Job ID = 1299525 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:20:48 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 : NET - Reading information from the socket failed ) 2019-06-03T09:20:48 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 : NET - Reading information from the socket failed ) 2019-06-03T09:20:48 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 ) 2019-06-03T09:20:48 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 ) 2019-06-03T09:25:57 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 ) 2019-06-03T09:25:57 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 ) 2019-06-03T09:25:57 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 ) 2019-06-03T09:25:57 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 ) 2019-06-03T09:29:00 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 ) 2019-06-03T09:29:00 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 : 14,694,725 reads read : 29,389,450 reads written : 29,389,450 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: 00:24:40 14694725 reads; of these: 14694725 (100.00%) were paired; of these: 5991773 (40.77%) aligned concordantly 0 times 6725160 (45.77%) aligned concordantly exactly 1 time 1977792 (13.46%) aligned concordantly >1 times ---- 5991773 pairs aligned concordantly 0 times; of these: 214053 (3.57%) aligned discordantly 1 time ---- 5777720 pairs aligned 0 times concordantly or discordantly; of these: 11555440 mates make up the pairs; of these: 11155118 (96.54%) aligned 0 times 236384 (2.05%) aligned exactly 1 time 163938 (1.42%) aligned >1 times 62.04% overall alignment rate Time searching: 00:24:40 Overall time: 00:24:40 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] 5461503 / 8912490 = 0.6128 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 19:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.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 19:06:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.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 19:06:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.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 19:06:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:06:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:06:51: 1000000 INFO @ Mon, 03 Jun 2019 19:06:51: 1000000 INFO @ Mon, 03 Jun 2019 19:06:51: 1000000 INFO @ Mon, 03 Jun 2019 19:07:01: 2000000 INFO @ Mon, 03 Jun 2019 19:07:02: 2000000 INFO @ Mon, 03 Jun 2019 19:07:02: 2000000 INFO @ Mon, 03 Jun 2019 19:07:12: 3000000 INFO @ Mon, 03 Jun 2019 19:07:12: 3000000 INFO @ Mon, 03 Jun 2019 19:07:13: 3000000 INFO @ Mon, 03 Jun 2019 19:07:21: 4000000 INFO @ Mon, 03 Jun 2019 19:07:22: 4000000 INFO @ Mon, 03 Jun 2019 19:07:24: 4000000 INFO @ Mon, 03 Jun 2019 19:07:30: 5000000 INFO @ Mon, 03 Jun 2019 19:07:32: 5000000 INFO @ Mon, 03 Jun 2019 19:07:34: 5000000 INFO @ Mon, 03 Jun 2019 19:07:40: 6000000 INFO @ Mon, 03 Jun 2019 19:07:42: 6000000 INFO @ Mon, 03 Jun 2019 19:07:44: 6000000 INFO @ Mon, 03 Jun 2019 19:07:50: 7000000 INFO @ Mon, 03 Jun 2019 19:07:52: 7000000 INFO @ Mon, 03 Jun 2019 19:07:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:07:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:07:53: #1 total tags in treatment: 3332259 INFO @ Mon, 03 Jun 2019 19:07:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:07:53: #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 19:07:53: #1 tags after filtering in treatment: 3243643 INFO @ Mon, 03 Jun 2019 19:07:53: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 19:07:53: #1 finished! INFO @ Mon, 03 Jun 2019 19:07:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:07:53: #2 number of paired peaks: 986 WARNING @ Mon, 03 Jun 2019 19:07:53: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Mon, 03 Jun 2019 19:07:53: start model_add_line... INFO @ Mon, 03 Jun 2019 19:07:53: start X-correlation... INFO @ Mon, 03 Jun 2019 19:07:53: end of X-cor INFO @ Mon, 03 Jun 2019 19:07:53: #2 finished! INFO @ Mon, 03 Jun 2019 19:07:53: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 19:07:53: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 19:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10_model.r INFO @ Mon, 03 Jun 2019 19:07:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:07:54: 7000000 INFO @ Mon, 03 Jun 2019 19:07:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:07:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:07:55: #1 total tags in treatment: 3332259 INFO @ Mon, 03 Jun 2019 19:07:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:07:55: #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 19:07:55: #1 tags after filtering in treatment: 3243643 INFO @ Mon, 03 Jun 2019 19:07:55: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 19:07:55: #1 finished! INFO @ Mon, 03 Jun 2019 19:07:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:07:55: #2 number of paired peaks: 986 WARNING @ Mon, 03 Jun 2019 19:07:55: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Mon, 03 Jun 2019 19:07:55: start model_add_line... INFO @ Mon, 03 Jun 2019 19:07:55: start X-correlation... INFO @ Mon, 03 Jun 2019 19:07:55: end of X-cor INFO @ Mon, 03 Jun 2019 19:07:55: #2 finished! INFO @ Mon, 03 Jun 2019 19:07:55: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 19:07:55: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 19:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20_model.r INFO @ Mon, 03 Jun 2019 19:07:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:07:57: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:07:57: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:07:57: #1 total tags in treatment: 3332259 INFO @ Mon, 03 Jun 2019 19:07:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:07:57: #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 19:07:57: #1 tags after filtering in treatment: 3243643 INFO @ Mon, 03 Jun 2019 19:07:57: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 19:07:57: #1 finished! INFO @ Mon, 03 Jun 2019 19:07:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:07:58: #2 number of paired peaks: 986 WARNING @ Mon, 03 Jun 2019 19:07:58: Fewer paired peaks (986) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 986 pairs to build model! INFO @ Mon, 03 Jun 2019 19:07:58: start model_add_line... INFO @ Mon, 03 Jun 2019 19:07:58: start X-correlation... INFO @ Mon, 03 Jun 2019 19:07:58: end of X-cor INFO @ Mon, 03 Jun 2019 19:07:58: #2 finished! INFO @ Mon, 03 Jun 2019 19:07:58: #2 predicted fragment length is 149 bps INFO @ Mon, 03 Jun 2019 19:07:58: #2 alternative fragment length(s) may be 149 bps INFO @ Mon, 03 Jun 2019 19:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05_model.r INFO @ Mon, 03 Jun 2019 19:07:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:08:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:08:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:08:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:08:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:08:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:08:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.10_summits.bed INFO @ Mon, 03 Jun 2019 19:08:10: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1007 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:08:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:08:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:08:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.20_summits.bed INFO @ Mon, 03 Jun 2019 19:08:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474588/SRX474588.05_summits.bed INFO @ Mon, 03 Jun 2019 19:08:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2399 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。