Job ID = 4178443 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-12-05T03:41:12 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 ) 2019-12-05T03:43:35 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 : 18,171,780 reads read : 36,343,560 reads written : 36,343,560 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: 00:35:32 18171780 reads; of these: 18171780 (100.00%) were paired; of these: 4255230 (23.42%) aligned concordantly 0 times 12618669 (69.44%) aligned concordantly exactly 1 time 1297881 (7.14%) aligned concordantly >1 times ---- 4255230 pairs aligned concordantly 0 times; of these: 2592000 (60.91%) aligned discordantly 1 time ---- 1663230 pairs aligned 0 times concordantly or discordantly; of these: 3326460 mates make up the pairs; of these: 1990628 (59.84%) aligned 0 times 846194 (25.44%) aligned exactly 1 time 489638 (14.72%) aligned >1 times 94.52% overall alignment rate Time searching: 00:35:32 Overall time: 00:35:32 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 16 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] 491511 / 16439917 = 0.0299 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.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 13:42:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:42:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:42:49: 1000000 INFO @ Thu, 05 Dec 2019 13:42:59: 2000000 INFO @ Thu, 05 Dec 2019 13:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.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 13:43:09: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:43:09: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:43:09: 3000000 INFO @ Thu, 05 Dec 2019 13:43:20: 1000000 INFO @ Thu, 05 Dec 2019 13:43:20: 4000000 INFO @ Thu, 05 Dec 2019 13:43:32: 2000000 INFO @ Thu, 05 Dec 2019 13:43:32: 5000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:43:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.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 13:43:39: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:43:39: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:43:43: 3000000 INFO @ Thu, 05 Dec 2019 13:43:43: 6000000 INFO @ Thu, 05 Dec 2019 13:43:51: 1000000 INFO @ Thu, 05 Dec 2019 13:43:55: 4000000 INFO @ Thu, 05 Dec 2019 13:43:56: 7000000 INFO @ Thu, 05 Dec 2019 13:44:04: 2000000 INFO @ Thu, 05 Dec 2019 13:44:07: 5000000 INFO @ Thu, 05 Dec 2019 13:44:08: 8000000 INFO @ Thu, 05 Dec 2019 13:44:15: 3000000 INFO @ Thu, 05 Dec 2019 13:44:18: 6000000 INFO @ Thu, 05 Dec 2019 13:44:20: 9000000 INFO @ Thu, 05 Dec 2019 13:44:27: 4000000 INFO @ Thu, 05 Dec 2019 13:44:30: 7000000 INFO @ Thu, 05 Dec 2019 13:44:32: 10000000 INFO @ Thu, 05 Dec 2019 13:44:39: 5000000 INFO @ Thu, 05 Dec 2019 13:44:42: 8000000 INFO @ Thu, 05 Dec 2019 13:44:44: 11000000 INFO @ Thu, 05 Dec 2019 13:44:51: 6000000 INFO @ Thu, 05 Dec 2019 13:44:54: 9000000 INFO @ Thu, 05 Dec 2019 13:44:56: 12000000 INFO @ Thu, 05 Dec 2019 13:45:03: 7000000 INFO @ Thu, 05 Dec 2019 13:45:06: 10000000 INFO @ Thu, 05 Dec 2019 13:45:08: 13000000 INFO @ Thu, 05 Dec 2019 13:45:15: 8000000 INFO @ Thu, 05 Dec 2019 13:45:18: 11000000 INFO @ Thu, 05 Dec 2019 13:45:20: 14000000 INFO @ Thu, 05 Dec 2019 13:45:27: 9000000 INFO @ Thu, 05 Dec 2019 13:45:30: 12000000 INFO @ Thu, 05 Dec 2019 13:45:32: 15000000 INFO @ Thu, 05 Dec 2019 13:45:39: 10000000 INFO @ Thu, 05 Dec 2019 13:45:42: 13000000 INFO @ Thu, 05 Dec 2019 13:45:44: 16000000 INFO @ Thu, 05 Dec 2019 13:45:51: 11000000 INFO @ Thu, 05 Dec 2019 13:45:54: 14000000 INFO @ Thu, 05 Dec 2019 13:45:56: 17000000 INFO @ Thu, 05 Dec 2019 13:46:03: 12000000 INFO @ Thu, 05 Dec 2019 13:46:06: 15000000 INFO @ Thu, 05 Dec 2019 13:46:08: 18000000 INFO @ Thu, 05 Dec 2019 13:46:14: 13000000 INFO @ Thu, 05 Dec 2019 13:46:17: 16000000 INFO @ Thu, 05 Dec 2019 13:46:19: 19000000 INFO @ Thu, 05 Dec 2019 13:46:26: 14000000 INFO @ Thu, 05 Dec 2019 13:46:29: 17000000 INFO @ Thu, 05 Dec 2019 13:46:31: 20000000 INFO @ Thu, 05 Dec 2019 13:46:38: 15000000 INFO @ Thu, 05 Dec 2019 13:46:41: 18000000 INFO @ Thu, 05 Dec 2019 13:46:43: 21000000 INFO @ Thu, 05 Dec 2019 13:46:50: 16000000 INFO @ Thu, 05 Dec 2019 13:46:53: 19000000 INFO @ Thu, 05 Dec 2019 13:46:54: 22000000 INFO @ Thu, 05 Dec 2019 13:47:01: 17000000 INFO @ Thu, 05 Dec 2019 13:47:04: 20000000 INFO @ Thu, 05 Dec 2019 13:47:06: 23000000 INFO @ Thu, 05 Dec 2019 13:47:13: 18000000 INFO @ Thu, 05 Dec 2019 13:47:16: 21000000 INFO @ Thu, 05 Dec 2019 13:47:18: 24000000 INFO @ Thu, 05 Dec 2019 13:47:25: 19000000 INFO @ Thu, 05 Dec 2019 13:47:28: 22000000 INFO @ Thu, 05 Dec 2019 13:47:30: 25000000 INFO @ Thu, 05 Dec 2019 13:47:37: 20000000 INFO @ Thu, 05 Dec 2019 13:47:40: 23000000 INFO @ Thu, 05 Dec 2019 13:47:42: 26000000 INFO @ Thu, 05 Dec 2019 13:47:49: 21000000 INFO @ Thu, 05 Dec 2019 13:47:52: 24000000 INFO @ Thu, 05 Dec 2019 13:47:54: 27000000 INFO @ Thu, 05 Dec 2019 13:48:01: 22000000 INFO @ Thu, 05 Dec 2019 13:48:04: 25000000 INFO @ Thu, 05 Dec 2019 13:48:06: 28000000 INFO @ Thu, 05 Dec 2019 13:48:13: 23000000 INFO @ Thu, 05 Dec 2019 13:48:16: 26000000 INFO @ Thu, 05 Dec 2019 13:48:18: 29000000 INFO @ Thu, 05 Dec 2019 13:48:25: 24000000 INFO @ Thu, 05 Dec 2019 13:48:28: 27000000 INFO @ Thu, 05 Dec 2019 13:48:30: 30000000 INFO @ Thu, 05 Dec 2019 13:48:37: 25000000 INFO @ Thu, 05 Dec 2019 13:48:40: 28000000 INFO @ Thu, 05 Dec 2019 13:48:42: 31000000 INFO @ Thu, 05 Dec 2019 13:48:49: 26000000 INFO @ Thu, 05 Dec 2019 13:48:52: 29000000 INFO @ Thu, 05 Dec 2019 13:48:54: 32000000 INFO @ Thu, 05 Dec 2019 13:49:01: 27000000 INFO @ Thu, 05 Dec 2019 13:49:04: 30000000 INFO @ Thu, 05 Dec 2019 13:49:06: 33000000 INFO @ Thu, 05 Dec 2019 13:49:10: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 13:49:10: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 13:49:10: #1 total tags in treatment: 13512064 INFO @ Thu, 05 Dec 2019 13:49:10: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:49:10: #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 13:49:11: #1 tags after filtering in treatment: 10674745 INFO @ Thu, 05 Dec 2019 13:49:11: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Dec 2019 13:49:11: #1 finished! INFO @ Thu, 05 Dec 2019 13:49:11: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:49:12: #2 number of paired peaks: 8247 INFO @ Thu, 05 Dec 2019 13:49:12: start model_add_line... INFO @ Thu, 05 Dec 2019 13:49:12: start X-correlation... INFO @ Thu, 05 Dec 2019 13:49:12: end of X-cor INFO @ Thu, 05 Dec 2019 13:49:12: #2 finished! INFO @ Thu, 05 Dec 2019 13:49:12: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Dec 2019 13:49:12: #2 alternative fragment length(s) may be 3,300 bps INFO @ Thu, 05 Dec 2019 13:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05_model.r INFO @ Thu, 05 Dec 2019 13:49:12: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:49:13: 28000000 INFO @ Thu, 05 Dec 2019 13:49:16: 31000000 INFO @ Thu, 05 Dec 2019 13:49:24: 29000000 INFO @ Thu, 05 Dec 2019 13:49:27: 32000000 INFO @ Thu, 05 Dec 2019 13:49:35: 30000000 INFO @ Thu, 05 Dec 2019 13:49:38: 33000000 INFO @ Thu, 05 Dec 2019 13:49:42: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 13:49:42: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 13:49:42: #1 total tags in treatment: 13512064 INFO @ Thu, 05 Dec 2019 13:49:42: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:49:42: #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 13:49:42: #1 tags after filtering in treatment: 10674745 INFO @ Thu, 05 Dec 2019 13:49:42: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Dec 2019 13:49:42: #1 finished! INFO @ Thu, 05 Dec 2019 13:49:42: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:49:44: #2 number of paired peaks: 8247 INFO @ Thu, 05 Dec 2019 13:49:44: start model_add_line... INFO @ Thu, 05 Dec 2019 13:49:44: start X-correlation... INFO @ Thu, 05 Dec 2019 13:49:44: end of X-cor INFO @ Thu, 05 Dec 2019 13:49:44: #2 finished! INFO @ Thu, 05 Dec 2019 13:49:44: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Dec 2019 13:49:44: #2 alternative fragment length(s) may be 3,300 bps INFO @ Thu, 05 Dec 2019 13:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10_model.r INFO @ Thu, 05 Dec 2019 13:49:44: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:49:45: 31000000 INFO @ Thu, 05 Dec 2019 13:49:55: 32000000 INFO @ Thu, 05 Dec 2019 13:50:05: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Dec 2019 13:50:09: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 13:50:09: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 13:50:09: #1 total tags in treatment: 13512064 INFO @ Thu, 05 Dec 2019 13:50:09: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:50:09: #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 13:50:09: #1 tags after filtering in treatment: 10674745 INFO @ Thu, 05 Dec 2019 13:50:09: #1 Redundant rate of treatment: 0.21 INFO @ Thu, 05 Dec 2019 13:50:09: #1 finished! INFO @ Thu, 05 Dec 2019 13:50:09: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:50:11: #2 number of paired peaks: 8247 INFO @ Thu, 05 Dec 2019 13:50:11: start model_add_line... INFO @ Thu, 05 Dec 2019 13:50:11: start X-correlation... INFO @ Thu, 05 Dec 2019 13:50:11: end of X-cor INFO @ Thu, 05 Dec 2019 13:50:11: #2 finished! INFO @ Thu, 05 Dec 2019 13:50:11: #2 predicted fragment length is 300 bps INFO @ Thu, 05 Dec 2019 13:50:11: #2 alternative fragment length(s) may be 3,300 bps INFO @ Thu, 05 Dec 2019 13:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20_model.r INFO @ Thu, 05 Dec 2019 13:50:11: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:50:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:50:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:50:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:50:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.05_summits.bed INFO @ Thu, 05 Dec 2019 13:50:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2561 records, 4 fields): 167 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:50:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 05 Dec 2019 13:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.10_summits.bed INFO @ Thu, 05 Dec 2019 13:51:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:51:19: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:51:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117267/SRX4117267.20_summits.bed INFO @ Thu, 05 Dec 2019 13:51:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (757 records, 4 fields): 5 millis CompletedMACS2peakCalling