: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:39:31: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:39:42: 1000000 INFO @ Mon, 03 Jun 2019 17:39:42: 1000000 INFO @ Mon, 03 Jun 2019 17:39:43: 1000000 INFO @ Mon, 03 Jun 2019 17:39:53: 2000000 INFO @ Mon, 03 Jun 2019 17:39:54: 2000000 INFO @ Mon, 03 Jun 2019 17:39:54: 2000000 INFO @ Mon, 03 Jun 2019 17:40:04: 3000000 INFO @ Mon, 03 Jun 2019 17:40:05: 3000000 INFO @ Mon, 03 Jun 2019 17:40:06: 3000000 INFO @ Mon, 03 Jun 2019 17:40:16: 4000000 INFO @ Mon, 03 Jun 2019 17:40:17: 4000000 INFO @ Mon, 03 Jun 2019 17:40:18: 4000000 INFO @ Mon, 03 Jun 2019 17:40:26: 5000000 INFO @ Mon, 03 Jun 2019 17:40:28: 5000000 INFO @ Mon, 03 Jun 2019 17:40:30: 5000000 INFO @ Mon, 03 Jun 2019 17:40:36: 6000000 INFO @ Mon, 03 Jun 2019 17:40:36: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:40:36: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:40:36: #1 total tags in treatment: 2669766 INFO @ Mon, 03 Jun 2019 17:40:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:36: #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 17:40:36: #1 tags after filtering in treatment: 2538211 INFO @ Mon, 03 Jun 2019 17:40:36: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:40:36: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:40:36: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 17:40:36: start model_add_line... INFO @ Mon, 03 Jun 2019 17:40:36: start X-correlation... INFO @ Mon, 03 Jun 2019 17:40:36: end of X-cor INFO @ Mon, 03 Jun 2019 17:40:36: #2 finished! INFO @ Mon, 03 Jun 2019 17:40:36: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:40:36: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 17:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10_model.r INFO @ Mon, 03 Jun 2019 17:40:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:40:38: 6000000 INFO @ Mon, 03 Jun 2019 17:40:39: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:40:39: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:40:39: #1 total tags in treatment: 2669766 INFO @ Mon, 03 Jun 2019 17:40:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:39: #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 17:40:39: #1 tags after filtering in treatment: 2538211 INFO @ Mon, 03 Jun 2019 17:40:39: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:40:39: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:40:39: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 17:40:39: start model_add_line... INFO @ Mon, 03 Jun 2019 17:40:39: start X-correlation... INFO @ Mon, 03 Jun 2019 17:40:39: end of X-cor INFO @ Mon, 03 Jun 2019 17:40:39: #2 finished! INFO @ Mon, 03 Jun 2019 17:40:39: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:40:39: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 17:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20_model.r INFO @ Mon, 03 Jun 2019 17:40:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:40:41: 6000000 INFO @ Mon, 03 Jun 2019 17:40:42: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 17:40:42: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 17:40:42: #1 total tags in treatment: 2669766 INFO @ Mon, 03 Jun 2019 17:40:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:40:42: #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 17:40:42: #1 tags after filtering in treatment: 2538211 INFO @ Mon, 03 Jun 2019 17:40:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:40:42: #1 finished! INFO @ Mon, 03 Jun 2019 17:40:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:40:42: #2 number of paired peaks: 1487 INFO @ Mon, 03 Jun 2019 17:40:42: start model_add_line... INFO @ Mon, 03 Jun 2019 17:40:42: start X-correlation... INFO @ Mon, 03 Jun 2019 17:40:42: end of X-cor INFO @ Mon, 03 Jun 2019 17:40:42: #2 finished! INFO @ Mon, 03 Jun 2019 17:40:42: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 17:40:42: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 17:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05_model.r INFO @ Mon, 03 Jun 2019 17:40:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:40:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:40:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:40:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.10_summits.bed INFO @ Mon, 03 Jun 2019 17:40:54: Done! pass1 - making usageList (10 chroms): 7 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.20_summits.bed INFO @ Mon, 03 Jun 2019 17:40:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650847/SRX4650847.05_summits.bed INFO @ Mon, 03 Jun 2019 17:40:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (370 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。