Job ID = 2010572 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:23:34 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 ) 2019-07-05T14:23:34 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 ) 2019-07-05T14:23:34 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 ) spots read : 8,428,700 reads read : 16,857,400 reads written : 16,857,400 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: 00:02:33 8428700 reads; of these: 8428700 (100.00%) were paired; of these: 6869643 (81.50%) aligned concordantly 0 times 1209556 (14.35%) aligned concordantly exactly 1 time 349501 (4.15%) aligned concordantly >1 times ---- 6869643 pairs aligned concordantly 0 times; of these: 13399 (0.20%) aligned discordantly 1 time ---- 6856244 pairs aligned 0 times concordantly or discordantly; of these: 13712488 mates make up the pairs; of these: 13604044 (99.21%) aligned 0 times 54324 (0.40%) aligned exactly 1 time 54120 (0.39%) aligned >1 times 19.30% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 398771 / 1570766 = 0.2539 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 23:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.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 23:28:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.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 23:28:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.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 23:28:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:45: 1000000 INFO @ Fri, 05 Jul 2019 23:28:45: 1000000 INFO @ Fri, 05 Jul 2019 23:28:48: 1000000 INFO @ Fri, 05 Jul 2019 23:28:55: 2000000 INFO @ Fri, 05 Jul 2019 23:28:56: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:28:58: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:28:58: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:28:58: #1 total tags in treatment: 1162053 INFO @ Fri, 05 Jul 2019 23:28:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:28:58: #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 23:28:58: #1 tags after filtering in treatment: 763686 INFO @ Fri, 05 Jul 2019 23:28:58: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:28:58: #1 finished! INFO @ Fri, 05 Jul 2019 23:28:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:28:59: 2000000 INFO @ Fri, 05 Jul 2019 23:28:59: #2 number of paired peaks: 989 WARNING @ Fri, 05 Jul 2019 23:28:59: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 05 Jul 2019 23:28:59: start model_add_line... INFO @ Fri, 05 Jul 2019 23:28:59: start X-correlation... INFO @ Fri, 05 Jul 2019 23:28:59: end of X-cor INFO @ Fri, 05 Jul 2019 23:28:59: #2 finished! INFO @ Fri, 05 Jul 2019 23:28:59: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 23:28:59: #2 alternative fragment length(s) may be 2,302,322,341,345,356,434,452,488,557 bps INFO @ Fri, 05 Jul 2019 23:28:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10_model.r INFO @ Fri, 05 Jul 2019 23:29:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:00: #1 total tags in treatment: 1162053 INFO @ Fri, 05 Jul 2019 23:29:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:00: #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 23:29:00: #1 tags after filtering in treatment: 763686 INFO @ Fri, 05 Jul 2019 23:29:00: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:29:00: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:00: #2 number of paired peaks: 989 WARNING @ Fri, 05 Jul 2019 23:29:00: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 05 Jul 2019 23:29:00: start model_add_line... INFO @ Fri, 05 Jul 2019 23:29:00: start X-correlation... INFO @ Fri, 05 Jul 2019 23:29:00: end of X-cor INFO @ Fri, 05 Jul 2019 23:29:00: #2 finished! INFO @ Fri, 05 Jul 2019 23:29:00: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 23:29:00: #2 alternative fragment length(s) may be 2,302,322,341,345,356,434,452,488,557 bps INFO @ Fri, 05 Jul 2019 23:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05_model.r INFO @ Fri, 05 Jul 2019 23:29:03: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:03: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:03: #1 total tags in treatment: 1162053 INFO @ Fri, 05 Jul 2019 23:29:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:03: #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 23:29:03: #1 tags after filtering in treatment: 763686 INFO @ Fri, 05 Jul 2019 23:29:03: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 05 Jul 2019 23:29:03: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:03: #2 number of paired peaks: 989 WARNING @ Fri, 05 Jul 2019 23:29:03: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 05 Jul 2019 23:29:03: start model_add_line... INFO @ Fri, 05 Jul 2019 23:29:03: start X-correlation... INFO @ Fri, 05 Jul 2019 23:29:03: end of X-cor INFO @ Fri, 05 Jul 2019 23:29:03: #2 finished! INFO @ Fri, 05 Jul 2019 23:29:03: #2 predicted fragment length is 302 bps INFO @ Fri, 05 Jul 2019 23:29:03: #2 alternative fragment length(s) may be 2,302,322,341,345,356,434,452,488,557 bps INFO @ Fri, 05 Jul 2019 23:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20_model.r INFO @ Fri, 05 Jul 2019 23:29:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:29:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:29:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:29:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:29:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:29:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:29:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:29:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.20_summits.bed INFO @ Fri, 05 Jul 2019 23:29:42: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (182 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.05_summits.bed INFO @ Fri, 05 Jul 2019 23:29:42: Done! INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381273/SRX381273.10_summits.bed INFO @ Fri, 05 Jul 2019 23:29:42: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 4 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling