Job ID = 1294741 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T00:45:19 fasterq-dump.2.9.6 sys: connection not found while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download-internal.ncbi.nlm.nih.gov:443' 2019-06-03T00:45:19 fasterq-dump.2.9.6 err: connection not found while validating within network system module - error with https open 'https://sra-download-internal.ncbi.nlm.nih.gov/traces/sra12/SRR/000849/SRR870040' 2019-06-03T00:45:19 fasterq-dump.2.9.6 err: invalid accession 'SRR870040' 2019-06-03T00:46:42 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 ) 2019-06-03T00:46:42 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 ) 2019-06-03T00:49:08 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 ) 2019-06-03T00:49:08 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 ) 2019-06-03T00:49:50 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 ) 2019-06-03T00:49:50 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 ) 2019-06-03T00:56:00 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 ) 2019-06-03T00:56:44 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 : 16,854,886 reads read : 16,854,886 reads written : 16,854,886 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: 00:03:50 16854886 reads; of these: 16854886 (100.00%) were unpaired; of these: 1176776 (6.98%) aligned 0 times 14757317 (87.56%) aligned exactly 1 time 920793 (5.46%) aligned >1 times 93.02% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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_rmdupse_core] 1644217 / 15678110 = 0.1049 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 10:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.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 10:07:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:07:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.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 10:07:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:07:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.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 10:07:32: #1 read tag files... INFO @ Mon, 03 Jun 2019 10:07:32: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 10:07:41: 1000000 INFO @ Mon, 03 Jun 2019 10:07:41: 1000000 INFO @ Mon, 03 Jun 2019 10:07:41: 1000000 INFO @ Mon, 03 Jun 2019 10:07:50: 2000000 INFO @ Mon, 03 Jun 2019 10:07:50: 2000000 INFO @ Mon, 03 Jun 2019 10:07:50: 2000000 INFO @ Mon, 03 Jun 2019 10:07:58: 3000000 INFO @ Mon, 03 Jun 2019 10:07:59: 3000000 INFO @ Mon, 03 Jun 2019 10:07:59: 3000000 INFO @ Mon, 03 Jun 2019 10:08:07: 4000000 INFO @ Mon, 03 Jun 2019 10:08:08: 4000000 INFO @ Mon, 03 Jun 2019 10:08:08: 4000000 INFO @ Mon, 03 Jun 2019 10:08:16: 5000000 INFO @ Mon, 03 Jun 2019 10:08:17: 5000000 INFO @ Mon, 03 Jun 2019 10:08:18: 5000000 INFO @ Mon, 03 Jun 2019 10:08:26: 6000000 INFO @ Mon, 03 Jun 2019 10:08:26: 6000000 INFO @ Mon, 03 Jun 2019 10:08:27: 6000000 INFO @ Mon, 03 Jun 2019 10:08:35: 7000000 INFO @ Mon, 03 Jun 2019 10:08:36: 7000000 INFO @ Mon, 03 Jun 2019 10:08:37: 7000000 INFO @ Mon, 03 Jun 2019 10:08:44: 8000000 INFO @ Mon, 03 Jun 2019 10:08:44: 8000000 INFO @ Mon, 03 Jun 2019 10:08:46: 8000000 INFO @ Mon, 03 Jun 2019 10:08:52: 9000000 INFO @ Mon, 03 Jun 2019 10:08:53: 9000000 INFO @ Mon, 03 Jun 2019 10:08:54: 9000000 INFO @ Mon, 03 Jun 2019 10:09:00: 10000000 INFO @ Mon, 03 Jun 2019 10:09:02: 10000000 INFO @ Mon, 03 Jun 2019 10:09:03: 10000000 INFO @ Mon, 03 Jun 2019 10:09:08: 11000000 INFO @ Mon, 03 Jun 2019 10:09:10: 11000000 INFO @ Mon, 03 Jun 2019 10:09:12: 11000000 INFO @ Mon, 03 Jun 2019 10:09:16: 12000000 INFO @ Mon, 03 Jun 2019 10:09:19: 12000000 INFO @ Mon, 03 Jun 2019 10:09:21: 12000000 INFO @ Mon, 03 Jun 2019 10:09:26: 13000000 INFO @ Mon, 03 Jun 2019 10:09:29: 13000000 INFO @ Mon, 03 Jun 2019 10:09:31: 13000000 INFO @ Mon, 03 Jun 2019 10:09:35: 14000000 INFO @ Mon, 03 Jun 2019 10:09:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:09:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:09:35: #1 total tags in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:09:35: #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 10:09:36: #1 tags after filtering in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:09:36: #1 finished! INFO @ Mon, 03 Jun 2019 10:09:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:09:37: #2 number of paired peaks: 375 WARNING @ Mon, 03 Jun 2019 10:09:37: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 03 Jun 2019 10:09:37: start model_add_line... INFO @ Mon, 03 Jun 2019 10:09:37: start X-correlation... INFO @ Mon, 03 Jun 2019 10:09:37: end of X-cor INFO @ Mon, 03 Jun 2019 10:09:37: #2 finished! INFO @ Mon, 03 Jun 2019 10:09:37: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 10:09:37: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 10:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10_model.r INFO @ Mon, 03 Jun 2019 10:09:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:09:38: 14000000 INFO @ Mon, 03 Jun 2019 10:09:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:09:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:09:39: #1 total tags in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:09:39: #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 10:09:39: 14000000 INFO @ Mon, 03 Jun 2019 10:09:39: #1 tags after filtering in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:09:39: #1 finished! INFO @ Mon, 03 Jun 2019 10:09:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:09:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:09:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 10:09:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 10:09:39: #1 total tags in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 10:09:39: #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 10:09:40: #1 tags after filtering in treatment: 14033893 INFO @ Mon, 03 Jun 2019 10:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 10:09:40: #1 finished! INFO @ Mon, 03 Jun 2019 10:09:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 10:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 10:09:40: #2 number of paired peaks: 375 WARNING @ Mon, 03 Jun 2019 10:09:40: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 03 Jun 2019 10:09:40: start model_add_line... INFO @ Mon, 03 Jun 2019 10:09:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:09:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:09:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:09:41: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 10:09:41: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 10:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05_model.r INFO @ Mon, 03 Jun 2019 10:09:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:09:41: #2 number of paired peaks: 375 WARNING @ Mon, 03 Jun 2019 10:09:41: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Mon, 03 Jun 2019 10:09:41: start model_add_line... INFO @ Mon, 03 Jun 2019 10:09:41: start X-correlation... INFO @ Mon, 03 Jun 2019 10:09:41: end of X-cor INFO @ Mon, 03 Jun 2019 10:09:41: #2 finished! INFO @ Mon, 03 Jun 2019 10:09:41: #2 predicted fragment length is 190 bps INFO @ Mon, 03 Jun 2019 10:09:41: #2 alternative fragment length(s) may be 190 bps INFO @ Mon, 03 Jun 2019 10:09:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20_model.r INFO @ Mon, 03 Jun 2019 10:09:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 10:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 10:10:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:10:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:10:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 10:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10_peaks.xls INFO @ Mon, 03 Jun 2019 10:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.10_summits.bed INFO @ Mon, 03 Jun 2019 10:10:39: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3152 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05_peaks.xls INFO @ Mon, 03 Jun 2019 10:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.05_summits.bed INFO @ Mon, 03 Jun 2019 10:10:42: Done! pass1 - making usageList (12 chroms): 14 millis pass2 - checking and writing primary data (8782 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 10:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20_peaks.xls INFO @ Mon, 03 Jun 2019 10:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 10:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287851/SRX287851.20_summits.bed INFO @ Mon, 03 Jun 2019 10:10:43: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (619 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。