Job ID = 1297415 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:01:02 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 ) 2019-06-03T08:01:02 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 ) 2019-06-03T08:01:02 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 ) 2019-06-03T08:04:50 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 : 53,415,089 reads read : 106,830,178 reads written : 106,830,178 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: 00:11:57 53415089 reads; of these: 53415089 (100.00%) were paired; of these: 50595026 (94.72%) aligned concordantly 0 times 2230642 (4.18%) aligned concordantly exactly 1 time 589421 (1.10%) aligned concordantly >1 times ---- 50595026 pairs aligned concordantly 0 times; of these: 8700 (0.02%) aligned discordantly 1 time ---- 50586326 pairs aligned 0 times concordantly or discordantly; of these: 101172652 mates make up the pairs; of these: 100550064 (99.38%) aligned 0 times 243150 (0.24%) aligned exactly 1 time 379438 (0.38%) aligned >1 times 5.88% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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] 156134 / 2825060 = 0.0553 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 17:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.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 17:31:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:31:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.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 17:31:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:31:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.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 17:31:58: #1 read tag files... INFO @ Mon, 03 Jun 2019 17:31:58: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 17:32:05: 1000000 INFO @ Mon, 03 Jun 2019 17:32:05: 1000000 INFO @ Mon, 03 Jun 2019 17:32:06: 1000000 INFO @ Mon, 03 Jun 2019 17:32:11: 2000000 INFO @ Mon, 03 Jun 2019 17:32:13: 2000000 INFO @ Mon, 03 Jun 2019 17:32:13: 2000000 INFO @ Mon, 03 Jun 2019 17:32:18: 3000000 INFO @ Mon, 03 Jun 2019 17:32:20: 3000000 INFO @ Mon, 03 Jun 2019 17:32:21: 3000000 INFO @ Mon, 03 Jun 2019 17:32:24: 4000000 INFO @ Mon, 03 Jun 2019 17:32:27: 4000000 INFO @ Mon, 03 Jun 2019 17:32:28: 4000000 INFO @ Mon, 03 Jun 2019 17:32:31: 5000000 INFO @ Mon, 03 Jun 2019 17:32:34: 5000000 INFO @ Mon, 03 Jun 2019 17:32:35: 5000000 INFO @ Mon, 03 Jun 2019 17:32:37: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:32:37: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:32:37: #1 total tags in treatment: 2664204 INFO @ Mon, 03 Jun 2019 17:32:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:32:37: #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 17:32:37: #1 tags after filtering in treatment: 2531187 INFO @ Mon, 03 Jun 2019 17:32:37: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:32:37: #1 finished! INFO @ Mon, 03 Jun 2019 17:32:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:32:37: #2 number of paired peaks: 1464 INFO @ Mon, 03 Jun 2019 17:32:37: start model_add_line... INFO @ Mon, 03 Jun 2019 17:32:37: start X-correlation... INFO @ Mon, 03 Jun 2019 17:32:37: end of X-cor INFO @ Mon, 03 Jun 2019 17:32:37: #2 finished! INFO @ Mon, 03 Jun 2019 17:32:37: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:32:37: #2 alternative fragment length(s) may be 4,131,146 bps INFO @ Mon, 03 Jun 2019 17:32:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20_model.r INFO @ Mon, 03 Jun 2019 17:32:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:32:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:32:39: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:32:39: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:32:39: #1 total tags in treatment: 2664204 INFO @ Mon, 03 Jun 2019 17:32:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:32:39: #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 17:32:40: #1 tags after filtering in treatment: 2531187 INFO @ Mon, 03 Jun 2019 17:32:40: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:32:40: #1 finished! INFO @ Mon, 03 Jun 2019 17:32:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:32:40: #2 number of paired peaks: 1464 INFO @ Mon, 03 Jun 2019 17:32:40: start model_add_line... INFO @ Mon, 03 Jun 2019 17:32:40: start X-correlation... INFO @ Mon, 03 Jun 2019 17:32:40: end of X-cor INFO @ Mon, 03 Jun 2019 17:32:40: #2 finished! INFO @ Mon, 03 Jun 2019 17:32:40: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:32:40: #2 alternative fragment length(s) may be 4,131,146 bps INFO @ Mon, 03 Jun 2019 17:32:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05_model.r INFO @ Mon, 03 Jun 2019 17:32:40: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:32:42: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 17:32:42: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 17:32:42: #1 total tags in treatment: 2664204 INFO @ Mon, 03 Jun 2019 17:32:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 17:32:42: #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 17:32:42: #1 tags after filtering in treatment: 2531187 INFO @ Mon, 03 Jun 2019 17:32:42: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 17:32:42: #1 finished! INFO @ Mon, 03 Jun 2019 17:32:42: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 17:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 17:32:42: #2 number of paired peaks: 1464 INFO @ Mon, 03 Jun 2019 17:32:42: start model_add_line... INFO @ Mon, 03 Jun 2019 17:32:42: start X-correlation... INFO @ Mon, 03 Jun 2019 17:32:42: end of X-cor INFO @ Mon, 03 Jun 2019 17:32:42: #2 finished! INFO @ Mon, 03 Jun 2019 17:32:42: #2 predicted fragment length is 146 bps INFO @ Mon, 03 Jun 2019 17:32:42: #2 alternative fragment length(s) may be 4,131,146 bps INFO @ Mon, 03 Jun 2019 17:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10_model.r INFO @ Mon, 03 Jun 2019 17:32:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 17:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 17:32:45: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:32:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:32:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20_peaks.xls INFO @ Mon, 03 Jun 2019 17:32:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.20_summits.bed INFO @ Mon, 03 Jun 2019 17:32:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:32:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 17:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05_peaks.xls INFO @ Mon, 03 Jun 2019 17:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.05_summits.bed INFO @ Mon, 03 Jun 2019 17:32:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 17:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10_peaks.xls INFO @ Mon, 03 Jun 2019 17:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 17:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650850/SRX4650850.10_summits.bed INFO @ Mon, 03 Jun 2019 17:32:54: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (185 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。