Job ID = 1295165 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T03:20:50 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 ) 2019-06-03T03:20:50 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 : 15,661,916 reads read : 31,323,832 reads written : 31,323,832 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: 00:39:10 15661916 reads; of these: 15661916 (100.00%) were paired; of these: 9563289 (61.06%) aligned concordantly 0 times 4242313 (27.09%) aligned concordantly exactly 1 time 1856314 (11.85%) aligned concordantly >1 times ---- 9563289 pairs aligned concordantly 0 times; of these: 70800 (0.74%) aligned discordantly 1 time ---- 9492489 pairs aligned 0 times concordantly or discordantly; of these: 18984978 mates make up the pairs; of these: 14505586 (76.41%) aligned 0 times 1236102 (6.51%) aligned exactly 1 time 3243290 (17.08%) aligned >1 times 53.69% overall alignment rate Time searching: 00:39:10 Overall time: 00:39:10 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_sort_core] merging from 8 files... [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] 4444934 / 6135535 = 0.7245 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 13:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.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 13:08:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:08:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.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 13:08:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:08:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.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 13:08:47: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:08:47: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:08:54: 1000000 INFO @ Mon, 03 Jun 2019 13:08:54: 1000000 INFO @ Mon, 03 Jun 2019 13:08:56: 1000000 INFO @ Mon, 03 Jun 2019 13:09:00: 2000000 INFO @ Mon, 03 Jun 2019 13:09:01: 2000000 INFO @ Mon, 03 Jun 2019 13:09:04: 2000000 INFO @ Mon, 03 Jun 2019 13:09:06: 3000000 INFO @ Mon, 03 Jun 2019 13:09:08: 3000000 INFO @ Mon, 03 Jun 2019 13:09:12: 4000000 INFO @ Mon, 03 Jun 2019 13:09:13: 3000000 INFO @ Mon, 03 Jun 2019 13:09:14: 4000000 INFO @ Mon, 03 Jun 2019 13:09:19: 5000000 INFO @ Mon, 03 Jun 2019 13:09:21: 4000000 INFO @ Mon, 03 Jun 2019 13:09:22: 5000000 INFO @ Mon, 03 Jun 2019 13:09:26: 6000000 INFO @ Mon, 03 Jun 2019 13:09:29: 6000000 INFO @ Mon, 03 Jun 2019 13:09:30: 5000000 INFO @ Mon, 03 Jun 2019 13:09:32: 7000000 INFO @ Mon, 03 Jun 2019 13:09:35: 7000000 INFO @ Mon, 03 Jun 2019 13:09:38: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 13:09:38: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 13:09:38: #1 total tags in treatment: 1697856 INFO @ Mon, 03 Jun 2019 13:09:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:09:38: #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 13:09:38: #1 tags after filtering in treatment: 1548990 INFO @ Mon, 03 Jun 2019 13:09:38: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 13:09:38: #1 finished! INFO @ Mon, 03 Jun 2019 13:09:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:09:38: #2 number of paired peaks: 4402 INFO @ Mon, 03 Jun 2019 13:09:38: start model_add_line... INFO @ Mon, 03 Jun 2019 13:09:38: start X-correlation... INFO @ Mon, 03 Jun 2019 13:09:38: end of X-cor INFO @ Mon, 03 Jun 2019 13:09:38: #2 finished! INFO @ Mon, 03 Jun 2019 13:09:38: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 13:09:38: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 13:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10_model.r INFO @ Mon, 03 Jun 2019 13:09:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:09:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:09:38: 6000000 INFO @ Mon, 03 Jun 2019 13:09:41: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 13:09:41: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 13:09:41: #1 total tags in treatment: 1697856 INFO @ Mon, 03 Jun 2019 13:09:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:09:41: #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 13:09:41: #1 tags after filtering in treatment: 1548990 INFO @ Mon, 03 Jun 2019 13:09:41: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 13:09:41: #1 finished! INFO @ Mon, 03 Jun 2019 13:09:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:09:41: #2 number of paired peaks: 4402 INFO @ Mon, 03 Jun 2019 13:09:41: start model_add_line... INFO @ Mon, 03 Jun 2019 13:09:41: start X-correlation... INFO @ Mon, 03 Jun 2019 13:09:41: end of X-cor INFO @ Mon, 03 Jun 2019 13:09:41: #2 finished! INFO @ Mon, 03 Jun 2019 13:09:41: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 13:09:41: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 13:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20_model.r INFO @ Mon, 03 Jun 2019 13:09:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:09:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.10_summits.bed INFO @ Mon, 03 Jun 2019 13:09:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1286 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:09:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:09:47: 7000000 INFO @ Mon, 03 Jun 2019 13:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.20_summits.bed INFO @ Mon, 03 Jun 2019 13:09:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:09:55: #1 tag size is determined as 40 bps INFO @ Mon, 03 Jun 2019 13:09:55: #1 tag size = 40 INFO @ Mon, 03 Jun 2019 13:09:55: #1 total tags in treatment: 1697856 INFO @ Mon, 03 Jun 2019 13:09:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:09:55: #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 13:09:55: #1 tags after filtering in treatment: 1548990 INFO @ Mon, 03 Jun 2019 13:09:55: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 13:09:55: #1 finished! INFO @ Mon, 03 Jun 2019 13:09:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:09:55: #2 number of paired peaks: 4402 INFO @ Mon, 03 Jun 2019 13:09:55: start model_add_line... INFO @ Mon, 03 Jun 2019 13:09:55: start X-correlation... INFO @ Mon, 03 Jun 2019 13:09:55: end of X-cor INFO @ Mon, 03 Jun 2019 13:09:55: #2 finished! INFO @ Mon, 03 Jun 2019 13:09:55: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 13:09:55: #2 alternative fragment length(s) may be 112 bps INFO @ Mon, 03 Jun 2019 13:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05_model.r INFO @ Mon, 03 Jun 2019 13:09:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:09:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 13:10:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3287356/SRX3287356.05_summits.bed INFO @ Mon, 03 Jun 2019 13:10:03: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (2679 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。