Job ID = 1300851 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-06-03T10:20:53 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' 2019-06-03T10:20:53 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/sra72/SRR/007805/SRR7992752' 2019-06-03T10:20:53 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7992752' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:20:53 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T10:22:08 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 ) 2019-06-03T10:22:08 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 ) 2019-06-03T10:22:08 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 ) 2019-06-03T10:27:19 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 ) 2019-06-03T10:27:19 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 ) 2019-06-03T10:27:19 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 ) spots read : 26,259,900 reads read : 26,259,900 reads written : 26,259,900 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: 00:06:43 26259900 reads; of these: 26259900 (100.00%) were unpaired; of these: 10109820 (38.50%) aligned 0 times 11816542 (45.00%) aligned exactly 1 time 4333538 (16.50%) aligned >1 times 61.50% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 6532168 / 16150080 = 0.4045 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 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.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 19:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.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 19:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.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 19:52:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:52:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:52:45: 1000000 INFO @ Mon, 03 Jun 2019 19:52:46: 1000000 INFO @ Mon, 03 Jun 2019 19:52:47: 1000000 INFO @ Mon, 03 Jun 2019 19:52:53: 2000000 INFO @ Mon, 03 Jun 2019 19:52:55: 2000000 INFO @ Mon, 03 Jun 2019 19:52:57: 2000000 INFO @ Mon, 03 Jun 2019 19:53:01: 3000000 INFO @ Mon, 03 Jun 2019 19:53:05: 3000000 INFO @ Mon, 03 Jun 2019 19:53:07: 3000000 INFO @ Mon, 03 Jun 2019 19:53:10: 4000000 INFO @ Mon, 03 Jun 2019 19:53:14: 4000000 INFO @ Mon, 03 Jun 2019 19:53:17: 4000000 INFO @ Mon, 03 Jun 2019 19:53:18: 5000000 INFO @ Mon, 03 Jun 2019 19:53:24: 5000000 INFO @ Mon, 03 Jun 2019 19:53:26: 6000000 INFO @ Mon, 03 Jun 2019 19:53:27: 5000000 INFO @ Mon, 03 Jun 2019 19:53:33: 6000000 INFO @ Mon, 03 Jun 2019 19:53:35: 7000000 INFO @ Mon, 03 Jun 2019 19:53:37: 6000000 INFO @ Mon, 03 Jun 2019 19:53:43: 7000000 INFO @ Mon, 03 Jun 2019 19:53:43: 8000000 INFO @ Mon, 03 Jun 2019 19:53:48: 7000000 INFO @ Mon, 03 Jun 2019 19:53:51: 9000000 INFO @ Mon, 03 Jun 2019 19:53:52: 8000000 INFO @ Mon, 03 Jun 2019 19:53:56: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:53:56: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:53:56: #1 total tags in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:53:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:53:56: #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 19:53:56: #1 tags after filtering in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:53:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:53:56: #1 finished! INFO @ Mon, 03 Jun 2019 19:53:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:53:57: #2 number of paired peaks: 2233 INFO @ Mon, 03 Jun 2019 19:53:57: start model_add_line... INFO @ Mon, 03 Jun 2019 19:53:58: start X-correlation... INFO @ Mon, 03 Jun 2019 19:53:58: end of X-cor INFO @ Mon, 03 Jun 2019 19:53:58: #2 finished! INFO @ Mon, 03 Jun 2019 19:53:58: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 19:53:58: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 19:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05_model.r INFO @ Mon, 03 Jun 2019 19:53:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:53:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:53:58: 8000000 INFO @ Mon, 03 Jun 2019 19:54:01: 9000000 INFO @ Mon, 03 Jun 2019 19:54:07: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:54:07: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:54:07: #1 total tags in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:54:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:54:07: #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 19:54:07: #1 tags after filtering in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:54:07: #1 finished! INFO @ Mon, 03 Jun 2019 19:54:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:54:07: 9000000 INFO @ Mon, 03 Jun 2019 19:54:08: #2 number of paired peaks: 2233 INFO @ Mon, 03 Jun 2019 19:54:08: start model_add_line... INFO @ Mon, 03 Jun 2019 19:54:08: start X-correlation... INFO @ Mon, 03 Jun 2019 19:54:08: end of X-cor INFO @ Mon, 03 Jun 2019 19:54:08: #2 finished! INFO @ Mon, 03 Jun 2019 19:54:08: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 19:54:08: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 19:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20_model.r INFO @ Mon, 03 Jun 2019 19:54:08: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:54:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:54:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:54:13: #1 total tags in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:54:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:54:13: #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 19:54:13: #1 tags after filtering in treatment: 9617912 INFO @ Mon, 03 Jun 2019 19:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:54:13: #1 finished! INFO @ Mon, 03 Jun 2019 19:54:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:54:14: #2 number of paired peaks: 2233 INFO @ Mon, 03 Jun 2019 19:54:14: start model_add_line... INFO @ Mon, 03 Jun 2019 19:54:14: start X-correlation... INFO @ Mon, 03 Jun 2019 19:54:14: end of X-cor INFO @ Mon, 03 Jun 2019 19:54:14: #2 finished! INFO @ Mon, 03 Jun 2019 19:54:14: #2 predicted fragment length is 207 bps INFO @ Mon, 03 Jun 2019 19:54:14: #2 alternative fragment length(s) may be 207 bps INFO @ Mon, 03 Jun 2019 19:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10_model.r INFO @ Mon, 03 Jun 2019 19:54:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:54:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:54:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:54:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:54:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:54:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.05_summits.bed INFO @ Mon, 03 Jun 2019 19:54:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6936 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:54:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.20_summits.bed INFO @ Mon, 03 Jun 2019 19:54:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4041 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4823794/SRX4823794.10_summits.bed INFO @ Mon, 03 Jun 2019 19:55:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5489 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。