Job ID = 1294324 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-06-02T21:19:56 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 ) 2019-06-02T21:19:56 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 ) 2019-06-02T21:19:56 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 ) 2019-06-02T21:20:41 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 ) 2019-06-02T21:21:16 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 ) 2019-06-02T21:21:46 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2019-06-02T21:21:46 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '130.14.250.27' from '172.19.7.9' 2019-06-02T21:21:46 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (130.14.250.27) from '172.19.7.9' 2019-06-02T21:21:46 fasterq-dump.2.9.6 err: timeout exhausted while reading file within network system module - Failed to KHttpFileRead('https://sra-download.ncbi.nlm.nih.gov/traces/sra44/SRR/004997/SRR5117070' (130.14.250.27), 32768) from '172.19.7.9' spots read : 10,636,465 reads read : 21,272,930 reads written : 21,272,930 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: 00:25:20 10636465 reads; of these: 10636465 (100.00%) were paired; of these: 804823 (7.57%) aligned concordantly 0 times 7407814 (69.65%) aligned concordantly exactly 1 time 2423828 (22.79%) aligned concordantly >1 times ---- 804823 pairs aligned concordantly 0 times; of these: 80459 (10.00%) aligned discordantly 1 time ---- 724364 pairs aligned 0 times concordantly or discordantly; of these: 1448728 mates make up the pairs; of these: 810078 (55.92%) aligned 0 times 366009 (25.26%) aligned exactly 1 time 272641 (18.82%) aligned >1 times 96.19% overall alignment rate Time searching: 00:25:20 Overall time: 00:25:20 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 12 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] 4703195 / 9875838 = 0.4762 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 07:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.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 07:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.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 07:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.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 07:03:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:03:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:03:07: 1000000 INFO @ Mon, 03 Jun 2019 07:03:08: 1000000 INFO @ Mon, 03 Jun 2019 07:03:09: 1000000 INFO @ Mon, 03 Jun 2019 07:03:15: 2000000 INFO @ Mon, 03 Jun 2019 07:03:17: 2000000 INFO @ Mon, 03 Jun 2019 07:03:17: 2000000 INFO @ Mon, 03 Jun 2019 07:03:22: 3000000 INFO @ Mon, 03 Jun 2019 07:03:25: 3000000 INFO @ Mon, 03 Jun 2019 07:03:25: 3000000 INFO @ Mon, 03 Jun 2019 07:03:29: 4000000 INFO @ Mon, 03 Jun 2019 07:03:34: 4000000 INFO @ Mon, 03 Jun 2019 07:03:34: 4000000 INFO @ Mon, 03 Jun 2019 07:03:36: 5000000 INFO @ Mon, 03 Jun 2019 07:03:41: 5000000 INFO @ Mon, 03 Jun 2019 07:03:42: 5000000 INFO @ Mon, 03 Jun 2019 07:03:43: 6000000 INFO @ Mon, 03 Jun 2019 07:03:49: 6000000 INFO @ Mon, 03 Jun 2019 07:03:50: 7000000 INFO @ Mon, 03 Jun 2019 07:03:50: 6000000 INFO @ Mon, 03 Jun 2019 07:03:57: 8000000 INFO @ Mon, 03 Jun 2019 07:03:57: 7000000 INFO @ Mon, 03 Jun 2019 07:03:58: 7000000 INFO @ Mon, 03 Jun 2019 07:04:04: 9000000 INFO @ Mon, 03 Jun 2019 07:04:05: 8000000 INFO @ Mon, 03 Jun 2019 07:04:06: 8000000 INFO @ Mon, 03 Jun 2019 07:04:11: 10000000 INFO @ Mon, 03 Jun 2019 07:04:13: 9000000 INFO @ Mon, 03 Jun 2019 07:04:14: 9000000 INFO @ Mon, 03 Jun 2019 07:04:18: 11000000 INFO @ Mon, 03 Jun 2019 07:04:18: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:04:18: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:04:18: #1 total tags in treatment: 5144960 INFO @ Mon, 03 Jun 2019 07:04:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:04:18: #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 07:04:18: #1 tags after filtering in treatment: 4602349 INFO @ Mon, 03 Jun 2019 07:04:18: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 07:04:18: #1 finished! INFO @ Mon, 03 Jun 2019 07:04:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:04:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:04:19: #2 number of paired peaks: 4695 INFO @ Mon, 03 Jun 2019 07:04:19: start model_add_line... INFO @ Mon, 03 Jun 2019 07:04:19: start X-correlation... INFO @ Mon, 03 Jun 2019 07:04:19: end of X-cor INFO @ Mon, 03 Jun 2019 07:04:19: #2 finished! INFO @ Mon, 03 Jun 2019 07:04:19: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:04:19: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05_model.r INFO @ Mon, 03 Jun 2019 07:04:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:04:20: 10000000 INFO @ Mon, 03 Jun 2019 07:04:22: 10000000 INFO @ Mon, 03 Jun 2019 07:04:28: 11000000 INFO @ Mon, 03 Jun 2019 07:04:28: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:04:28: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:04:28: #1 total tags in treatment: 5144960 INFO @ Mon, 03 Jun 2019 07:04:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:04:28: #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 07:04:29: #1 tags after filtering in treatment: 4602349 INFO @ Mon, 03 Jun 2019 07:04:29: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 07:04:29: #1 finished! INFO @ Mon, 03 Jun 2019 07:04:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:04:29: #2 number of paired peaks: 4695 INFO @ Mon, 03 Jun 2019 07:04:29: start model_add_line... INFO @ Mon, 03 Jun 2019 07:04:29: start X-correlation... INFO @ Mon, 03 Jun 2019 07:04:29: end of X-cor INFO @ Mon, 03 Jun 2019 07:04:29: #2 finished! INFO @ Mon, 03 Jun 2019 07:04:29: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:04:29: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10_model.r INFO @ Mon, 03 Jun 2019 07:04:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:04:30: 11000000 INFO @ Mon, 03 Jun 2019 07:04:31: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 07:04:31: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 07:04:31: #1 total tags in treatment: 5144960 INFO @ Mon, 03 Jun 2019 07:04:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:04:31: #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 07:04:31: #1 tags after filtering in treatment: 4602349 INFO @ Mon, 03 Jun 2019 07:04:31: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 07:04:31: #1 finished! INFO @ Mon, 03 Jun 2019 07:04:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:04:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:04:32: #2 number of paired peaks: 4695 INFO @ Mon, 03 Jun 2019 07:04:32: start model_add_line... INFO @ Mon, 03 Jun 2019 07:04:32: start X-correlation... INFO @ Mon, 03 Jun 2019 07:04:32: end of X-cor INFO @ Mon, 03 Jun 2019 07:04:32: #2 finished! INFO @ Mon, 03 Jun 2019 07:04:32: #2 predicted fragment length is 229 bps INFO @ Mon, 03 Jun 2019 07:04:32: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 03 Jun 2019 07:04:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20_model.r INFO @ Mon, 03 Jun 2019 07:04:32: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:04:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:04:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.05_summits.bed INFO @ Mon, 03 Jun 2019 07:04:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4444 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:04:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.10_summits.bed INFO @ Mon, 03 Jun 2019 07:04:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2804 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:04:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:04:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:04:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2432263/SRX2432263.20_summits.bed INFO @ Mon, 03 Jun 2019 07:04:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1543 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。