Job ID = 1299819 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:31:51 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 ) 2019-06-03T09:34:56 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 ) 2019-06-03T09:34:56 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 ) 2019-06-03T09:37:48 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 ) 2019-06-03T09:38:24 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 ) 2019-06-03T09:39:19 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 ) 2019-06-03T09:41:12 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 ) 2019-06-03T09:41:12 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 ) 2019-06-03T09:43:59 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 ) 2019-06-03T09:48:53 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 : 14,568,344 reads read : 29,136,688 reads written : 29,136,688 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: 00:47:29 14568344 reads; of these: 14568344 (100.00%) were paired; of these: 1168641 (8.02%) aligned concordantly 0 times 9588325 (65.82%) aligned concordantly exactly 1 time 3811378 (26.16%) aligned concordantly >1 times ---- 1168641 pairs aligned concordantly 0 times; of these: 85621 (7.33%) aligned discordantly 1 time ---- 1083020 pairs aligned 0 times concordantly or discordantly; of these: 2166040 mates make up the pairs; of these: 1765151 (81.49%) aligned 0 times 277042 (12.79%) aligned exactly 1 time 123847 (5.72%) aligned >1 times 93.94% overall alignment rate Time searching: 00:47:29 Overall time: 00:47:29 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] 1167616 / 13454080 = 0.0868 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 19:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.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 19:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.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 19:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:47:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.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 19:47:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:47:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:47:55: 1000000 INFO @ Mon, 03 Jun 2019 19:47:56: 1000000 INFO @ Mon, 03 Jun 2019 19:47:56: 1000000 INFO @ Mon, 03 Jun 2019 19:48:04: 2000000 INFO @ Mon, 03 Jun 2019 19:48:06: 2000000 INFO @ Mon, 03 Jun 2019 19:48:06: 2000000 INFO @ Mon, 03 Jun 2019 19:48:12: 3000000 INFO @ Mon, 03 Jun 2019 19:48:16: 3000000 INFO @ Mon, 03 Jun 2019 19:48:17: 3000000 INFO @ Mon, 03 Jun 2019 19:48:20: 4000000 INFO @ Mon, 03 Jun 2019 19:48:27: 4000000 INFO @ Mon, 03 Jun 2019 19:48:27: 4000000 INFO @ Mon, 03 Jun 2019 19:48:30: 5000000 INFO @ Mon, 03 Jun 2019 19:48:36: 5000000 INFO @ Mon, 03 Jun 2019 19:48:37: 5000000 INFO @ Mon, 03 Jun 2019 19:48:38: 6000000 INFO @ Mon, 03 Jun 2019 19:48:46: 6000000 INFO @ Mon, 03 Jun 2019 19:48:47: 7000000 INFO @ Mon, 03 Jun 2019 19:48:48: 6000000 INFO @ Mon, 03 Jun 2019 19:48:56: 8000000 INFO @ Mon, 03 Jun 2019 19:48:56: 7000000 INFO @ Mon, 03 Jun 2019 19:48:58: 7000000 INFO @ Mon, 03 Jun 2019 19:49:05: 9000000 INFO @ Mon, 03 Jun 2019 19:49:06: 8000000 INFO @ Mon, 03 Jun 2019 19:49:09: 8000000 INFO @ Mon, 03 Jun 2019 19:49:13: 10000000 INFO @ Mon, 03 Jun 2019 19:49:15: 9000000 INFO @ Mon, 03 Jun 2019 19:49:19: 9000000 INFO @ Mon, 03 Jun 2019 19:49:22: 11000000 INFO @ Mon, 03 Jun 2019 19:49:25: 10000000 INFO @ Mon, 03 Jun 2019 19:49:29: 10000000 INFO @ Mon, 03 Jun 2019 19:49:30: 12000000 INFO @ Mon, 03 Jun 2019 19:49:35: 11000000 INFO @ Mon, 03 Jun 2019 19:49:39: 13000000 INFO @ Mon, 03 Jun 2019 19:49:40: 11000000 INFO @ Mon, 03 Jun 2019 19:49:45: 12000000 INFO @ Mon, 03 Jun 2019 19:49:47: 14000000 INFO @ Mon, 03 Jun 2019 19:49:49: 12000000 INFO @ Mon, 03 Jun 2019 19:49:54: 13000000 INFO @ Mon, 03 Jun 2019 19:49:56: 15000000 INFO @ Mon, 03 Jun 2019 19:50:00: 13000000 INFO @ Mon, 03 Jun 2019 19:50:04: 16000000 INFO @ Mon, 03 Jun 2019 19:50:04: 14000000 INFO @ Mon, 03 Jun 2019 19:50:10: 14000000 INFO @ Mon, 03 Jun 2019 19:50:12: 17000000 INFO @ Mon, 03 Jun 2019 19:50:14: 15000000 INFO @ Mon, 03 Jun 2019 19:50:20: 15000000 INFO @ Mon, 03 Jun 2019 19:50:21: 18000000 INFO @ Mon, 03 Jun 2019 19:50:23: 16000000 INFO @ Mon, 03 Jun 2019 19:50:29: 19000000 INFO @ Mon, 03 Jun 2019 19:50:31: 16000000 INFO @ Mon, 03 Jun 2019 19:50:33: 17000000 INFO @ Mon, 03 Jun 2019 19:50:38: 20000000 INFO @ Mon, 03 Jun 2019 19:50:42: 17000000 INFO @ Mon, 03 Jun 2019 19:50:44: 18000000 INFO @ Mon, 03 Jun 2019 19:50:47: 21000000 INFO @ Mon, 03 Jun 2019 19:50:53: 18000000 INFO @ Mon, 03 Jun 2019 19:50:53: 19000000 INFO @ Mon, 03 Jun 2019 19:50:56: 22000000 INFO @ Mon, 03 Jun 2019 19:51:02: 20000000 INFO @ Mon, 03 Jun 2019 19:51:03: 19000000 INFO @ Mon, 03 Jun 2019 19:51:05: 23000000 INFO @ Mon, 03 Jun 2019 19:51:11: 21000000 INFO @ Mon, 03 Jun 2019 19:51:13: 20000000 INFO @ Mon, 03 Jun 2019 19:51:14: 24000000 INFO @ Mon, 03 Jun 2019 19:51:20: 22000000 INFO @ Mon, 03 Jun 2019 19:51:23: 21000000 INFO @ Mon, 03 Jun 2019 19:51:24: 25000000 INFO @ Mon, 03 Jun 2019 19:51:24: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:24: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:24: #1 total tags in treatment: 12234491 INFO @ Mon, 03 Jun 2019 19:51:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:24: #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 19:51:25: #1 tags after filtering in treatment: 10874638 INFO @ Mon, 03 Jun 2019 19:51:25: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:51:25: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:26: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 19:51:26: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 19:51:26: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:26: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:26: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:26: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:26: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 19:51:26: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 19:51:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05_model.r INFO @ Mon, 03 Jun 2019 19:51:26: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:28: 23000000 INFO @ Mon, 03 Jun 2019 19:51:32: 22000000 INFO @ Mon, 03 Jun 2019 19:51:38: 24000000 INFO @ Mon, 03 Jun 2019 19:51:42: 23000000 INFO @ Mon, 03 Jun 2019 19:51:47: 25000000 INFO @ Mon, 03 Jun 2019 19:51:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:51:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:51:48: #1 total tags in treatment: 12234491 INFO @ Mon, 03 Jun 2019 19:51:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:51:48: #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 19:51:48: #1 tags after filtering in treatment: 10874638 INFO @ Mon, 03 Jun 2019 19:51:48: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:51:48: #1 finished! INFO @ Mon, 03 Jun 2019 19:51:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:51:49: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 19:51:49: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 19:51:49: start model_add_line... INFO @ Mon, 03 Jun 2019 19:51:49: start X-correlation... INFO @ Mon, 03 Jun 2019 19:51:49: end of X-cor INFO @ Mon, 03 Jun 2019 19:51:49: #2 finished! INFO @ Mon, 03 Jun 2019 19:51:49: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 19:51:49: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 19:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10_model.r INFO @ Mon, 03 Jun 2019 19:51:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:51:51: 24000000 INFO @ Mon, 03 Jun 2019 19:52:00: 25000000 INFO @ Mon, 03 Jun 2019 19:52:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:52:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:52:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:52:00: #1 total tags in treatment: 12234491 INFO @ Mon, 03 Jun 2019 19:52:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:52:00: #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 19:52:01: #1 tags after filtering in treatment: 10874638 INFO @ Mon, 03 Jun 2019 19:52:01: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:52:01: #1 finished! INFO @ Mon, 03 Jun 2019 19:52:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:52:02: #2 number of paired peaks: 116 WARNING @ Mon, 03 Jun 2019 19:52:02: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Mon, 03 Jun 2019 19:52:02: start model_add_line... INFO @ Mon, 03 Jun 2019 19:52:02: start X-correlation... INFO @ Mon, 03 Jun 2019 19:52:02: end of X-cor INFO @ Mon, 03 Jun 2019 19:52:02: #2 finished! INFO @ Mon, 03 Jun 2019 19:52:02: #2 predicted fragment length is 106 bps INFO @ Mon, 03 Jun 2019 19:52:02: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 03 Jun 2019 19:52:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20_model.r INFO @ Mon, 03 Jun 2019 19:52:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:52:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.05_summits.bed INFO @ Mon, 03 Jun 2019 19:52:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1040 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:52:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:52:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:52:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:52:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:52:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.10_summits.bed INFO @ Mon, 03 Jun 2019 19:52:40: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:52:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:52:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:52:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474610/SRX474610.20_summits.bed INFO @ Mon, 03 Jun 2019 19:52:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (533 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。