Job ID = 4178464 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T03:38:27 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 ) 2019-12-05T03:44:11 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2019-12-05T03:44:11 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 25,238,226 reads read : 50,476,452 reads written : 50,476,452 rm: cannot remove ‘[DSE]RR*’: 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: 00:21:42 25238226 reads; of these: 25238226 (100.00%) were paired; of these: 16094222 (63.77%) aligned concordantly 0 times 7849446 (31.10%) aligned concordantly exactly 1 time 1294558 (5.13%) aligned concordantly >1 times ---- 16094222 pairs aligned concordantly 0 times; of these: 324669 (2.02%) aligned discordantly 1 time ---- 15769553 pairs aligned 0 times concordantly or discordantly; of these: 31539106 mates make up the pairs; of these: 30950100 (98.13%) aligned 0 times 332597 (1.05%) aligned exactly 1 time 256409 (0.81%) aligned >1 times 38.68% overall alignment rate Time searching: 00:21:42 Overall time: 00:21:42 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] 1257799 / 9432285 = 0.1334 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.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 @ Thu, 05 Dec 2019 13:14:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:14:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:14:47: 1000000 INFO @ Thu, 05 Dec 2019 13:14:53: 2000000 INFO @ Thu, 05 Dec 2019 13:15:00: 3000000 INFO @ Thu, 05 Dec 2019 13:15:06: 4000000 INFO @ Thu, 05 Dec 2019 13:15:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.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 @ Thu, 05 Dec 2019 13:15:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:15:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:15:13: 5000000 INFO @ Thu, 05 Dec 2019 13:15:18: 1000000 INFO @ Thu, 05 Dec 2019 13:15:20: 6000000 INFO @ Thu, 05 Dec 2019 13:15:25: 2000000 INFO @ Thu, 05 Dec 2019 13:15:27: 7000000 INFO @ Thu, 05 Dec 2019 13:15:32: 3000000 INFO @ Thu, 05 Dec 2019 13:15:34: 8000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:15:39: 4000000 INFO @ Thu, 05 Dec 2019 13:15:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.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 @ Thu, 05 Dec 2019 13:15:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:15:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:15:41: 9000000 INFO @ Thu, 05 Dec 2019 13:15:47: 5000000 INFO @ Thu, 05 Dec 2019 13:15:48: 1000000 INFO @ Thu, 05 Dec 2019 13:15:48: 10000000 INFO @ Thu, 05 Dec 2019 13:15:54: 6000000 INFO @ Thu, 05 Dec 2019 13:15:54: 2000000 INFO @ Thu, 05 Dec 2019 13:15:56: 11000000 INFO @ Thu, 05 Dec 2019 13:16:02: 3000000 INFO @ Thu, 05 Dec 2019 13:16:02: 7000000 INFO @ Thu, 05 Dec 2019 13:16:03: 12000000 INFO @ Thu, 05 Dec 2019 13:16:08: 4000000 INFO @ Thu, 05 Dec 2019 13:16:09: 8000000 INFO @ Thu, 05 Dec 2019 13:16:11: 13000000 INFO @ Thu, 05 Dec 2019 13:16:15: 5000000 INFO @ Thu, 05 Dec 2019 13:16:17: 9000000 INFO @ Thu, 05 Dec 2019 13:16:18: 14000000 INFO @ Thu, 05 Dec 2019 13:16:22: 6000000 INFO @ Thu, 05 Dec 2019 13:16:24: 10000000 INFO @ Thu, 05 Dec 2019 13:16:26: 15000000 INFO @ Thu, 05 Dec 2019 13:16:29: 7000000 INFO @ Thu, 05 Dec 2019 13:16:32: 11000000 INFO @ Thu, 05 Dec 2019 13:16:34: 16000000 INFO @ Thu, 05 Dec 2019 13:16:36: 8000000 INFO @ Thu, 05 Dec 2019 13:16:40: 12000000 INFO @ Thu, 05 Dec 2019 13:16:41: 17000000 INFO @ Thu, 05 Dec 2019 13:16:41: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:16:41: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:16:41: #1 total tags in treatment: 7935333 INFO @ Thu, 05 Dec 2019 13:16:41: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:16:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:16:41: #1 tags after filtering in treatment: 6480475 INFO @ Thu, 05 Dec 2019 13:16:41: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Dec 2019 13:16:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:16:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:16:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:16:42: #2 number of paired peaks: 4237 INFO @ Thu, 05 Dec 2019 13:16:42: start model_add_line... INFO @ Thu, 05 Dec 2019 13:16:42: start X-correlation... INFO @ Thu, 05 Dec 2019 13:16:42: end of X-cor INFO @ Thu, 05 Dec 2019 13:16:42: #2 finished! INFO @ Thu, 05 Dec 2019 13:16:42: #2 predicted fragment length is 176 bps INFO @ Thu, 05 Dec 2019 13:16:42: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 05 Dec 2019 13:16:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05_model.r INFO @ Thu, 05 Dec 2019 13:16:43: 9000000 INFO @ Thu, 05 Dec 2019 13:16:43: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:16:47: 13000000 INFO @ Thu, 05 Dec 2019 13:16:49: 10000000 INFO @ Thu, 05 Dec 2019 13:16:53: 14000000 INFO @ Thu, 05 Dec 2019 13:16:56: 11000000 INFO @ Thu, 05 Dec 2019 13:17:01: 15000000 INFO @ Thu, 05 Dec 2019 13:17:03: 12000000 INFO @ Thu, 05 Dec 2019 13:17:08: 16000000 INFO @ Thu, 05 Dec 2019 13:17:09: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:17:10: 13000000 INFO @ Thu, 05 Dec 2019 13:17:15: 17000000 INFO @ Thu, 05 Dec 2019 13:17:15: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:17:15: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:17:15: #1 total tags in treatment: 7935333 INFO @ Thu, 05 Dec 2019 13:17:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:17:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:17:15: #1 tags after filtering in treatment: 6480475 INFO @ Thu, 05 Dec 2019 13:17:15: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Dec 2019 13:17:15: #1 finished! INFO @ Thu, 05 Dec 2019 13:17:15: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:17:16: #2 number of paired peaks: 4237 INFO @ Thu, 05 Dec 2019 13:17:16: start model_add_line... INFO @ Thu, 05 Dec 2019 13:17:16: start X-correlation... INFO @ Thu, 05 Dec 2019 13:17:16: end of X-cor INFO @ Thu, 05 Dec 2019 13:17:16: #2 finished! INFO @ Thu, 05 Dec 2019 13:17:16: #2 predicted fragment length is 176 bps INFO @ Thu, 05 Dec 2019 13:17:16: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 05 Dec 2019 13:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10_model.r INFO @ Thu, 05 Dec 2019 13:17:16: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:17:16: 14000000 INFO @ Thu, 05 Dec 2019 13:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.05_summits.bed INFO @ Thu, 05 Dec 2019 13:17:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1907 records, 4 fields): 262 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:17:23: 15000000 INFO @ Thu, 05 Dec 2019 13:17:29: 16000000 INFO @ Thu, 05 Dec 2019 13:17:35: 17000000 INFO @ Thu, 05 Dec 2019 13:17:36: #1 tag size is determined as 79 bps INFO @ Thu, 05 Dec 2019 13:17:36: #1 tag size = 79 INFO @ Thu, 05 Dec 2019 13:17:36: #1 total tags in treatment: 7935333 INFO @ Thu, 05 Dec 2019 13:17:36: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:17:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:17:36: #1 tags after filtering in treatment: 6480475 INFO @ Thu, 05 Dec 2019 13:17:36: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 05 Dec 2019 13:17:36: #1 finished! INFO @ Thu, 05 Dec 2019 13:17:36: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:17:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:17:36: #2 number of paired peaks: 4237 INFO @ Thu, 05 Dec 2019 13:17:36: start model_add_line... INFO @ Thu, 05 Dec 2019 13:17:37: start X-correlation... INFO @ Thu, 05 Dec 2019 13:17:37: end of X-cor INFO @ Thu, 05 Dec 2019 13:17:37: #2 finished! INFO @ Thu, 05 Dec 2019 13:17:37: #2 predicted fragment length is 176 bps INFO @ Thu, 05 Dec 2019 13:17:37: #2 alternative fragment length(s) may be 4,176 bps INFO @ Thu, 05 Dec 2019 13:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20_model.r INFO @ Thu, 05 Dec 2019 13:17:37: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:17:42: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.10_summits.bed INFO @ Thu, 05 Dec 2019 13:17:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1261 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:18:03: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5462367/SRX5462367.20_summits.bed INFO @ Thu, 05 Dec 2019 13:18:10: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (737 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。