Job ID = 2010606 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:32:27 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 ) 2019-07-05T14:36:33 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 ) 2019-07-05T14:36:34 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 ) 2019-07-05T14:38:20 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 : 4,132,605 reads read : 8,265,210 reads written : 8,265,210 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: 00:02:36 4132605 reads; of these: 4132605 (100.00%) were paired; of these: 1887906 (45.68%) aligned concordantly 0 times 1826860 (44.21%) aligned concordantly exactly 1 time 417839 (10.11%) aligned concordantly >1 times ---- 1887906 pairs aligned concordantly 0 times; of these: 24066 (1.27%) aligned discordantly 1 time ---- 1863840 pairs aligned 0 times concordantly or discordantly; of these: 3727680 mates make up the pairs; of these: 3591024 (96.33%) aligned 0 times 87013 (2.33%) aligned exactly 1 time 49643 (1.33%) aligned >1 times 56.55% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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_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] 109745 / 2264117 = 0.0485 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 23:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.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 23:43:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.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 23:43:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.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 23:43:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:43:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:43:36: 1000000 INFO @ Fri, 05 Jul 2019 23:43:38: 1000000 INFO @ Fri, 05 Jul 2019 23:43:41: 1000000 INFO @ Fri, 05 Jul 2019 23:43:44: 2000000 INFO @ Fri, 05 Jul 2019 23:43:46: 2000000 INFO @ Fri, 05 Jul 2019 23:43:51: 2000000 INFO @ Fri, 05 Jul 2019 23:43:51: 3000000 INFO @ Fri, 05 Jul 2019 23:43:55: 3000000 INFO @ Fri, 05 Jul 2019 23:43:59: 4000000 INFO @ Fri, 05 Jul 2019 23:44:01: 3000000 INFO @ Fri, 05 Jul 2019 23:44:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:44:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:44:03: #1 total tags in treatment: 2135309 INFO @ Fri, 05 Jul 2019 23:44:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:03: #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 23:44:03: #1 tags after filtering in treatment: 1379386 INFO @ Fri, 05 Jul 2019 23:44:03: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:44:03: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:03: #2 number of paired peaks: 1028 INFO @ Fri, 05 Jul 2019 23:44:03: start model_add_line... INFO @ Fri, 05 Jul 2019 23:44:03: start X-correlation... INFO @ Fri, 05 Jul 2019 23:44:03: end of X-cor INFO @ Fri, 05 Jul 2019 23:44:03: #2 finished! INFO @ Fri, 05 Jul 2019 23:44:03: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 23:44:03: #2 alternative fragment length(s) may be 1,236,262,283,311,575,594 bps INFO @ Fri, 05 Jul 2019 23:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05_model.r INFO @ Fri, 05 Jul 2019 23:44:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:44:03: 4000000 INFO @ Fri, 05 Jul 2019 23:44:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:44:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:44:07: #1 total tags in treatment: 2135309 INFO @ Fri, 05 Jul 2019 23:44:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:07: #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 23:44:07: #1 tags after filtering in treatment: 1379386 INFO @ Fri, 05 Jul 2019 23:44:07: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:44:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:08: #2 number of paired peaks: 1028 INFO @ Fri, 05 Jul 2019 23:44:08: start model_add_line... INFO @ Fri, 05 Jul 2019 23:44:08: start X-correlation... INFO @ Fri, 05 Jul 2019 23:44:08: end of X-cor INFO @ Fri, 05 Jul 2019 23:44:08: #2 finished! INFO @ Fri, 05 Jul 2019 23:44:08: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 23:44:08: #2 alternative fragment length(s) may be 1,236,262,283,311,575,594 bps INFO @ Fri, 05 Jul 2019 23:44:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10_model.r INFO @ Fri, 05 Jul 2019 23:44:08: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:44:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:44:11: 4000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:44:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:44:15: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:44:15: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:44:15: #1 total tags in treatment: 2135309 INFO @ Fri, 05 Jul 2019 23:44:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:44:15: #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 23:44:15: #1 tags after filtering in treatment: 1379386 INFO @ Fri, 05 Jul 2019 23:44:15: #1 Redundant rate of treatment: 0.35 INFO @ Fri, 05 Jul 2019 23:44:15: #1 finished! INFO @ Fri, 05 Jul 2019 23:44:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:44:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:44:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:44:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:44:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.05_summits.bed INFO @ Fri, 05 Jul 2019 23:44:16: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 23:44:16: #2 number of paired peaks: 1028 INFO @ Fri, 05 Jul 2019 23:44:16: start model_add_line... INFO @ Fri, 05 Jul 2019 23:44:16: start X-correlation... INFO @ Fri, 05 Jul 2019 23:44:16: end of X-cor INFO @ Fri, 05 Jul 2019 23:44:16: #2 finished! INFO @ Fri, 05 Jul 2019 23:44:16: #2 predicted fragment length is 283 bps INFO @ Fri, 05 Jul 2019 23:44:16: #2 alternative fragment length(s) may be 1,236,262,283,311,575,594 bps INFO @ Fri, 05 Jul 2019 23:44:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20_model.r INFO @ Fri, 05 Jul 2019 23:44:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:44:16: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:44:18: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.10_summits.bed INFO @ Fri, 05 Jul 2019 23:44:20: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (173 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:44:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381306/SRX381306.20_summits.bed INFO @ Fri, 05 Jul 2019 23:44:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling