Job ID = 1294337 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:29:32 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 ) 2019-06-02T21:29:32 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 : 19,633,255 reads read : 39,266,510 reads written : 39,266,510 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: 00:24:35 19633255 reads; of these: 19633255 (100.00%) were paired; of these: 7741083 (39.43%) aligned concordantly 0 times 9700845 (49.41%) aligned concordantly exactly 1 time 2191327 (11.16%) aligned concordantly >1 times ---- 7741083 pairs aligned concordantly 0 times; of these: 10995 (0.14%) aligned discordantly 1 time ---- 7730088 pairs aligned 0 times concordantly or discordantly; of these: 15460176 mates make up the pairs; of these: 15205366 (98.35%) aligned 0 times 192299 (1.24%) aligned exactly 1 time 62511 (0.40%) aligned >1 times 61.28% overall alignment rate Time searching: 00:24:35 Overall time: 00:24:35 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 12 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] 3407574 / 11894552 = 0.2865 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 07:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.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 07:03:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.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 07:03:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.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 07:03:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:09: 1000000 INFO @ Mon, 03 Jun 2019 07:03:09: 1000000 INFO @ Mon, 03 Jun 2019 07:03:09: 1000000 INFO @ Mon, 03 Jun 2019 07:03:16: 2000000 INFO @ Mon, 03 Jun 2019 07:03:16: 2000000 INFO @ Mon, 03 Jun 2019 07:03:16: 2000000 INFO @ Mon, 03 Jun 2019 07:03:23: 3000000 INFO @ Mon, 03 Jun 2019 07:03:23: 3000000 INFO @ Mon, 03 Jun 2019 07:03:24: 3000000 INFO @ Mon, 03 Jun 2019 07:03:30: 4000000 INFO @ Mon, 03 Jun 2019 07:03:31: 4000000 INFO @ Mon, 03 Jun 2019 07:03:31: 4000000 INFO @ Mon, 03 Jun 2019 07:03:37: 5000000 INFO @ Mon, 03 Jun 2019 07:03:38: 5000000 INFO @ Mon, 03 Jun 2019 07:03:38: 5000000 INFO @ Mon, 03 Jun 2019 07:03:45: 6000000 INFO @ Mon, 03 Jun 2019 07:03:45: 6000000 INFO @ Mon, 03 Jun 2019 07:03:46: 6000000 INFO @ Mon, 03 Jun 2019 07:03:52: 7000000 INFO @ Mon, 03 Jun 2019 07:03:53: 7000000 INFO @ Mon, 03 Jun 2019 07:03:53: 7000000 INFO @ Mon, 03 Jun 2019 07:03:59: 8000000 INFO @ Mon, 03 Jun 2019 07:04:01: 8000000 INFO @ Mon, 03 Jun 2019 07:04:01: 8000000 INFO @ Mon, 03 Jun 2019 07:04:07: 9000000 INFO @ Mon, 03 Jun 2019 07:04:09: 9000000 INFO @ Mon, 03 Jun 2019 07:04:09: 9000000 INFO @ Mon, 03 Jun 2019 07:04:14: 10000000 INFO @ Mon, 03 Jun 2019 07:04:16: 10000000 INFO @ Mon, 03 Jun 2019 07:04:17: 10000000 INFO @ Mon, 03 Jun 2019 07:04:21: 11000000 INFO @ Mon, 03 Jun 2019 07:04:24: 11000000 INFO @ Mon, 03 Jun 2019 07:04:24: 11000000 INFO @ Mon, 03 Jun 2019 07:04:28: 12000000 INFO @ Mon, 03 Jun 2019 07:04:32: 12000000 INFO @ Mon, 03 Jun 2019 07:04:32: 12000000 INFO @ Mon, 03 Jun 2019 07:04:35: 13000000 INFO @ Mon, 03 Jun 2019 07:04:40: 13000000 INFO @ Mon, 03 Jun 2019 07:04:40: 13000000 INFO @ Mon, 03 Jun 2019 07:04:42: 14000000 INFO @ Mon, 03 Jun 2019 07:04:47: 14000000 INFO @ Mon, 03 Jun 2019 07:04:48: 14000000 INFO @ Mon, 03 Jun 2019 07:04:50: 15000000 INFO @ Mon, 03 Jun 2019 07:04:55: 15000000 INFO @ Mon, 03 Jun 2019 07:04:56: 15000000 INFO @ Mon, 03 Jun 2019 07:04:57: 16000000 INFO @ Mon, 03 Jun 2019 07:05:03: 16000000 INFO @ Mon, 03 Jun 2019 07:05:03: 16000000 INFO @ Mon, 03 Jun 2019 07:05:04: 17000000 INFO @ Mon, 03 Jun 2019 07:05:06: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:05:06: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:05:06: #1 total tags in treatment: 8485723 INFO @ Mon, 03 Jun 2019 07:05:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:05:06: #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 07:05:06: #1 tags after filtering in treatment: 7321835 INFO @ Mon, 03 Jun 2019 07:05:06: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 07:05:06: #1 finished! INFO @ Mon, 03 Jun 2019 07:05:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:05:07: #2 number of paired peaks: 1924 INFO @ Mon, 03 Jun 2019 07:05:07: start model_add_line... INFO @ Mon, 03 Jun 2019 07:05:07: start X-correlation... INFO @ Mon, 03 Jun 2019 07:05:07: end of X-cor INFO @ Mon, 03 Jun 2019 07:05:07: #2 finished! INFO @ Mon, 03 Jun 2019 07:05:07: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 07:05:07: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 03 Jun 2019 07:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05_model.r INFO @ Mon, 03 Jun 2019 07:05:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:05:10: 17000000 INFO @ Mon, 03 Jun 2019 07:05:11: 17000000 INFO @ Mon, 03 Jun 2019 07:05:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:05:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:05:12: #1 total tags in treatment: 8485723 INFO @ Mon, 03 Jun 2019 07:05:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:05:12: #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 07:05:12: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:05:12: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:05:12: #1 total tags in treatment: 8485723 INFO @ Mon, 03 Jun 2019 07:05:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:05:12: #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 07:05:12: #1 tags after filtering in treatment: 7321835 INFO @ Mon, 03 Jun 2019 07:05:12: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 07:05:12: #1 finished! INFO @ Mon, 03 Jun 2019 07:05:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:05:13: #1 tags after filtering in treatment: 7321835 INFO @ Mon, 03 Jun 2019 07:05:13: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 07:05:13: #1 finished! INFO @ Mon, 03 Jun 2019 07:05:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:05:13: #2 number of paired peaks: 1924 INFO @ Mon, 03 Jun 2019 07:05:13: start model_add_line... INFO @ Mon, 03 Jun 2019 07:05:13: start X-correlation... INFO @ Mon, 03 Jun 2019 07:05:13: end of X-cor INFO @ Mon, 03 Jun 2019 07:05:13: #2 finished! INFO @ Mon, 03 Jun 2019 07:05:13: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 07:05:13: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 03 Jun 2019 07:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10_model.r INFO @ Mon, 03 Jun 2019 07:05:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:05:13: #2 number of paired peaks: 1924 INFO @ Mon, 03 Jun 2019 07:05:13: start model_add_line... INFO @ Mon, 03 Jun 2019 07:05:14: start X-correlation... INFO @ Mon, 03 Jun 2019 07:05:14: end of X-cor INFO @ Mon, 03 Jun 2019 07:05:14: #2 finished! INFO @ Mon, 03 Jun 2019 07:05:14: #2 predicted fragment length is 139 bps INFO @ Mon, 03 Jun 2019 07:05:14: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 03 Jun 2019 07:05:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20_model.r INFO @ Mon, 03 Jun 2019 07:05:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:05:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:05:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:05:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:05:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:05:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:05:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:05:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.05_summits.bed INFO @ Mon, 03 Jun 2019 07:05:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12753 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.20_summits.bed INFO @ Mon, 03 Jun 2019 07:05:48: Done! INFO @ Mon, 03 Jun 2019 07:05:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252227/SRX252227.10_summits.bed INFO @ Mon, 03 Jun 2019 07:05:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3380 records, 4 fields): 10 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6356 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。