Job ID = 1299762 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:30:48 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 ) 2019-06-03T09:37:48 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 ) 2019-06-03T09:38:24 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 ) 2019-06-03T09:45:38 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 : 16,461,638 reads read : 32,923,276 reads written : 32,923,276 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: 00:44:17 16461638 reads; of these: 16461638 (100.00%) were paired; of these: 1789413 (10.87%) aligned concordantly 0 times 10172041 (61.79%) aligned concordantly exactly 1 time 4500184 (27.34%) aligned concordantly >1 times ---- 1789413 pairs aligned concordantly 0 times; of these: 143934 (8.04%) aligned discordantly 1 time ---- 1645479 pairs aligned 0 times concordantly or discordantly; of these: 3290958 mates make up the pairs; of these: 2727591 (82.88%) aligned 0 times 325617 (9.89%) aligned exactly 1 time 237750 (7.22%) aligned >1 times 91.72% overall alignment rate Time searching: 00:44:17 Overall time: 00:44:17 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] 1775976 / 14781201 = 0.1202 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 19:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.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 19:42:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:42:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.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 19:42:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:42:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.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 19:42:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:42:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:42:35: 1000000 INFO @ Mon, 03 Jun 2019 19:42:36: 1000000 INFO @ Mon, 03 Jun 2019 19:42:38: 1000000 INFO @ Mon, 03 Jun 2019 19:42:42: 2000000 INFO @ Mon, 03 Jun 2019 19:42:43: 2000000 INFO @ Mon, 03 Jun 2019 19:42:47: 2000000 INFO @ Mon, 03 Jun 2019 19:42:48: 3000000 INFO @ Mon, 03 Jun 2019 19:42:50: 3000000 INFO @ Mon, 03 Jun 2019 19:42:55: 4000000 INFO @ Mon, 03 Jun 2019 19:42:56: 3000000 INFO @ Mon, 03 Jun 2019 19:42:57: 4000000 INFO @ Mon, 03 Jun 2019 19:43:01: 5000000 INFO @ Mon, 03 Jun 2019 19:43:04: 5000000 INFO @ Mon, 03 Jun 2019 19:43:05: 4000000 INFO @ Mon, 03 Jun 2019 19:43:07: 6000000 INFO @ Mon, 03 Jun 2019 19:43:11: 6000000 INFO @ Mon, 03 Jun 2019 19:43:13: 5000000 INFO @ Mon, 03 Jun 2019 19:43:14: 7000000 INFO @ Mon, 03 Jun 2019 19:43:18: 7000000 INFO @ Mon, 03 Jun 2019 19:43:20: 8000000 INFO @ Mon, 03 Jun 2019 19:43:22: 6000000 INFO @ Mon, 03 Jun 2019 19:43:25: 8000000 INFO @ Mon, 03 Jun 2019 19:43:26: 9000000 INFO @ Mon, 03 Jun 2019 19:43:31: 7000000 INFO @ Mon, 03 Jun 2019 19:43:32: 9000000 INFO @ Mon, 03 Jun 2019 19:43:33: 10000000 INFO @ Mon, 03 Jun 2019 19:43:39: 10000000 INFO @ Mon, 03 Jun 2019 19:43:39: 11000000 INFO @ Mon, 03 Jun 2019 19:43:39: 8000000 INFO @ Mon, 03 Jun 2019 19:43:45: 12000000 INFO @ Mon, 03 Jun 2019 19:43:46: 11000000 INFO @ Mon, 03 Jun 2019 19:43:48: 9000000 INFO @ Mon, 03 Jun 2019 19:43:52: 13000000 INFO @ Mon, 03 Jun 2019 19:43:52: 12000000 INFO @ Mon, 03 Jun 2019 19:43:56: 10000000 INFO @ Mon, 03 Jun 2019 19:43:58: 14000000 INFO @ Mon, 03 Jun 2019 19:43:59: 13000000 INFO @ Mon, 03 Jun 2019 19:44:04: 11000000 INFO @ Mon, 03 Jun 2019 19:44:05: 15000000 INFO @ Mon, 03 Jun 2019 19:44:06: 14000000 INFO @ Mon, 03 Jun 2019 19:44:11: 16000000 INFO @ Mon, 03 Jun 2019 19:44:13: 15000000 INFO @ Mon, 03 Jun 2019 19:44:14: 12000000 INFO @ Mon, 03 Jun 2019 19:44:17: 17000000 INFO @ Mon, 03 Jun 2019 19:44:20: 16000000 INFO @ Mon, 03 Jun 2019 19:44:23: 13000000 INFO @ Mon, 03 Jun 2019 19:44:24: 18000000 INFO @ Mon, 03 Jun 2019 19:44:27: 17000000 INFO @ Mon, 03 Jun 2019 19:44:30: 19000000 INFO @ Mon, 03 Jun 2019 19:44:32: 14000000 INFO @ Mon, 03 Jun 2019 19:44:34: 18000000 INFO @ Mon, 03 Jun 2019 19:44:37: 20000000 INFO @ Mon, 03 Jun 2019 19:44:40: 15000000 INFO @ Mon, 03 Jun 2019 19:44:41: 19000000 INFO @ Mon, 03 Jun 2019 19:44:43: 21000000 INFO @ Mon, 03 Jun 2019 19:44:48: 20000000 INFO @ Mon, 03 Jun 2019 19:44:49: 16000000 INFO @ Mon, 03 Jun 2019 19:44:49: 22000000 INFO @ Mon, 03 Jun 2019 19:44:55: 21000000 INFO @ Mon, 03 Jun 2019 19:44:56: 23000000 INFO @ Mon, 03 Jun 2019 19:44:58: 17000000 INFO @ Mon, 03 Jun 2019 19:45:02: 22000000 INFO @ Mon, 03 Jun 2019 19:45:02: 24000000 INFO @ Mon, 03 Jun 2019 19:45:06: 18000000 INFO @ Mon, 03 Jun 2019 19:45:08: 25000000 INFO @ Mon, 03 Jun 2019 19:45:08: 23000000 INFO @ Mon, 03 Jun 2019 19:45:15: 19000000 INFO @ Mon, 03 Jun 2019 19:45:16: 24000000 INFO @ Mon, 03 Jun 2019 19:45:16: 26000000 INFO @ Mon, 03 Jun 2019 19:45:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:21: #1 total tags in treatment: 12904393 INFO @ Mon, 03 Jun 2019 19:45:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:21: #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 19:45:21: #1 tags after filtering in treatment: 11997161 INFO @ Mon, 03 Jun 2019 19:45:21: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 19:45:21: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:22: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 19:45:22: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 19:45:22: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:22: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:22: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:22: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:22: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 19:45:22: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 03 Jun 2019 19:45:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20_model.r INFO @ Mon, 03 Jun 2019 19:45:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:23: 25000000 INFO @ Mon, 03 Jun 2019 19:45:23: 20000000 INFO @ Mon, 03 Jun 2019 19:45:30: 26000000 INFO @ Mon, 03 Jun 2019 19:45:31: 21000000 INFO @ Mon, 03 Jun 2019 19:45:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:45:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:45:35: #1 total tags in treatment: 12904393 INFO @ Mon, 03 Jun 2019 19:45:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:45:35: #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 19:45:35: #1 tags after filtering in treatment: 11997161 INFO @ Mon, 03 Jun 2019 19:45:35: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 19:45:35: #1 finished! INFO @ Mon, 03 Jun 2019 19:45:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:45:36: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 19:45:36: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 19:45:36: start model_add_line... INFO @ Mon, 03 Jun 2019 19:45:36: start X-correlation... INFO @ Mon, 03 Jun 2019 19:45:36: end of X-cor INFO @ Mon, 03 Jun 2019 19:45:36: #2 finished! INFO @ Mon, 03 Jun 2019 19:45:36: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 19:45:36: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 03 Jun 2019 19:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10_model.r INFO @ Mon, 03 Jun 2019 19:45:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:45:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:45:41: 22000000 INFO @ Mon, 03 Jun 2019 19:45:50: 23000000 INFO @ Mon, 03 Jun 2019 19:45:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:45:58: 24000000 INFO @ Mon, 03 Jun 2019 19:46:07: 25000000 INFO @ Mon, 03 Jun 2019 19:46:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.20_summits.bed INFO @ Mon, 03 Jun 2019 19:46:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:15: 26000000 INFO @ Mon, 03 Jun 2019 19:46:21: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:46:21: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:46:21: #1 total tags in treatment: 12904393 INFO @ Mon, 03 Jun 2019 19:46:21: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:46:21: #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 19:46:21: #1 tags after filtering in treatment: 11997161 INFO @ Mon, 03 Jun 2019 19:46:21: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 19:46:21: #1 finished! INFO @ Mon, 03 Jun 2019 19:46:21: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:46:22: #2 number of paired peaks: 400 WARNING @ Mon, 03 Jun 2019 19:46:22: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Mon, 03 Jun 2019 19:46:22: start model_add_line... INFO @ Mon, 03 Jun 2019 19:46:22: start X-correlation... INFO @ Mon, 03 Jun 2019 19:46:22: end of X-cor INFO @ Mon, 03 Jun 2019 19:46:22: #2 finished! INFO @ Mon, 03 Jun 2019 19:46:22: #2 predicted fragment length is 102 bps INFO @ Mon, 03 Jun 2019 19:46:22: #2 alternative fragment length(s) may be 102 bps INFO @ Mon, 03 Jun 2019 19:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05_model.r INFO @ Mon, 03 Jun 2019 19:46:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.10_summits.bed INFO @ Mon, 03 Jun 2019 19:46:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1103 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474604/SRX474604.05_summits.bed INFO @ Mon, 03 Jun 2019 19:47:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1408 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。