Job ID = 2010594 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:26:17 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 ) 2019-07-05T14:26:17 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 ) 2019-07-05T14:26:17 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 ) 2019-07-05T14:26:17 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 ) 2019-07-05T14:26:17 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 ) 2019-07-05T14:27:32 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 ) 2019-07-05T14:27:32 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 ) 2019-07-05T14:27:32 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 ) 2019-07-05T14:27:33 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 ) 2019-07-05T14:27:33 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 ) 2019-07-05T14:27:33 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 ) spots read : 4,316,278 reads read : 8,632,556 reads written : 8,632,556 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: 00:02:48 4316278 reads; of these: 4316278 (100.00%) were paired; of these: 1348574 (31.24%) aligned concordantly 0 times 2755813 (63.85%) aligned concordantly exactly 1 time 211891 (4.91%) aligned concordantly >1 times ---- 1348574 pairs aligned concordantly 0 times; of these: 38173 (2.83%) aligned discordantly 1 time ---- 1310401 pairs aligned 0 times concordantly or discordantly; of these: 2620802 mates make up the pairs; of these: 2431108 (92.76%) aligned 0 times 154348 (5.89%) aligned exactly 1 time 35346 (1.35%) aligned >1 times 71.84% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 260910 / 3000095 = 0.0870 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 23:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.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 23:36:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.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 23:36:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.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 23:36:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:36:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:36:47: 1000000 INFO @ Fri, 05 Jul 2019 23:36:48: 1000000 INFO @ Fri, 05 Jul 2019 23:36:49: 1000000 INFO @ Fri, 05 Jul 2019 23:36:59: 2000000 INFO @ Fri, 05 Jul 2019 23:36:59: 2000000 INFO @ Fri, 05 Jul 2019 23:37:02: 2000000 INFO @ Fri, 05 Jul 2019 23:37:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:37:11: 3000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:37:15: 3000000 INFO @ Fri, 05 Jul 2019 23:37:19: 4000000 INFO @ Fri, 05 Jul 2019 23:37:24: 4000000 INFO @ Fri, 05 Jul 2019 23:37:27: 4000000 INFO @ Fri, 05 Jul 2019 23:37:29: 5000000 INFO @ Fri, 05 Jul 2019 23:37:36: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:37:36: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:37:36: #1 total tags in treatment: 2708758 INFO @ Fri, 05 Jul 2019 23:37:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:37:36: #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 23:37:36: #1 tags after filtering in treatment: 749470 INFO @ Fri, 05 Jul 2019 23:37:36: #1 Redundant rate of treatment: 0.72 INFO @ Fri, 05 Jul 2019 23:37:36: #1 finished! INFO @ Fri, 05 Jul 2019 23:37:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:37:36: #2 number of paired peaks: 810 WARNING @ Fri, 05 Jul 2019 23:37:36: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 05 Jul 2019 23:37:36: start model_add_line... INFO @ Fri, 05 Jul 2019 23:37:36: start X-correlation... INFO @ Fri, 05 Jul 2019 23:37:36: end of X-cor INFO @ Fri, 05 Jul 2019 23:37:36: #2 finished! INFO @ Fri, 05 Jul 2019 23:37:36: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 23:37:36: #2 alternative fragment length(s) may be 0,89,140,174,176,550,567,580,596 bps INFO @ Fri, 05 Jul 2019 23:37:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20_model.r INFO @ Fri, 05 Jul 2019 23:37:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:37:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:37:37: 5000000 INFO @ Fri, 05 Jul 2019 23:37:39: 5000000 INFO @ Fri, 05 Jul 2019 23:37:40: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.20_summits.bed INFO @ Fri, 05 Jul 2019 23:37:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:37:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:37:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:37:45: #1 total tags in treatment: 2708758 INFO @ Fri, 05 Jul 2019 23:37:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:37:45: #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 23:37:45: #1 tags after filtering in treatment: 749470 INFO @ Fri, 05 Jul 2019 23:37:45: #1 Redundant rate of treatment: 0.72 INFO @ Fri, 05 Jul 2019 23:37:45: #1 finished! INFO @ Fri, 05 Jul 2019 23:37:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:37:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:37:45: #2 number of paired peaks: 810 WARNING @ Fri, 05 Jul 2019 23:37:45: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 05 Jul 2019 23:37:45: start model_add_line... INFO @ Fri, 05 Jul 2019 23:37:45: start X-correlation... INFO @ Fri, 05 Jul 2019 23:37:45: end of X-cor INFO @ Fri, 05 Jul 2019 23:37:45: #2 finished! INFO @ Fri, 05 Jul 2019 23:37:45: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 23:37:45: #2 alternative fragment length(s) may be 0,89,140,174,176,550,567,580,596 bps INFO @ Fri, 05 Jul 2019 23:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05_model.r INFO @ Fri, 05 Jul 2019 23:37:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:37:47: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:37:47: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:37:47: #1 total tags in treatment: 2708758 INFO @ Fri, 05 Jul 2019 23:37:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:37:47: #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 23:37:47: #1 tags after filtering in treatment: 749470 INFO @ Fri, 05 Jul 2019 23:37:47: #1 Redundant rate of treatment: 0.72 INFO @ Fri, 05 Jul 2019 23:37:47: #1 finished! INFO @ Fri, 05 Jul 2019 23:37:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:37:47: #2 number of paired peaks: 810 WARNING @ Fri, 05 Jul 2019 23:37:47: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Fri, 05 Jul 2019 23:37:47: start model_add_line... INFO @ Fri, 05 Jul 2019 23:37:47: start X-correlation... INFO @ Fri, 05 Jul 2019 23:37:47: end of X-cor INFO @ Fri, 05 Jul 2019 23:37:47: #2 finished! INFO @ Fri, 05 Jul 2019 23:37:47: #2 predicted fragment length is 140 bps INFO @ Fri, 05 Jul 2019 23:37:47: #2 alternative fragment length(s) may be 0,89,140,174,176,550,567,580,596 bps INFO @ Fri, 05 Jul 2019 23:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10_model.r INFO @ Fri, 05 Jul 2019 23:37:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:37:49: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:37:50: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.10_summits.bed INFO @ Fri, 05 Jul 2019 23:38:16: Done! INFO @ Fri, 05 Jul 2019 23:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381295/SRX381295.05_summits.bed INFO @ Fri, 05 Jul 2019 23:38:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 3 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling