Job ID = 2010637 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2019-07-05T14:43:59 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 ) 2019-07-05T14:45:10 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 ) 2019-07-05T14:45:11 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 ) 2019-07-05T14:46:23 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 ) 2019-07-05T14:46:23 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 ) 2019-07-05T14:46:23 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 : 2,896,250 reads read : 5,792,500 reads written : 5,792,500 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: 00:01:34 2896250 reads; of these: 2896250 (100.00%) were paired; of these: 1718053 (59.32%) aligned concordantly 0 times 923487 (31.89%) aligned concordantly exactly 1 time 254710 (8.79%) aligned concordantly >1 times ---- 1718053 pairs aligned concordantly 0 times; of these: 12486 (0.73%) aligned discordantly 1 time ---- 1705567 pairs aligned 0 times concordantly or discordantly; of these: 3411134 mates make up the pairs; of these: 3231484 (94.73%) aligned 0 times 135652 (3.98%) aligned exactly 1 time 43998 (1.29%) aligned >1 times 44.21% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 636148 / 1185020 = 0.5368 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 23:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.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 23:50:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:50:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.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 23:50:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:50:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.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 23:50:44: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:50:44: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:50:50: 1000000 INFO @ Fri, 05 Jul 2019 23:50:51: 1000000 INFO @ Fri, 05 Jul 2019 23:50:52: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:52: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:52: #1 total tags in treatment: 545316 INFO @ Fri, 05 Jul 2019 23:50:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:52: #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 23:50:52: #1 tags after filtering in treatment: 403737 INFO @ Fri, 05 Jul 2019 23:50:52: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:52: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:52: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 23:50:52: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:52: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:52: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:52: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:52: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:52: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:50:52: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 05 Jul 2019 23:50:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05_model.r INFO @ Fri, 05 Jul 2019 23:50:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:50:53: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:53: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:53: #1 total tags in treatment: 545316 INFO @ Fri, 05 Jul 2019 23:50:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:53: #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 23:50:53: #1 tags after filtering in treatment: 403737 INFO @ Fri, 05 Jul 2019 23:50:53: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:53: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:53: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 23:50:53: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:53: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:53: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:53: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:53: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:53: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:50:53: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 05 Jul 2019 23:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10_model.r INFO @ Fri, 05 Jul 2019 23:50:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:50:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.05_summits.bed INFO @ Fri, 05 Jul 2019 23:50:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 23:50:55: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:50:55: 1000000 INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.10_summits.bed INFO @ Fri, 05 Jul 2019 23:50:55: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:50:58: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:50:58: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:50:58: #1 total tags in treatment: 545316 INFO @ Fri, 05 Jul 2019 23:50:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:50:58: #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 23:50:58: #1 tags after filtering in treatment: 403737 INFO @ Fri, 05 Jul 2019 23:50:58: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 05 Jul 2019 23:50:58: #1 finished! INFO @ Fri, 05 Jul 2019 23:50:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:50:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:50:58: #2 number of paired peaks: 205 WARNING @ Fri, 05 Jul 2019 23:50:58: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 05 Jul 2019 23:50:58: start model_add_line... INFO @ Fri, 05 Jul 2019 23:50:58: start X-correlation... INFO @ Fri, 05 Jul 2019 23:50:58: end of X-cor INFO @ Fri, 05 Jul 2019 23:50:58: #2 finished! INFO @ Fri, 05 Jul 2019 23:50:58: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:50:58: #2 alternative fragment length(s) may be 241 bps INFO @ Fri, 05 Jul 2019 23:50:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20_model.r INFO @ Fri, 05 Jul 2019 23:50:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:50:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386364/SRX386364.20_summits.bed INFO @ Fri, 05 Jul 2019 23:51:00: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。