Job ID = 2010001 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T11:45:30 fasterq-dump.2.9.6 sys: connection busy while validating within network system module - Failed to Make Connection in KClientHttpOpen to 'sra-download.ncbi.nlm.nih.gov:443' 2019-07-05T11:45:30 fasterq-dump.2.9.6 err: connection busy while validating within network system module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra12/SRR/004891/SRR5008423' 2019-07-05T11:45:30 fasterq-dump.2.9.6 err: invalid accession 'SRR5008423' 2019-07-05T11:47:13 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 ) 2019-07-05T11:50:53 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 ) 2019-07-05T11:50:53 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 ) 2019-07-05T11:50:53 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 : 5,796,339 reads read : 11,592,678 reads written : 11,592,678 rm: cannot remove ‘[DSE]RR*’: 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: 00:04:43 5796339 reads; of these: 5796339 (100.00%) were paired; of these: 883871 (15.25%) aligned concordantly 0 times 3627105 (62.58%) aligned concordantly exactly 1 time 1285363 (22.18%) aligned concordantly >1 times ---- 883871 pairs aligned concordantly 0 times; of these: 18544 (2.10%) aligned discordantly 1 time ---- 865327 pairs aligned 0 times concordantly or discordantly; of these: 1730654 mates make up the pairs; of these: 1470694 (84.98%) aligned 0 times 182380 (10.54%) aligned exactly 1 time 77580 (4.48%) aligned >1 times 87.31% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 772238 / 4926273 = 0.1568 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 @ Fri, 05 Jul 2019 21:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 21:04:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:04:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 21:04:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:04:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:04:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Fri, 05 Jul 2019 21:04:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 21:04:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 21:04:45: 1000000 INFO @ Fri, 05 Jul 2019 21:04:46: 1000000 INFO @ Fri, 05 Jul 2019 21:04:47: 1000000 INFO @ Fri, 05 Jul 2019 21:04:52: 2000000 INFO @ Fri, 05 Jul 2019 21:04:55: 2000000 INFO @ Fri, 05 Jul 2019 21:04:55: 2000000 INFO @ Fri, 05 Jul 2019 21:04:59: 3000000 INFO @ Fri, 05 Jul 2019 21:05:03: 3000000 INFO @ Fri, 05 Jul 2019 21:05:03: 3000000 INFO @ Fri, 05 Jul 2019 21:05:06: 4000000 INFO @ Fri, 05 Jul 2019 21:05:11: 4000000 INFO @ Fri, 05 Jul 2019 21:05:11: 4000000 INFO @ Fri, 05 Jul 2019 21:05:12: 5000000 INFO @ Fri, 05 Jul 2019 21:05:19: 5000000 INFO @ Fri, 05 Jul 2019 21:05:20: 5000000 INFO @ Fri, 05 Jul 2019 21:05:20: 6000000 INFO @ Fri, 05 Jul 2019 21:05:26: 7000000 INFO @ Fri, 05 Jul 2019 21:05:27: 6000000 INFO @ Fri, 05 Jul 2019 21:05:28: 6000000 INFO @ Fri, 05 Jul 2019 21:05:33: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 21:05:35: 7000000 INFO @ Fri, 05 Jul 2019 21:05:36: 7000000 INFO @ Fri, 05 Jul 2019 21:05:37: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:37: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:37: #1 total tags in treatment: 4140909 INFO @ Fri, 05 Jul 2019 21:05:37: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:38: #1 tags after filtering in treatment: 1578873 INFO @ Fri, 05 Jul 2019 21:05:38: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:05:38: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:38: #2 number of paired peaks: 1049 INFO @ Fri, 05 Jul 2019 21:05:38: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:38: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:38: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:38: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:38: #2 predicted fragment length is 366 bps INFO @ Fri, 05 Jul 2019 21:05:38: #2 alternative fragment length(s) may be 4,366 bps INFO @ Fri, 05 Jul 2019 21:05:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05_model.r INFO @ Fri, 05 Jul 2019 21:05:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 21:05:44: 8000000 INFO @ Fri, 05 Jul 2019 21:05:44: 8000000 INFO @ Fri, 05 Jul 2019 21:05:48: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:48: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:48: #1 total tags in treatment: 4140909 INFO @ Fri, 05 Jul 2019 21:05:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:48: #1 tags after filtering in treatment: 1578873 INFO @ Fri, 05 Jul 2019 21:05:48: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:05:48: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:49: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 21:05:49: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 21:05:49: #1 total tags in treatment: 4140909 INFO @ Fri, 05 Jul 2019 21:05:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 21:05:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 21:05:49: #1 tags after filtering in treatment: 1578873 INFO @ Fri, 05 Jul 2019 21:05:49: #1 Redundant rate of treatment: 0.62 INFO @ Fri, 05 Jul 2019 21:05:49: #1 finished! INFO @ Fri, 05 Jul 2019 21:05:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 21:05:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 21:05:49: #2 number of paired peaks: 1049 INFO @ Fri, 05 Jul 2019 21:05:49: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:49: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:49: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:49: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:49: #2 predicted fragment length is 366 bps INFO @ Fri, 05 Jul 2019 21:05:49: #2 alternative fragment length(s) may be 4,366 bps INFO @ Fri, 05 Jul 2019 21:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10_model.r INFO @ Fri, 05 Jul 2019 21:05:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:05:49: #2 number of paired peaks: 1049 INFO @ Fri, 05 Jul 2019 21:05:49: start model_add_line... INFO @ Fri, 05 Jul 2019 21:05:49: start X-correlation... INFO @ Fri, 05 Jul 2019 21:05:49: end of X-cor INFO @ Fri, 05 Jul 2019 21:05:49: #2 finished! INFO @ Fri, 05 Jul 2019 21:05:49: #2 predicted fragment length is 366 bps INFO @ Fri, 05 Jul 2019 21:05:49: #2 alternative fragment length(s) may be 4,366 bps INFO @ Fri, 05 Jul 2019 21:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20_model.r INFO @ Fri, 05 Jul 2019 21:05:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 21:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 21:05:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:05:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05_peaks.xls INFO @ Fri, 05 Jul 2019 21:05:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:05:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.05_summits.bed INFO @ Fri, 05 Jul 2019 21:05:54: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (545 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 21:06:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:06:04: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 21:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10_peaks.xls INFO @ Fri, 05 Jul 2019 21:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.10_summits.bed INFO @ Fri, 05 Jul 2019 21:06:05: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (498 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 21:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20_peaks.xls INFO @ Fri, 05 Jul 2019 21:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 21:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339864/SRX2339864.20_summits.bed INFO @ Fri, 05 Jul 2019 21:06:06: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling