Job ID = 1299938 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:40:40 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 ) 2019-06-03T09:40:40 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 ) 2019-06-03T09:40:40 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 ) 2019-06-03T09:40:40 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T09:40:40 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading inform004C) ) 2019-06-03T09:40:40 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 ) 2019-06-03T09:42:54 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 : 20,610,707 reads read : 41,221,414 reads written : 41,221,414 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: 01:00:36 20610707 reads; of these: 20610707 (100.00%) were paired; of these: 2147361 (10.42%) aligned concordantly 0 times 13114023 (63.63%) aligned concordantly exactly 1 time 5349323 (25.95%) aligned concordantly >1 times ---- 2147361 pairs aligned concordantly 0 times; of these: 57522 (2.68%) aligned discordantly 1 time ---- 2089839 pairs aligned 0 times concordantly or discordantly; of these: 4179678 mates make up the pairs; of these: 3637038 (87.02%) aligned 0 times 375854 (8.99%) aligned exactly 1 time 166786 (3.99%) aligned >1 times 91.18% overall alignment rate Time searching: 01:00:36 Overall time: 01:00:36 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] 3989790 / 18485114 = 0.2158 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 20:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.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 20:09:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.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 20:09:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.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 20:09:12: #1 read tag files... INFO @ Mon, 03 Jun 2019 20:09:12: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 20:09:20: 1000000 INFO @ Mon, 03 Jun 2019 20:09:22: 1000000 INFO @ Mon, 03 Jun 2019 20:09:22: 1000000 INFO @ Mon, 03 Jun 2019 20:09:29: 2000000 INFO @ Mon, 03 Jun 2019 20:09:32: 2000000 INFO @ Mon, 03 Jun 2019 20:09:32: 2000000 INFO @ Mon, 03 Jun 2019 20:09:37: 3000000 INFO @ Mon, 03 Jun 2019 20:09:42: 3000000 INFO @ Mon, 03 Jun 2019 20:09:42: 3000000 INFO @ Mon, 03 Jun 2019 20:09:46: 4000000 INFO @ Mon, 03 Jun 2019 20:09:52: 4000000 INFO @ Mon, 03 Jun 2019 20:09:53: 4000000 INFO @ Mon, 03 Jun 2019 20:09:55: 5000000 INFO @ Mon, 03 Jun 2019 20:10:02: 5000000 INFO @ Mon, 03 Jun 2019 20:10:03: 6000000 INFO @ Mon, 03 Jun 2019 20:10:04: 5000000 INFO @ Mon, 03 Jun 2019 20:10:12: 7000000 INFO @ Mon, 03 Jun 2019 20:10:12: 6000000 INFO @ Mon, 03 Jun 2019 20:10:14: 6000000 INFO @ Mon, 03 Jun 2019 20:10:21: 8000000 INFO @ Mon, 03 Jun 2019 20:10:22: 7000000 INFO @ Mon, 03 Jun 2019 20:10:24: 7000000 INFO @ Mon, 03 Jun 2019 20:10:29: 9000000 INFO @ Mon, 03 Jun 2019 20:10:32: 8000000 INFO @ Mon, 03 Jun 2019 20:10:34: 8000000 INFO @ Mon, 03 Jun 2019 20:10:38: 10000000 INFO @ Mon, 03 Jun 2019 20:10:41: 9000000 INFO @ Mon, 03 Jun 2019 20:10:44: 9000000 INFO @ Mon, 03 Jun 2019 20:10:46: 11000000 INFO @ Mon, 03 Jun 2019 20:10:51: 10000000 INFO @ Mon, 03 Jun 2019 20:10:54: 10000000 INFO @ Mon, 03 Jun 2019 20:10:55: 12000000 INFO @ Mon, 03 Jun 2019 20:11:01: 11000000 INFO @ Mon, 03 Jun 2019 20:11:03: 13000000 INFO @ Mon, 03 Jun 2019 20:11:05: 11000000 INFO @ Mon, 03 Jun 2019 20:11:11: 12000000 INFO @ Mon, 03 Jun 2019 20:11:12: 14000000 INFO @ Mon, 03 Jun 2019 20:11:15: 12000000 INFO @ Mon, 03 Jun 2019 20:11:20: 15000000 INFO @ Mon, 03 Jun 2019 20:11:21: 13000000 INFO @ Mon, 03 Jun 2019 20:11:25: 13000000 INFO @ Mon, 03 Jun 2019 20:11:29: 16000000 INFO @ Mon, 03 Jun 2019 20:11:30: 14000000 INFO @ Mon, 03 Jun 2019 20:11:35: 14000000 INFO @ Mon, 03 Jun 2019 20:11:37: 17000000 INFO @ Mon, 03 Jun 2019 20:11:40: 15000000 INFO @ Mon, 03 Jun 2019 20:11:45: 15000000 INFO @ Mon, 03 Jun 2019 20:11:45: 18000000 INFO @ Mon, 03 Jun 2019 20:11:49: 16000000 INFO @ Mon, 03 Jun 2019 20:11:53: 19000000 INFO @ Mon, 03 Jun 2019 20:11:55: 16000000 INFO @ Mon, 03 Jun 2019 20:11:59: 17000000 INFO @ Mon, 03 Jun 2019 20:12:02: 20000000 INFO @ Mon, 03 Jun 2019 20:12:04: 17000000 INFO @ Mon, 03 Jun 2019 20:12:08: 18000000 INFO @ Mon, 03 Jun 2019 20:12:10: 21000000 INFO @ Mon, 03 Jun 2019 20:12:14: 18000000 INFO @ Mon, 03 Jun 2019 20:12:17: 19000000 INFO @ Mon, 03 Jun 2019 20:12:18: 22000000 INFO @ Mon, 03 Jun 2019 20:12:23: 19000000 INFO @ Mon, 03 Jun 2019 20:12:26: 23000000 INFO @ Mon, 03 Jun 2019 20:12:26: 20000000 INFO @ Mon, 03 Jun 2019 20:12:32: 20000000 INFO @ Mon, 03 Jun 2019 20:12:34: 24000000 INFO @ Mon, 03 Jun 2019 20:12:36: 21000000 INFO @ Mon, 03 Jun 2019 20:12:42: 21000000 INFO @ Mon, 03 Jun 2019 20:12:42: 25000000 INFO @ Mon, 03 Jun 2019 20:12:45: 22000000 INFO @ Mon, 03 Jun 2019 20:12:51: 26000000 INFO @ Mon, 03 Jun 2019 20:12:51: 22000000 INFO @ Mon, 03 Jun 2019 20:12:54: 23000000 INFO @ Mon, 03 Jun 2019 20:12:59: 27000000 INFO @ Mon, 03 Jun 2019 20:13:01: 23000000 INFO @ Mon, 03 Jun 2019 20:13:04: 24000000 INFO @ Mon, 03 Jun 2019 20:13:07: 28000000 INFO @ Mon, 03 Jun 2019 20:13:10: 24000000 INFO @ Mon, 03 Jun 2019 20:13:13: 25000000 INFO @ Mon, 03 Jun 2019 20:13:15: 29000000 INFO @ Mon, 03 Jun 2019 20:13:20: 25000000 INFO @ Mon, 03 Jun 2019 20:13:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:13:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:13:20: #1 total tags in treatment: 14477883 INFO @ Mon, 03 Jun 2019 20:13:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:13:20: #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 20:13:20: #1 tags after filtering in treatment: 13454210 INFO @ Mon, 03 Jun 2019 20:13:20: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:13:20: #1 finished! INFO @ Mon, 03 Jun 2019 20:13:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:13:21: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 20:13:21: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 20:13:21: start model_add_line... INFO @ Mon, 03 Jun 2019 20:13:22: start X-correlation... INFO @ Mon, 03 Jun 2019 20:13:22: end of X-cor INFO @ Mon, 03 Jun 2019 20:13:22: #2 finished! INFO @ Mon, 03 Jun 2019 20:13:22: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 20:13:22: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 20:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05_model.r INFO @ Mon, 03 Jun 2019 20:13:22: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:13:22: 26000000 INFO @ Mon, 03 Jun 2019 20:13:29: 26000000 INFO @ Mon, 03 Jun 2019 20:13:31: 27000000 INFO @ Mon, 03 Jun 2019 20:13:38: 27000000 INFO @ Mon, 03 Jun 2019 20:13:40: 28000000 INFO @ Mon, 03 Jun 2019 20:13:47: 28000000 INFO @ Mon, 03 Jun 2019 20:13:49: 29000000 INFO @ Mon, 03 Jun 2019 20:13:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:13:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:13:55: #1 total tags in treatment: 14477883 INFO @ Mon, 03 Jun 2019 20:13:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:13:55: #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 20:13:55: #1 tags after filtering in treatment: 13454210 INFO @ Mon, 03 Jun 2019 20:13:55: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:13:55: #1 finished! INFO @ Mon, 03 Jun 2019 20:13:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:13:57: 29000000 INFO @ Mon, 03 Jun 2019 20:13:57: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 20:13:57: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 20:13:57: start model_add_line... INFO @ Mon, 03 Jun 2019 20:13:57: start X-correlation... INFO @ Mon, 03 Jun 2019 20:13:57: end of X-cor INFO @ Mon, 03 Jun 2019 20:13:57: #2 finished! INFO @ Mon, 03 Jun 2019 20:13:57: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 20:13:57: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 20:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20_model.r INFO @ Mon, 03 Jun 2019 20:13:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:14:02: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 20:14:02: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 20:14:02: #1 total tags in treatment: 14477883 INFO @ Mon, 03 Jun 2019 20:14:02: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 20:14:02: #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 20:14:03: #1 tags after filtering in treatment: 13454210 INFO @ Mon, 03 Jun 2019 20:14:03: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 20:14:03: #1 finished! INFO @ Mon, 03 Jun 2019 20:14:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 20:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 20:14:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:14:04: #2 number of paired peaks: 234 WARNING @ Mon, 03 Jun 2019 20:14:04: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Mon, 03 Jun 2019 20:14:04: start model_add_line... INFO @ Mon, 03 Jun 2019 20:14:04: start X-correlation... INFO @ Mon, 03 Jun 2019 20:14:04: end of X-cor INFO @ Mon, 03 Jun 2019 20:14:04: #2 finished! INFO @ Mon, 03 Jun 2019 20:14:04: #2 predicted fragment length is 110 bps INFO @ Mon, 03 Jun 2019 20:14:04: #2 alternative fragment length(s) may be 110 bps INFO @ Mon, 03 Jun 2019 20:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10_model.r INFO @ Mon, 03 Jun 2019 20:14:04: #3 Call peaks... INFO @ Mon, 03 Jun 2019 20:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 20:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05_peaks.xls INFO @ Mon, 03 Jun 2019 20:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.05_summits.bed INFO @ Mon, 03 Jun 2019 20:14:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:14:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:14:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 20:15:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20_peaks.xls INFO @ Mon, 03 Jun 2019 20:15:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:15:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.20_summits.bed INFO @ Mon, 03 Jun 2019 20:15:00: Done! pass1 - making usageList (8 chroms): 3 millis pass2 - checking and writing primary data (759 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 20:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10_peaks.xls INFO @ Mon, 03 Jun 2019 20:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 20:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474613/SRX474613.10_summits.bed INFO @ Mon, 03 Jun 2019 20:15:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1058 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。