Job ID = 1298132 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-03T08:05:27 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' 2019-06-03T08:05:27 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/sra70/SRR/007616/SRR7799045' 2019-06-03T08:05:27 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7799045' ) -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T08:05:27 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcNS,rcNoTarg,rcValidating,rcConnection,rcNotFound) 2019-06-03T08:07:55 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 ) 2019-06-03T08:07:55 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 ) 2019-06-03T08:08:33 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 ) 2019-06-03T08:10:50 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 ) 2019-06-03T08:11:40 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 ) 2019-06-03T08:14:03 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 ) 2019-06-03T08:20:48 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 ) 2019-06-03T08:24:14 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 ) 2019-06-03T08:26:06 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 ) 2019-06-03T08:38:52 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 : 41,872,250 reads read : 83,744,500 reads written : 83,744,500 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: 00:00:01 Multiseed full-index search: 00:10:44 41872250 reads; of these: 41872250 (100.00%) were paired; of these: 39921362 (95.34%) aligned concordantly 0 times 1536323 (3.67%) aligned concordantly exactly 1 time 414565 (0.99%) aligned concordantly >1 times ---- 39921362 pairs aligned concordantly 0 times; of these: 6681 (0.02%) aligned discordantly 1 time ---- 39914681 pairs aligned 0 times concordantly or discordantly; of these: 79829362 mates make up the pairs; of these: 78896402 (98.83%) aligned 0 times 305270 (0.38%) aligned exactly 1 time 627690 (0.79%) aligned >1 times 5.79% overall alignment rate Time searching: 00:10:45 Overall time: 00:10:45 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_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] 86869 / 1953356 = 0.0445 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 18:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.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 18:05:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:05:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.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 18:05:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:05:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.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 18:05:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 18:05:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 18:05:14: 1000000 INFO @ Mon, 03 Jun 2019 18:05:15: 1000000 INFO @ Mon, 03 Jun 2019 18:05:15: 1000000 INFO @ Mon, 03 Jun 2019 18:05:22: 2000000 INFO @ Mon, 03 Jun 2019 18:05:24: 2000000 INFO @ Mon, 03 Jun 2019 18:05:25: 2000000 INFO @ Mon, 03 Jun 2019 18:05:30: 3000000 INFO @ Mon, 03 Jun 2019 18:05:34: 3000000 INFO @ Mon, 03 Jun 2019 18:05:36: 3000000 INFO @ Mon, 03 Jun 2019 18:05:38: 4000000 INFO @ Mon, 03 Jun 2019 18:05:42: 4000000 INFO @ Mon, 03 Jun 2019 18:05:43: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 18:05:43: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 18:05:43: #1 total tags in treatment: 1864150 INFO @ Mon, 03 Jun 2019 18:05:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:05:43: #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 18:05:43: #1 tags after filtering in treatment: 1793798 INFO @ Mon, 03 Jun 2019 18:05:43: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 18:05:43: #1 finished! INFO @ Mon, 03 Jun 2019 18:05:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:05:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:05:43: #2 number of paired peaks: 2399 INFO @ Mon, 03 Jun 2019 18:05:43: start model_add_line... INFO @ Mon, 03 Jun 2019 18:05:43: start X-correlation... INFO @ Mon, 03 Jun 2019 18:05:43: end of X-cor INFO @ Mon, 03 Jun 2019 18:05:43: #2 finished! INFO @ Mon, 03 Jun 2019 18:05:43: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:05:43: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 18:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10_model.r INFO @ Mon, 03 Jun 2019 18:05:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:05:46: 4000000 INFO @ Mon, 03 Jun 2019 18:05:48: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 18:05:48: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 18:05:48: #1 total tags in treatment: 1864150 INFO @ Mon, 03 Jun 2019 18:05:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:05:48: #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 18:05:48: #1 tags after filtering in treatment: 1793798 INFO @ Mon, 03 Jun 2019 18:05:48: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 18:05:48: #1 finished! INFO @ Mon, 03 Jun 2019 18:05:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:05:48: #2 number of paired peaks: 2399 INFO @ Mon, 03 Jun 2019 18:05:48: start model_add_line... INFO @ Mon, 03 Jun 2019 18:05:48: start X-correlation... INFO @ Mon, 03 Jun 2019 18:05:48: end of X-cor INFO @ Mon, 03 Jun 2019 18:05:48: #2 finished! INFO @ Mon, 03 Jun 2019 18:05:48: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:05:48: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 18:05:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20_model.r INFO @ Mon, 03 Jun 2019 18:05:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:05:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:05:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:05:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10_peaks.xls INFO @ Mon, 03 Jun 2019 18:05:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:05:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.10_summits.bed INFO @ Mon, 03 Jun 2019 18:05:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:05:52: #1 tag size is determined as 39 bps INFO @ Mon, 03 Jun 2019 18:05:52: #1 tag size = 39 INFO @ Mon, 03 Jun 2019 18:05:52: #1 total tags in treatment: 1864150 INFO @ Mon, 03 Jun 2019 18:05:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 18:05:52: #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 18:05:52: #1 tags after filtering in treatment: 1793798 INFO @ Mon, 03 Jun 2019 18:05:52: #1 Redundant rate of treatment: 0.04 INFO @ Mon, 03 Jun 2019 18:05:52: #1 finished! INFO @ Mon, 03 Jun 2019 18:05:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 18:05:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 18:05:52: #2 number of paired peaks: 2399 INFO @ Mon, 03 Jun 2019 18:05:52: start model_add_line... INFO @ Mon, 03 Jun 2019 18:05:52: start X-correlation... INFO @ Mon, 03 Jun 2019 18:05:52: end of X-cor INFO @ Mon, 03 Jun 2019 18:05:52: #2 finished! INFO @ Mon, 03 Jun 2019 18:05:52: #2 predicted fragment length is 142 bps INFO @ Mon, 03 Jun 2019 18:05:52: #2 alternative fragment length(s) may be 4,142 bps INFO @ Mon, 03 Jun 2019 18:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05_model.r INFO @ Mon, 03 Jun 2019 18:05:52: #3 Call peaks... INFO @ Mon, 03 Jun 2019 18:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 18:05:54: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20_peaks.xls INFO @ Mon, 03 Jun 2019 18:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.20_summits.bed INFO @ Mon, 03 Jun 2019 18:05:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 18:05:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 18:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05_peaks.xls INFO @ Mon, 03 Jun 2019 18:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 18:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650886/SRX4650886.05_summits.bed INFO @ Mon, 03 Jun 2019 18:06:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (328 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。