Job ID = 1299429 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T09:09:34 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 ) 2019-06-03T09:09:37 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 ) 2019-06-03T09:09:37 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 ) 2019-06-03T09:13:38 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 ) 2019-06-03T09:16:09 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 ) 2019-06-03T09:17:14 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 ) 2019-06-03T09:19:39 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 ) 2019-06-03T09:30:57 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 ) 2019-06-03T09:30:57 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 ) 2019-06-03T09:32:42 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 25,026,335 reads read : 50,052,670 reads written : 50,052,670 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: 00:14:51 25026335 reads; of these: 25026335 (100.00%) were paired; of these: 19713652 (78.77%) aligned concordantly 0 times 4268450 (17.06%) aligned concordantly exactly 1 time 1044233 (4.17%) aligned concordantly >1 times ---- 19713652 pairs aligned concordantly 0 times; of these: 38627 (0.20%) aligned discordantly 1 time ---- 19675025 pairs aligned 0 times concordantly or discordantly; of these: 39350050 mates make up the pairs; of these: 39147052 (99.48%) aligned 0 times 144525 (0.37%) aligned exactly 1 time 58473 (0.15%) aligned >1 times 21.79% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 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] 717550 / 5347934 = 0.1342 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 18:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.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 18:55:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:55:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.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 18:55:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.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 18:55:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:55:44: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:55:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:55:44: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:55:53: 1000000 INFO @ Mon, 03 Jun 2019 18:55:53: 1000000 INFO @ Mon, 03 Jun 2019 18:55:54: 1000000 INFO @ Mon, 03 Jun 2019 18:56:02: 2000000 INFO @ Mon, 03 Jun 2019 18:56:02: 2000000 INFO @ Mon, 03 Jun 2019 18:56:03: 2000000 INFO @ Mon, 03 Jun 2019 18:56:11: 3000000 INFO @ Mon, 03 Jun 2019 18:56:12: 3000000 INFO @ Mon, 03 Jun 2019 18:56:12: 3000000 INFO @ Mon, 03 Jun 2019 18:56:20: 4000000 INFO @ Mon, 03 Jun 2019 18:56:21: 4000000 INFO @ Mon, 03 Jun 2019 18:56:21: 4000000 INFO @ Mon, 03 Jun 2019 18:56:28: 5000000 INFO @ Mon, 03 Jun 2019 18:56:29: 5000000 INFO @ Mon, 03 Jun 2019 18:56:30: 5000000 INFO @ Mon, 03 Jun 2019 18:56:37: 6000000 INFO @ Mon, 03 Jun 2019 18:56:38: 6000000 INFO @ Mon, 03 Jun 2019 18:56:38: 6000000 INFO @ Mon, 03 Jun 2019 18:56:45: 7000000 INFO @ Mon, 03 Jun 2019 18:56:47: 7000000 INFO @ Mon, 03 Jun 2019 18:56:47: 7000000 INFO @ Mon, 03 Jun 2019 18:56:54: 8000000 INFO @ Mon, 03 Jun 2019 18:56:55: 8000000 INFO @ Mon, 03 Jun 2019 18:56:56: 8000000 INFO @ Mon, 03 Jun 2019 18:57:03: 9000000 INFO @ Mon, 03 Jun 2019 18:57:04: 9000000 INFO @ Mon, 03 Jun 2019 18:57:05: 9000000 INFO @ Mon, 03 Jun 2019 18:57:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:57:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:57:07: #1 total tags in treatment: 4597395 INFO @ Mon, 03 Jun 2019 18:57:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:57:07: #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 18:57:07: #1 tags after filtering in treatment: 4262329 INFO @ Mon, 03 Jun 2019 18:57:07: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 18:57:07: #1 finished! INFO @ Mon, 03 Jun 2019 18:57:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:57:08: #2 number of paired peaks: 613 WARNING @ Mon, 03 Jun 2019 18:57:08: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Mon, 03 Jun 2019 18:57:08: start model_add_line... INFO @ Mon, 03 Jun 2019 18:57:08: start X-correlation... INFO @ Mon, 03 Jun 2019 18:57:08: end of X-cor INFO @ Mon, 03 Jun 2019 18:57:08: #2 finished! INFO @ Mon, 03 Jun 2019 18:57:08: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 18:57:08: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 18:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20_model.r INFO @ Mon, 03 Jun 2019 18:57:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:57:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:57:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:57:08: #1 total tags in treatment: 4597395 INFO @ Mon, 03 Jun 2019 18:57:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:57:08: #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 18:57:08: #1 tags after filtering in treatment: 4262329 INFO @ Mon, 03 Jun 2019 18:57:08: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 18:57:08: #1 finished! INFO @ Mon, 03 Jun 2019 18:57:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:57:08: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 18:57:08: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 18:57:08: #1 total tags in treatment: 4597395 INFO @ Mon, 03 Jun 2019 18:57:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:57:08: #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 18:57:09: #1 tags after filtering in treatment: 4262329 INFO @ Mon, 03 Jun 2019 18:57:09: #1 Redundant rate of treatment: 0.07 INFO @ Mon, 03 Jun 2019 18:57:09: #1 finished! INFO @ Mon, 03 Jun 2019 18:57:09: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:57:09: #2 number of paired peaks: 613 WARNING @ Mon, 03 Jun 2019 18:57:09: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Mon, 03 Jun 2019 18:57:09: start model_add_line... INFO @ Mon, 03 Jun 2019 18:57:09: start X-correlation... INFO @ Mon, 03 Jun 2019 18:57:09: end of X-cor INFO @ Mon, 03 Jun 2019 18:57:09: #2 finished! INFO @ Mon, 03 Jun 2019 18:57:09: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 18:57:09: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 18:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10_model.r INFO @ Mon, 03 Jun 2019 18:57:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:57:09: #2 number of paired peaks: 613 WARNING @ Mon, 03 Jun 2019 18:57:09: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Mon, 03 Jun 2019 18:57:09: start model_add_line... INFO @ Mon, 03 Jun 2019 18:57:09: start X-correlation... INFO @ Mon, 03 Jun 2019 18:57:09: end of X-cor INFO @ Mon, 03 Jun 2019 18:57:09: #2 finished! INFO @ Mon, 03 Jun 2019 18:57:09: #2 predicted fragment length is 150 bps INFO @ Mon, 03 Jun 2019 18:57:09: #2 alternative fragment length(s) may be 150 bps INFO @ Mon, 03 Jun 2019 18:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05_model.r INFO @ Mon, 03 Jun 2019 18:57:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:57:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:57:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:57:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.20_summits.bed INFO @ Mon, 03 Jun 2019 18:57:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.10_summits.bed INFO @ Mon, 03 Jun 2019 18:57:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (784 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474579/SRX474579.05_summits.bed INFO @ Mon, 03 Jun 2019 18:57:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1824 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。